Starting phenix.real_space_refine on Fri May 16 02:38:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9njk_49485/05_2025/9njk_49485.cif Found real_map, /net/cci-nas-00/data/ceres_data/9njk_49485/05_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_49485/05_2025/9njk_49485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9njk_49485/05_2025/9njk_49485.map" model { file = "/net/cci-nas-00/data/ceres_data/9njk_49485/05_2025/9njk_49485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9njk_49485/05_2025/9njk_49485.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.97, per 1000 atoms: 0.65 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: 3.29 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 4.64 Time building geometry restraints manager: 3.87 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: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.890 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), 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 HIS 0.012 0.001 HIS E 352 PHE 0.016 0.001 PHE B 187 TYR 0.031 0.001 TYR B 249 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.16551 ( 677) hydrogen bonds : angle 6.20145 ( 1926) covalent geometry : bond 0.00275 (13967) covalent geometry : angle 0.62460 (18841) *********************** 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 : 1.666 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: 0.2192 time to fit residues: 37.1095 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 : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 30.0000 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 0.0570 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 40.0000 chunk 158 optimal weight: 5.9990 overall best weight: 5.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 GLN D 311 GLN ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4053 r_free = 0.4053 target = 0.096621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.066542 restraints weight = 55901.766| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 4.92 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13967 Z= 0.339 Angle : 0.768 9.116 18841 Z= 0.389 Chirality : 0.049 0.215 2173 Planarity : 0.005 0.071 2438 Dihedral : 5.987 54.033 1969 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.89 % Allowed : 9.11 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1751 helix: 0.47 (0.18), residues: 827 sheet: -0.36 (0.30), residues: 306 loop : -0.19 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 196 PHE 0.029 0.003 PHE E 187 TYR 0.026 0.002 TYR C 217 ARG 0.006 0.001 ARG B 228 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 677) hydrogen bonds : angle 5.67121 ( 1926) covalent geometry : bond 0.00741 (13967) covalent geometry : angle 0.76800 (18841) *********************** 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 97 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: E 269 MET cc_start: 0.9043 (mpp) cc_final: 0.8811 (mpp) REVERT: F 142 MET cc_start: 0.3297 (tpt) cc_final: 0.2926 (pmm) REVERT: F 152 MET cc_start: 0.9099 (ppp) cc_final: 0.8863 (ppp) REVERT: F 302 HIS cc_start: 0.9296 (t-90) cc_final: 0.9042 (t-90) REVERT: A 348 ASN cc_start: 0.7943 (p0) cc_final: 0.7694 (p0) outliers start: 13 outliers final: 8 residues processed: 92 average time/residue: 0.2063 time to fit residues: 31.3880 Evaluate side-chains 92 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain A residue 180 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 50 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 110 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.098351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.068877 restraints weight = 55019.362| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.90 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13967 Z= 0.138 Angle : 0.601 9.809 18841 Z= 0.294 Chirality : 0.042 0.185 2173 Planarity : 0.004 0.064 2438 Dihedral : 5.479 52.117 1969 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.55 % Allowed : 11.44 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.20), residues: 1751 helix: 0.82 (0.18), residues: 827 sheet: 0.05 (0.31), residues: 289 loop : -0.19 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 352 PHE 0.012 0.001 PHE E 187 TYR 0.011 0.001 TYR E 217 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 677) hydrogen bonds : angle 4.97409 ( 1926) covalent geometry : bond 0.00302 (13967) covalent geometry : angle 0.60089 (18841) *********************** 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 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: D 302 HIS cc_start: 0.8939 (OUTLIER) cc_final: 0.8583 (t70) REVERT: E 144 PHE cc_start: 0.7265 (p90) cc_final: 0.6951 (p90) REVERT: E 269 MET cc_start: 0.9005 (mpp) cc_final: 0.8648 (mpp) REVERT: E 283 MET cc_start: 0.8883 (mmp) cc_final: 0.8650 (mmp) REVERT: F 302 HIS cc_start: 0.9336 (t-90) cc_final: 0.9042 (t-90) outliers start: 8 outliers final: 6 residues processed: 98 average time/residue: 0.2189 time to fit residues: 34.8632 Evaluate side-chains 97 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 C residue 145 VAL Chi-restraints excluded: chain F residue 144 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 168 optimal weight: 1.9990 chunk 107 optimal weight: 40.