Starting phenix.real_space_refine on Thu Sep 18 04:05:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.map" model { file = "/net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njk_49485/09_2025/9njk_49485.cif" } resolution = 3.37 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= 0.012 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 102 5.16 5 C 8603 2.51 5 N 2427 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s 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: 13780 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2286 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 288} Chain breaks: 2 Chain: "C" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2279 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 288} Chain breaks: 2 Chain: "E" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2258 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 285} Chain breaks: 3 Chain: "F" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2286 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 287} Chain breaks: 3 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2290 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 288} Chain breaks: 2 Chain: "A" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2269 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 285} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.68, per 1000 atoms: 0.27 Number of scatterers: 13780 At special positions: 0 Unit cell: (100.035, 117.135, 192.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 8 15.00 Mg 4 11.99 O 2636 8.00 N 2427 7.00 C 8603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 587.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 10 sheets defined 53.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.581A pdb=" N VAL D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 190 through 204 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.799A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 246 Processing helix chain 'D' and resid 254 through 272 removed outlier: 3.796A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 272 " --> pdb=" O MET D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 290 removed outlier: 4.112A pdb=" N TYR D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 318 Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.842A pdb=" N ALA D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.565A pdb=" N LYS C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.518A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 125 through 140 Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.797A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.882A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 270 removed outlier: 3.653A pdb=" N LEU C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 289 removed outlier: 3.871A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 318 removed outlier: 4.446A pdb=" N GLN C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N MET C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 311 " --> pdb=" O MET C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.510A pdb=" N SER C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER C 354 " --> pdb=" O MET C 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.638A pdb=" N LYS E 85 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.832A pdb=" N VAL E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.635A pdb=" N LEU E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.737A pdb=" N LYS E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 removed outlier: 3.642A pdb=" N GLU E 156 " --> pdb=" O MET E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 Processing helix chain 'E' and resid 191 through 202 removed outlier: 3.534A pdb=" N ALA E 199 " --> pdb=" O CYS E 195 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.670A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 272 removed outlier: 3.601A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.665A pdb=" N THR E 288 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 318 removed outlier: 3.772A pdb=" N MET E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 354 removed outlier: 4.229A pdb=" N SER E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.615A pdb=" N VAL F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 removed outlier: 3.527A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.531A pdb=" N ILE F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 237 Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 282 through 287 removed outlier: 4.018A pdb=" N TYR F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 318 removed outlier: 3.537A pdb=" N GLN F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 354 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.624A pdb=" N GLN B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.665A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.568A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 227 through 236 removed outlier: 3.791A pdb=" N SER B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 269 removed outlier: 3.634A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.532A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 318 Processing helix chain 'B' and resid 348 through 354 removed outlier: 3.761A pdb=" N SER B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 removed outlier: 3.600A pdb=" N LYS A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 102 removed outlier: 3.594A 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 114 through 121 removed outlier: 3.598A pdb=" N LEU A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.896A pdb=" N MET A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 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 237 removed outlier: 4.239A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 254 through 272 removed outlier: 3.785A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 removed outlier: 4.050A pdb=" N THR A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 Processing helix chain 'A' and resid 349 through 354 Processing sheet with id=AA1, first strand: chain 'D' and resid 145 through 146 removed outlier: 5.783A pdb=" N LYS C 214 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU C 276 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 280 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER C 275 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL C 322 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N GLN C 326 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR C 181 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASN C 325 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 183 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 180 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N LEU C 358 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU C 182 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE C 360 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 184 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N LYS C 362 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY C 359 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL C 372 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS C 361 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N CYS C 370 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 391 " --> pdb=" O TYR C 388 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AA3, first strand: chain 'D' and resid 391 through 393 removed outlier: 3.534A pdb=" N VAL D 373 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN D 325 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY D 185 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE D 277 " --> pdb=" O VAL D 322 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N THR D 324 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 279 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU D 216 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP D 280 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE D 218 " --> pdb=" O ASP D 280 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 248 " --> pdb=" O CYS D 215 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 219 " --> pdb=" O ALA D 250 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 145 through 146 removed outlier: 5.779A pdb=" N LYS B 214 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 276 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER B 275 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 322 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 277 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N THR B 324 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL B 279 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR B 181 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 373 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AA6, first strand: chain 'E' and resid 391 through 393 removed outlier: 6.855A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 320 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LYS E 214 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE E 277 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU E 216 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL E 279 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE E 218 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'F' and resid 247 through 251 removed outlier: 6.998A pdb=" N CYS F 215 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA F 250 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR F 217 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS F 214 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE F 277 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU F 216 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL F 279 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE F 218 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.575A pdb=" N TYR A 249 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 248 " --> pdb=" O CYS A 215 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 214 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL A 278 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU A 216 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP A 280 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 218 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 275 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL A 322 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 325 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 185 " --> pdb=" O ASN A 325 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE A 180 " --> pdb=" O THR A 356 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU A 358 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU A 182 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N PHE A 360 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE A 184 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N LYS A 362 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 159 through 160 677 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4675 