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.098738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.069308 restraints weight = 54338.143| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.97 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1714 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= 0.127 Angle : 0.591 9.288 18841 Z= 0.285 Chirality : 0.042 0.179 2173 Planarity : 0.003 0.058 2438 Dihedral : 5.268 50.799 1969 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.37 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.20), residues: 1751 helix: 0.93 (0.18), residues: 827 sheet: 0.07 (0.31), residues: 303 loop : -0.06 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 352 PHE 0.008 0.001 PHE F 150 TYR 0.010 0.001 TYR E 217 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03136 ( 677) hydrogen bonds : angle 4.72196 ( 1926) covalent geometry : bond 0.00276 (13967) covalent geometry : angle 0.59137 (18841) *********************** 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 114 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 302 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8642 (t70) REVERT: E 144 PHE cc_start: 0.7250 (p90) cc_final: 0.6981 (p90) REVERT: E 191 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7843 (mtmm) REVERT: E 269 MET cc_start: 0.9018 (mpp) cc_final: 0.8641 (mpp) REVERT: F 302 HIS cc_start: 0.9336 (t-90) cc_final: 0.9006 (t-90) REVERT: F 350 MET cc_start: 0.9187 (ppp) cc_final: 0.8962 (ppp) REVERT: B 89 ASN cc_start: 0.8225 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 152 MET cc_start: 0.7287 (ppp) cc_final: 0.6950 (ppp) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.2062 time to fit residues: 36.8988 Evaluate side-chains 103 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 MET Chi-restraints excluded: chain D residue 145 VAL 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 C residue 145 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain A residue 142 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 124 optimal weight: 7.9990 chunk 160 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.099132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.069944 restraints weight = 54813.759| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 4.96 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13967 Z= 0.109 Angle : 0.591 9.756 18841 Z= 0.281 Chirality : 0.042 0.193 2173 Planarity : 0.003 0.055 2438 Dihedral : 5.104 49.339 1969 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.23 % Allowed : 14.11 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1751 helix: 1.00 (0.18), residues: 828 sheet: 0.24 (0.31), residues: 300 loop : 0.00 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 352 PHE 0.008 0.001 PHE A 274 TYR 0.010 0.001 TYR E 217 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 677) hydrogen bonds : angle 4.56043 ( 1926) covalent geometry : bond 0.00237 (13967) covalent geometry : angle 0.59128 (18841) *********************** 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 113 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: E 144 PHE cc_start: 0.7220 (p90) cc_final: 0.6963 (p90) REVERT: E 269 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8617 (mpp) REVERT: F 302 HIS cc_start: 0.9355 (t-90) cc_final: 0.9022 (t-90) REVERT: F 400 GLU cc_start: 0.6575 (mt-10) cc_final: 0.6173 (mm-30) REVERT: B 246 ASN cc_start: 0.7562 (m-40) cc_final: 0.7096 (p0) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 0.2061 time to fit residues: 36.5421 Evaluate side-chains 100 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 C residue 145 VAL Chi-restraints excluded: chain C residue 187 PHE 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 151 HIS Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 58 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 10.0000 chunk 49 optimal weight: 0.0670 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN B 89 ASN A 311 GLN A 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.099948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.070751 restraints weight = 56028.285| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 5.02 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13967 Z= 0.096 Angle : 0.576 9.394 18841 Z= 0.273 Chirality : 0.041 0.198 2173 Planarity : 0.003 0.051 2438 Dihedral : 4.912 47.078 1969 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.37 % Allowed : 13.97 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.20), residues: 1751 helix: 1.06 (0.18), residues: 834 sheet: 0.35 (0.31), residues: 302 loop : 0.05 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS E 352 PHE 0.008 0.001 PHE A 274 TYR 0.006 0.001 TYR C 217 ARG 0.002 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.02705 ( 677) hydrogen bonds : angle 4.43100 ( 1926) covalent geometry : bond 0.00207 (13967) covalent geometry : angle 0.57626 (18841) *********************** 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 113 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 144 PHE cc_start: 0.7102 (p90) cc_final: 0.6883 (p90) REVERT: E 191 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7802 (mtmm) REVERT: E 269 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8641 (mpp) REVERT: E 307 MET cc_start: 0.8894 (tpp) cc_final: 0.8410 (mmm) REVERT: F 302 HIS cc_start: 0.9383 (t-90) cc_final: 0.9033 (t70) REVERT: F 400 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6160 (mm-30) REVERT: B 89 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7748 (p0) REVERT: B 246 ASN cc_start: 0.7539 (m-40) cc_final: 0.7177 (p0) outliers start: 20 outliers final: 10 residues processed: 107 average time/residue: 0.2323 time to fit residues: 38.9166 Evaluate side-chains 100 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 C residue 145 VAL Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.099841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071110 restraints weight = 55530.494| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 4.96 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13967 Z= 0.094 Angle : 0.594 9.649 18841 Z= 0.278 Chirality : 0.042 0.298 2173 Planarity : 0.003 0.049 2438 Dihedral : 4.802 45.486 1969 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.16 % Allowed : 15.07 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1751 helix: 1.09 (0.18), residues: 834 sheet: 0.40 (0.31), residues: 307 loop : 0.12 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS E 352 PHE 0.009 0.001 PHE A 274 TYR 0.010 0.001 TYR E 217 ARG 0.006 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.02587 ( 677) hydrogen bonds : angle 4.37591 ( 1926) covalent geometry : bond 0.00203 (13967) covalent geometry : angle 0.59365 (18841) *********************** 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 104 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 144 PHE cc_start: 0.7136 (p90) cc_final: 0.6913 (p90) REVERT: E 191 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7823 (mtmm) REVERT: E 269 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: E 307 MET cc_start: 0.8934 (tpp) cc_final: 0.8430 (mmm) REVERT: F 302 HIS cc_start: 0.9402 (t-90) cc_final: 0.9037 (t70) REVERT: F 400 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6141 (mm-30) REVERT: B 246 ASN cc_start: 0.7524 (m-40) cc_final: 0.7233 (p0) outliers start: 17 outliers final: 14 residues processed: 99 average time/residue: 0.2146 time to fit residues: 33.8594 Evaluate side-chains 101 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 191 LYS 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 B residue 308 ARG Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 151 HIS 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 76 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 88 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 98 optimal weight: 30.0000 chunk 128 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.099643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.070678 restraints weight = 55191.887| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 4.97 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13967 Z= 0.103 Angle : 0.597 10.124 18841 Z= 0.280 Chirality : 0.042 0.289 2173 Planarity : 0.003 0.049 2438 Dihedral : 4.773 44.840 1969 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.44 % Allowed : 15.00 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.21), residues: 1751 helix: 1.12 (0.18), residues: 834 sheet: 0.38 (0.31), residues: 309 loop : 0.16 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 257 PHE 0.011 0.001 PHE D 274 TYR 0.007 0.001 TYR C 217 ARG 0.006 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.02625 ( 677) hydrogen bonds : angle 4.37147 ( 1926) covalent geometry : bond 0.00226 (13967) covalent geometry : angle 0.59665 (18841) *********************** 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 106 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 302 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8401 (t-170) REVERT: E 142 MET cc_start: 0.7305 (mmm) cc_final: 0.7036 (mmm) REVERT: E 191 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7808 (mtmm) REVERT: E 269 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8582 (mpp) REVERT: E 307 MET cc_start: 0.8990 (tpp) cc_final: 0.8490 (mmm) REVERT: F 302 HIS cc_start: 0.9420 (t-90) cc_final: 0.9056 (t70) REVERT: F 400 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6169 (mm-30) REVERT: B 246 ASN cc_start: 0.7618 (m-40) cc_final: 0.7256 (p0) outliers start: 21 outliers final: 14 residues processed: 100 average time/residue: 0.2261 time to fit residues: 36.0609 Evaluate side-chains 102 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 D residue 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 191 LYS 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 B residue 308 ARG 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 109 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 0.0670 chunk 141 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 103 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.100410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.072908 restraints weight = 55275.340| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 5.28 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13967 Z= 0.099 Angle : 0.618 11.041 18841 Z= 0.286 Chirality : 0.042 0.223 2173 Planarity : 0.003 0.049 