1.34 - 1.46: 2817 1.46 - 1.58: 6307 1.58 - 1.70: 12 1.70 - 1.82: 156 Bond restraints: 13967 Sorted by residual: bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N GLY E 185 " pdb=" CA GLY E 185 " ideal model delta sigma weight residual 1.448 1.474 -0.026 9.20e-03 1.18e+04 8.11e+00 bond pdb=" N GLU E 186 " pdb=" CA GLU E 186 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.74e+00 bond pdb=" N ASN E 166 " pdb=" CA ASN E 166 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.64e+00 ... (remaining 13962 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 18466 1.85 - 3.70: 294 3.70 - 5.55: 56 5.55 - 7.40: 19 7.40 - 9.25: 6 Bond angle restraints: 18841 Sorted by residual: angle pdb=" N LEU B 229 " pdb=" CA LEU B 229 " pdb=" C LEU B 229 " ideal model delta sigma weight residual 111.28 106.04 5.24 1.09e+00 8.42e-01 2.31e+01 angle pdb=" N VAL B 227 " pdb=" CA VAL B 227 " pdb=" C VAL B 227 " ideal model delta sigma weight residual 110.82 114.88 -4.06 9.70e-01 1.06e+00 1.75e+01 angle pdb=" C GLN B 300 " pdb=" N MET B 301 " pdb=" CA MET B 301 " ideal model delta sigma weight residual 121.14 114.46 6.68 1.75e+00 3.27e-01 1.46e+01 angle pdb=" CA GLY E 185 " pdb=" C GLY E 185 " pdb=" O GLY E 185 " ideal model delta sigma weight residual 121.83 118.10 3.73 1.02e+00 9.61e-01 1.34e+01 angle pdb=" N THR E 189 " pdb=" CA THR E 189 " pdb=" C THR E 189 " ideal model delta sigma weight residual 111.28 107.42 3.86 1.09e+00 8.42e-01 1.26e+01 ... (remaining 18836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7751 18.00 - 35.99: 624 35.99 - 53.99: 88 53.99 - 71.99: 18 71.99 - 89.98: 13 Dihedral angle restraints: 8494 sinusoidal: 3409 harmonic: 5085 Sorted by residual: dihedral pdb=" CA ARG C 273 " pdb=" C ARG C 273 " pdb=" N PHE C 274 " pdb=" CA PHE C 274 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 176 " pdb=" CG GLU A 176 " pdb=" CD GLU A 176 " pdb=" OE1 GLU A 176 " ideal model delta sinusoidal sigma weight residual 0.00 -85.49 85.49 1 3.00e+01 1.11e-03 9.83e+00 dihedral pdb=" CG ARG D 312 " pdb=" CD ARG D 312 " pdb=" NE ARG D 312 " pdb=" CZ ARG D 312 " ideal model delta sinusoidal sigma weight residual 180.00 137.90 42.10 2 1.50e+01 4.44e-03 9.59e+00 ... (remaining 8491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1359 0.030 - 0.059: 491 0.059 - 0.089: 168 0.089 - 0.118: 130 0.118 - 0.148: 25 Chirality restraints: 2173 Sorted by residual: chirality pdb=" CB ILE D 180 " pdb=" CA ILE D 180 " pdb=" CG1 ILE D 180 " pdb=" CG2 ILE D 180 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA VAL F 145 " pdb=" N VAL F 145 " pdb=" C VAL F 145 " pdb=" CB VAL F 145 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CB ILE A 180 " pdb=" CA ILE A 180 " pdb=" CG1 ILE A 180 " pdb=" CG2 ILE A 180 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 2170 not shown) Planarity restraints: 2438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 225 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO B 226 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 249 " -0.009 2.00e-02 2.50e+03 1.30e-02 3.36e+00 pdb=" CG TYR B 249 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 249 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 249 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 249 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 249 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 249 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 249 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 239 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 240 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 240 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 240 " 0.024 5.00e-02 4.00e+02 ... (remaining 2435 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 185 2.61 - 3.18: 12152 3.18 - 3.76: 21950 3.76 - 4.33: 29290 4.33 - 4.90: 47586 Nonbonded interactions: 111163 Sorted by model distance: nonbonded pdb=" OG SER B 192 " pdb="MG MG B 502 " model vdw 2.038 2.170 nonbonded pdb=" O1B ADP D 501 " pdb="MG MG D 502 " model vdw 2.055 2.170 nonbonded pdb=" O1B ADP B 501 " pdb="MG MG B 502 " model vdw 2.086 2.170 nonbonded pdb=" OG SER C 192 " pdb="MG MG C 502 " model vdw 2.093 2.170 nonbonded pdb=" O1B ADP C 501 " pdb="MG MG C 502 " model vdw 2.194 2.170 ... (remaining 111158 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' and (resid 81 through 287 or resid 296 through 400)) selection = (chain 'B' and (resid 81 through 287 or resid 296 through 327 or resid 348 throu \ gh 400)) selection = (chain 'C' and (resid 81 through 287 or resid 296 through 327 or resid 348 throu \ gh 400)) selection = (chain 'D' and (resid 81 through 287 or resid 296 through 327 or resid 348 throu \ gh 400)) selection = (chain 'E' and (resid 81 through 287 or resid 296 through 327 or resid 348 throu \ gh 400)) selection = (chain 'F' and (resid 81 through 287 or resid 296 through 327 or resid 348 throu \ gh 400)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.010 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.003 0.109 13967 Z= 0.147 Angle : 0.625 9.253 18841 Z= 0.320 Chirality : 0.042 0.148 2173 Planarity : 0.003 0.065 2438 Dihedral : 13.376 89.984 5214 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.07 % Allowed : 0.14 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.69 (0.21), residues: 1751 helix: 0.92 (0.18), residues: 810 sheet: 0.40 (0.31), residues: 301 loop : 0.08 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.031 0.001 TYR B 249 PHE 0.016 0.001 PHE B 187 HIS 0.012 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00275 (13967) covalent geometry : angle 0.62460 (18841) hydrogen bonds : bond 0.16551 ( 677) hydrogen bonds : angle 6.20145 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 142 MET cc_start: 0.8012 (pmm) cc_final: 0.7773 (pmm) REVERT: F 152 MET cc_start: 0.9170 (ppp) cc_final: 0.8851 (ppp) REVERT: F 283 MET cc_start: 0.6232 (mmp) cc_final: 0.5128 (tpp) outliers start: 1 outliers final: 0 residues processed: 107 average time/residue: 0.0983 time to fit residues: 16.6518 Evaluate side-chains 85 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN E 352 HIS F 134 ASN F 302 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.099608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.070629 restraints weight = 55231.955| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.01 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13967 Z= 0.137 Angle : 0.604 9.404 18841 Z= 0.297 Chirality : 0.043 0.170 2173 Planarity : 0.004 0.056 2438 Dihedral : 5.185 46.936 1969 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.41 % Allowed : 6.37 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.64 (0.20), residues: 1751 helix: 0.93 (0.18), residues: 828 sheet: 0.39 (0.31), residues: 308 loop : -0.08 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 188 TYR 0.013 0.001 TYR C 217 PHE 0.029 0.001 PHE E 187 HIS 0.008 0.001 HIS F 302 Details of bonding type rmsd covalent geometry : bond 0.00295 (13967) covalent geometry : angle 0.60427 (18841) hydrogen bonds : bond 0.03659 ( 677) hydrogen bonds : angle 4.95058 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: E 144 PHE cc_start: 0.7254 (p90) cc_final: 0.7046 (p90) REVERT: E 269 MET cc_start: 0.9033 (mpp) cc_final: 0.8702 (mpp) REVERT: F 152 MET cc_start: 0.9109 (ppp) cc_final: 0.8877 (ppp) REVERT: F 302 HIS cc_start: 0.9297 (t-90) cc_final: 0.9047 (t-90) REVERT: B 152 MET cc_start: 0.6895 (tmm) cc_final: 0.6640 (ppp) REVERT: B 283 MET cc_start: 0.8652 (mmm) cc_final: 0.8447 (mmt) REVERT: A 269 MET cc_start: 0.9128 (mmm) cc_final: 0.8635 (mmm) outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 0.0875 time to fit residues: 13.6166 Evaluate side-chains 90 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 0.0010 chunk 5 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 56 optimal weight: 0.6980 overall best weight: 2.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.098882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.069471 restraints weight = 55542.817| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 5.02 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13967 Z= 0.156 Angle : 0.594 8.397 18841 Z= 0.290 Chirality : 0.043 0.176 2173 Planarity : 0.004 0.058 2438 Dihedral : 5.211 48.209 1969 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.96 % Allowed : 8.15 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.66 (0.20), residues: 1751 helix: 0.97 (0.18), residues: 827 sheet: 0.30 (0.31), residues: 309 loop : -0.03 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.014 0.001 TYR B 217 PHE 0.013 0.001 PHE C 274 HIS 0.003 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00343 (13967) covalent geometry : angle 0.59374 (18841) hydrogen bonds : bond 0.03386 ( 677) hydrogen bonds : angle 4.77434 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: D 302 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (t70) REVERT: E 269 MET cc_start: 0.8966 (mpp) cc_final: 0.8543 (mpp) REVERT: F 302 HIS cc_start: 0.9344 (t-90) cc_final: 0.9049 (t-90) REVERT: F 400 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6127 (mm-30) REVERT: B 89 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7663 (p0) REVERT: B 152 MET cc_start: 0.6813 (tmm) cc_final: 0.6441 (ppp) REVERT: A 269 MET cc_start: 0.9188 (mmm) cc_final: 0.8771 (mmm) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 0.0941 time to fit residues: 15.4232 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 287 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 126 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 114 optimal weight: 40.0000 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN E 151 HIS B 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.099136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.069981 restraints weight = 55049.195| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 5.00 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13967 Z= 0.134 Angle : 0.595 9.704 18841 Z= 0.285 Chirality : 0.042 0.180 2173 Planarity : 0.003 0.056 2438 Dihedral : 5.137 48.474 1969 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.96 % Allowed : 10.75 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.74 (0.20), residues: 1751 helix: 1.03 (0.18), residues: 828 sheet: 0.32 (0.31), residues: 307 loop : 0.02 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.011 0.001 TYR C 217 PHE 0.009 0.001 PHE D 150 HIS 0.003 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00293 (13967) covalent geometry : angle 0.59501 (18841) hydrogen bonds : bond 0.03113 ( 677) hydrogen bonds : angle 4.64551 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: D 302 HIS cc_start: 0.8899 (OUTLIER) cc_final: 0.8654 (t70) REVERT: E 269 MET cc_start: 0.9020 (mpp) cc_final: 0.8615 (mpp) REVERT: F 302 HIS cc_start: 0.9326 (t-90) cc_final: 0.9011 (t-90) REVERT: F 350 MET cc_start: 0.9156 (ppp) cc_final: 0.8954 (ppp) REVERT: F 400 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6199 (mm-30) REVERT: B 89 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 152 MET cc_start: 0.6863 (tmm) cc_final: 0.6515 (ppp) REVERT: A 269 