2438 Dihedral : 4.718 43.765 1969 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.64 % Allowed : 15.34 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.21), residues: 1751 helix: 1.11 (0.18), residues: 839 sheet: 0.43 (0.31), residues: 307 loop : 0.15 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 257 PHE 0.017 0.001 PHE D 274 TYR 0.007 0.001 TYR D 217 ARG 0.005 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.02581 ( 677) hydrogen bonds : angle 4.31469 ( 1926) covalent geometry : bond 0.00216 (13967) covalent geometry : angle 0.61828 (18841) *********************** 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 114 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.6910 (mmm) cc_final: 0.6665 (mmm) REVERT: E 144 PHE cc_start: 0.7154 (p90) cc_final: 0.6895 (p90) REVERT: E 191 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7796 (mtmm) REVERT: E 269 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8643 (mpp) REVERT: E 307 MET cc_start: 0.8970 (tpp) cc_final: 0.8494 (mmm) REVERT: F 302 HIS cc_start: 0.9437 (t-90) cc_final: 0.8987 (t70) REVERT: F 400 GLU cc_start: 0.6179 (mt-10) cc_final: 0.5814 (mm-30) REVERT: B 89 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8038 (p0) REVERT: B 246 ASN cc_start: 0.7653 (m-40) cc_final: 0.7303 (p0) REVERT: B 348 ASN cc_start: 0.8892 (p0) cc_final: 0.8629 (p0) REVERT: A 348 ASN cc_start: 0.7828 (p0) cc_final: 0.7626 (p0) outliers start: 24 outliers final: 15 residues processed: 107 average time/residue: 0.2266 time to fit residues: 38.7751 Evaluate side-chains 105 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 311 GLN Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain F residue 268 MET Chi-restraints excluded: chain B residue 89 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 370 CYS 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 93 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.099674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070910 restraints weight = 55497.553| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 4.93 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 13967 Z= 0.200 Angle : 0.861 59.196 18841 Z= 0.475 Chirality : 0.045 0.433 2173 Planarity : 0.004 0.113 2438 Dihedral : 4.713 43.890 1969 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.48 % Favored : 98.46 % Rotamer: Outliers : 1.16 % Allowed : 15.96 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1751 helix: 1.09 (0.18), residues: 839 sheet: 0.42 (0.31), residues: 307 loop : 0.13 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.032 0.001 HIS E 352 PHE 0.017 0.001 PHE D 274 TYR 0.008 0.001 TYR C 217 ARG 0.005 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 677) hydrogen bonds : angle 4.34496 ( 1926) covalent geometry : bond 0.00421 (13967) covalent geometry : angle 0.86079 (18841) ********************** 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 105 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 142 MET cc_start: 0.7252 (mmm) cc_final: 0.6980 (mmm) REVERT: E 144 PHE cc_start: 0.7089 (p90) cc_final: 0.6840 (p90) REVERT: E 191 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7807 (mtmm) REVERT: E 269 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8568 (mpp) REVERT: F 302 HIS cc_start: 0.9453 (t-90) cc_final: 0.9072 (t70) REVERT: F 400 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6052 (mm-30) REVERT: B 246 ASN cc_start: 0.7635 (m-40) cc_final: 0.7296 (p0) outliers start: 17 outliers final: 15 residues processed: 99 average time/residue: 0.2193 time to fit residues: 34.7558 Evaluate side-chains 103 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 C residue 145 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain E residue 191 LYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain F residue 268 MET Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 370 CYS 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 25 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 58 optimal weight: 0.0370 chunk 61 optimal weight: 7.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.099685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.070910 restraints weight = 55805.343| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.87 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 13967 Z= 0.200 Angle : 0.861 59.196 18841 Z= 0.475 Chirality : 0.045 0.433 2173 Planarity : 0.004 0.113 2438 Dihedral : 4.713 43.890 1969 Min Nonbonded Distance : 1.376 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.48 % Favored : 98.46 % Rotamer: Outliers : 1.16 % Allowed : 15.89 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.35 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1751 helix: 1.09 (0.18), residues: 839 sheet: 0.42 (0.31), residues: 307 loop : 0.13 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.032 0.001 HIS E 352 PHE 0.017 0.001 PHE D 274 TYR 0.008 0.001 TYR C 217 ARG 0.005 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 677) hydrogen bonds : angle 4.34496 ( 1926) covalent geometry : bond 0.00421 (13967) covalent geometry : angle 0.86079 (18841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6382.43 seconds wall clock time: 112 minutes 16.53 seconds (6736.53 seconds total)