MET cc_start: 0.9184 (mmm) cc_final: 0.8735 (mmm) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.0952 time to fit residues: 16.0867 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 302 HIS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 287 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 83 optimal weight: 0.0470 chunk 166 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN B 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.099325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.070174 restraints weight = 55607.098| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 5.02 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13967 Z= 0.119 Angle : 0.593 9.063 18841 Z= 0.282 Chirality : 0.042 0.181 2173 Planarity : 0.003 0.053 2438 Dihedral : 5.044 47.988 1969 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.16 % Allowed : 12.40 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.80 (0.20), residues: 1751 helix: 1.08 (0.18), residues: 828 sheet: 0.37 (0.31), residues: 304 loop : 0.04 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.009 0.001 TYR C 217 PHE 0.009 0.001 PHE D 274 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00262 (13967) covalent geometry : angle 0.59327 (18841) hydrogen bonds : bond 0.02940 ( 677) hydrogen bonds : angle 4.54131 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.499 Fit side-chains REVERT: E 269 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8648 (mpp) REVERT: F 302 HIS cc_start: 0.9364 (t-90) cc_final: 0.9023 (t-90) REVERT: F 400 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6183 (mm-30) REVERT: B 152 MET cc_start: 0.6893 (tmm) cc_final: 0.6545 (ppp) outliers start: 17 outliers final: 10 residues processed: 103 average time/residue: 0.0954 time to fit residues: 15.6433 Evaluate side-chains 100 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 118 optimal weight: 10.0000 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 98 optimal weight: 30.0000 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 40.0000 chunk 127 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 302 HIS D 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.098577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.069172 restraints weight = 54942.939| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 4.98 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13967 Z= 0.152 Angle : 0.612 9.909 18841 Z= 0.294 Chirality : 0.042 0.209 2173 Planarity : 0.003 0.054 2438 Dihedral : 5.123 48.882 1969 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.71 % Allowed : 12.53 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.76 (0.21), residues: 1751 helix: 1.05 (0.18), residues: 833 sheet: 0.31 (0.31), residues: 303 loop : 0.03 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 153 TYR 0.011 0.001 TYR C 217 PHE 0.012 0.001 PHE D 274 HIS 0.002 0.001 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00336 (13967) covalent geometry : angle 0.61248 (18841) hydrogen bonds : bond 0.03109 ( 677) hydrogen bonds : angle 4.62106 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.494 Fit side-chains REVERT: D 187 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.8177 (p90) REVERT: E 269 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8668 (mpp) REVERT: E 307 MET cc_start: 0.8936 (tpp) cc_final: 0.8453 (mmm) REVERT: F 302 HIS cc_start: 0.9372 (t-90) cc_final: 0.9025 (t-90) REVERT: F 400 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6326 (mm-30) outliers start: 25 outliers final: 15 residues processed: 107 average time/residue: 0.0879 time to fit residues: 15.3777 Evaluate side-chains 104 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 302 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 49 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 73 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN E 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.099518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.070413 restraints weight = 54615.424| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.96 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13967 Z= 0.106 Angle : 0.615 10.367 18841 Z= 0.288 Chirality : 0.042 0.292 2173 Planarity : 0.003 0.053 2438 Dihedral : 4.939 47.345 1969 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.10 % Allowed : 13.90 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.84 (0.21), residues: 1751 helix: 1.08 (0.18), residues: 834 sheet: 0.40 (0.31), residues: 304 loop : 0.10 (0.26), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 308 TYR 0.007 0.001 TYR C 217 PHE 0.010 0.001 PHE D 274 HIS 0.002 0.000 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00231 (13967) covalent geometry : angle 0.61503 (18841) hydrogen bonds : bond 0.02747 ( 677) hydrogen bonds : angle 4.44315 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.580 Fit side-chains REVERT: E 269 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8692 (mpp) REVERT: F 302 HIS cc_start: 0.9399 (t-90) cc_final: 0.9042 (t-90) REVERT: F 400 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6289 (mm-30) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1056 time to fit residues: 17.0675 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 133 optimal weight: 0.0170 chunk 120 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 overall best weight: 1.4022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN A 311 GLN A 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.099641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.070505 restraints weight = 55130.100| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 4.91 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13967 Z= 0.120 Angle : 0.620 12.087 18841 Z= 0.292 Chirality : 0.042 0.288 2173 Planarity : 0.003 0.051 2438 Dihedral : 4.933 46.945 1969 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.03 % Allowed : 14.66 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.86 (0.21), residues: 1751 helix: 1.07 (0.18), residues: 841 sheet: 0.41 (0.31), residues: 302 loop : 0.14 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 308 TYR 0.009 0.001 TYR E 217 PHE 0.016 0.001 PHE D 274 HIS 0.003 0.000 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00263 (13967) covalent geometry : angle 0.62020 (18841) hydrogen bonds : bond 0.02838 ( 677) hydrogen bonds : angle 4.46523 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.469 Fit side-chains REVERT: E 142 MET cc_start: 0.7324 (mmm) cc_final: 0.7075 (mmm) REVERT: E 269 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8647 (mpp) REVERT: F 302 HIS cc_start: 0.9414 (t-90) cc_final: 0.9051 (t-90) REVERT: F 400 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6304 (mm-30) REVERT: A 348 ASN cc_start: 0.7552 (p0) cc_final: 0.7275 (p0) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.0911 time to fit residues: 14.5309 Evaluate side-chains 102 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 268 MET Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 78 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 0.0010 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 111 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.097828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068165 restraints weight = 54963.586| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 4.93 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13967 Z= 0.206 Angle : 0.694 14.655 18841 Z= 0.334 Chirality : 0.044 0.270 2173 Planarity : 0.004 0.054 2438 Dihedral : 5.311 50.255 1969 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.03 % Allowed : 14.93 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.63 (0.20), residues: 1751 helix: 0.89 (0.18), residues: 842 sheet: 0.19 (0.31), residues: 301 loop : 0.09 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.015 0.001 TYR C 249 PHE 0.022 0.002 PHE D 274 HIS 0.004 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00454 (13967) covalent geometry : angle 0.69362 (18841) hydrogen bonds : bond 0.03446 ( 677) hydrogen bonds : angle 4.81119 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: E 269 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8703 (mpp) REVERT: E 307 MET cc_start: 0.8937 (tpp) cc_final: 0.8459 (mmm) REVERT: F 302 HIS cc_start: 0.9422 (t-90) cc_final: 0.9044 (t70) REVERT: A 348 ASN cc_start: 0.7843 (p0) cc_final: 0.7584 (p0) outliers start: 15 outliers final: 13 residues processed: 99 average time/residue: 0.0972 time to fit residues: 15.7074 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.1980 chunk 149 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.069998 restraints weight = 54651.595| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 4.95 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13967 Z= 0.108 Angle : 0.647 13.365 18841 Z= 0.302 Chirality : 0.042 0.240 2173 Planarity : 0.003 0.053 2438 Dihedral : 4.993 48.666 1969 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.89 % Allowed : 15.14 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.76 (0.21), residues: 1751 helix: 0.97 (0.18), residues: 848 sheet: 0.36 (0.31), residues: 303 loop : 0.13 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 153 TYR 0.007 0.001 TYR C 217 PHE 0.013 0.001 PHE D 274 HIS 0.004 0.000 HIS D 302 Details of bonding type rmsd covalent geometry : bond 0.00237 (13967) covalent geometry : angle 0.64719 (18841) hydrogen bonds : bond 0.02755 ( 677) hydrogen bonds : angle 4.49276 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: F 302 HIS cc_start: 0.9440 (t-90) cc_final: 0.9067 (t-90) REVERT: A 348 ASN cc_start: 0.7804 (p0) cc_final: 0.7518 (p0) outliers start: 13 outliers final: 12 residues processed: 99 average time/residue: 0.0965 time to fit residues: 15.5291 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 258 GLN Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 150 optimal weight: 20.0000 chunk 110 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 163 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 GLN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.096904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.066694 restraints weight = 55688.182| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.95 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13967 Z= 0.330 Angle : 0.810 12.301 18841 Z= 0.398 Chirality : 0.048 0.253 2173 Planarity : 0.005 0.054 2438 Dihedral : 5.827 54.711 1969 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.16 % Allowed : 15.21 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % 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: 0.13 (0.20), residues: 1751 helix: 0.53 (0.18), residues: 844 sheet: -0.28 (0.31), residues: 300 loop : -0.11 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 312 TYR 0.023 0.002 TYR C 217 PHE 0.036 0.002 PHE D 317 HIS 0.007 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00727 (13967) covalent geometry : angle 0.80987 (18841) hydrogen bonds : bond 0.04215 ( 677) hydrogen bonds : angle 5.25477 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.09 seconds wall clock time: 54 minutes 13.55 seconds (3253.55 seconds total)