Starting phenix.real_space_refine on Fri Aug 7 17:09:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9a_71404/08_2026/9p9a_71404.map" } resolution = 3.5 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= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11978 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 5 5.89 5 P 23 5.49 5 Mg 5 5.21 5 S 65 5.16 5 C 7995 2.51 5 N 2277 2.21 5 O 2578 1.98 5 F 20 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12968 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2021 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1663 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain breaks: 5 Chain: "C" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2229 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain: "D" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2199 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Chain: "H" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2233 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "F" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2208 Classifications: {'peptide': 281} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Chain: "M" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, 'ALF': 1, 'TYD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'ALF': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' MG': 1, 'TYD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, 'ALF': 1, 'TYD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, 'ALF': 1, 'TYD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, 'ALF': 1, 'TYD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.76, per 1000 atoms: 0.21 Number of scatterers: 12968 At special positions: 0 Unit cell: (86.33, 128.04, 137.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 65 16.00 P 23 15.00 Al 5 13.00 Mg 5 11.99 F 20 9.00 O 2578 8.00 N 2277 7.00 C 7995 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 743.8 milliseconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 50.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 259 through 266 Processing helix chain 'A' and resid 269 through 284 removed outlier: 4.010A pdb=" N TRP A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 313 Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 334 through 354 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.918A pdb=" N VAL A 367 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.823A pdb=" N ILE A 380 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.300A pdb=" N ILE A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 388 " --> pdb=" O SER A 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 390 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 403 Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.583A pdb=" N GLN B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 removed outlier: 4.252A pdb=" N MET B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 334 through 354 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.657A pdb=" N GLN B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 380 removed outlier: 4.163A pdb=" N ILE B 380 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'C' and resid 162 through 177 removed outlier: 3.799A pdb=" N VAL C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 198 removed outlier: 3.671A pdb=" N MET C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 231 Processing helix chain 'C' and resid 243 through 256 removed outlier: 3.573A pdb=" N LEU C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 269 through 286 removed outlier: 3.527A pdb=" N TRP C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 311 removed outlier: 3.631A pdb=" N ARG C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.571A pdb=" N ILE C 325 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.589A pdb=" N ARG C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 4.005A pdb=" N VAL C 367 " --> pdb=" O SER C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 380 removed outlier: 4.306A pdb=" N ILE C 380 " --> pdb=" O MET C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 402 No H-bonds generated for 'chain 'C' and resid 400 through 402' Processing helix chain 'D' and resid 161 through 178 removed outlier: 3.587A pdb=" N ILE D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 198 removed outlier: 3.656A pdb=" N MET D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 231 Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.504A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 266 Processing helix chain 'D' and resid 269 through 285 removed outlier: 3.611A pdb=" N TRP D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS D 275 " --> pdb=" O GLU D 271 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 313 removed outlier: 4.127A pdb=" N GLU D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.640A pdb=" N ILE D 325 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.710A pdb=" N ALA D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 370 removed outlier: 3.709A pdb=" N VAL D 367 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 369 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 380 removed outlier: 3.953A pdb=" N ILE D 380 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 3.947A pdb=" N GLN D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 390 " --> pdb=" O ILE D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 402 No H-bonds generated for 'chain 'D' and resid 400 through 402' Processing helix chain 'H' and resid 161 through 178 removed outlier: 3.991A pdb=" N ILE H 165 " --> pdb=" O ASN H 161 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP H 171 " --> pdb=" O VAL H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 198 removed outlier: 3.593A pdb=" N MET H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 231 Processing helix chain 'H' and resid 243 through 257 removed outlier: 3.598A pdb=" N LEU H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 256 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN H 257 " --> pdb=" O CYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 266 Processing helix chain 'H' and resid 269 through 285 removed outlier: 3.571A pdb=" N MET H 278 " --> pdb=" O GLY H 274 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY H 281 " --> pdb=" O THR H 277 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN H 285 " --> pdb=" O GLY H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 312 removed outlier: 3.707A pdb=" N GLU H 311 " --> pdb=" O ARG H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 321 through 325 Processing helix chain 'H' and resid 334 through 354 removed outlier: 3.553A pdb=" N GLU H 338 " --> pdb=" O ASN H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 364 through 370 removed outlier: 3.942A pdb=" N VAL H 367 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG H 370 " --> pdb=" O VAL H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 376 through 380 removed outlier: 4.052A pdb=" N ILE H 380 " --> pdb=" O MET H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 384 through 390 removed outlier: 3.797A pdb=" N GLN H 388 " --> pdb=" O GLY H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 402 No H-bonds generated for 'chain 'H' and resid 400 through 402' Processing helix chain 'F' and resid 162 through 178 removed outlier: 3.649A pdb=" N VAL F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN F 178 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 198 Processing helix chain 'F' and resid 215 through 231 Processing helix chain 'F' and resid 243 through 257 removed outlier: 3.517A pdb=" N ALA F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.877A pdb=" N TRP F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY F 274 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 310 Processing helix chain 'F' and resid 321 through 325 removed outlier: 3.531A pdb=" N ILE F 325 " --> pdb=" O LEU F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 354 Processing helix chain 'F' and resid 364 through 369 removed outlier: 3.929A pdb=" N VAL F 367 " --> pdb=" O SER F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 380 removed outlier: 4.138A pdb=" N ILE F 380 " --> pdb=" O MET F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 389 removed outlier: 3.921A pdb=" N GLN F 388 " --> pdb=" O GLY F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 439 removed outlier: 3.893A pdb=" N LYS A 437 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 393 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 205 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ALA A 394 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE A 207 " --> pdb=" O ALA A 394 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU A 396 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA A 209 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ARG A 398 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 206 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N SER A 361 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A 208 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 236 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 238 removed outlier: 6.290A pdb=" N ILE B 317 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU B 360 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE B 319 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 206 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N SER B 361 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL B 208 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 393 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.694A pdb=" N LYS C 160 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE D 290 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 360 " --> pdb=" O ILE D 319 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 206 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N SER D 361 " --> pdb=" O ILE D 206 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 208 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU D 205 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N ALA D 394 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 207 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU D 396 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA D 209 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ARG D 398 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 393 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY D 425 " --> pdb=" O ILE D 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 288 through 291 removed outlier: 3.699A pdb=" N ALA C 210 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU C 205 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ALA C 394 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 207 " --> pdb=" O ALA C 394 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU C 396 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA C 209 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ARG C 398 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL C 393 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 437 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 288 through 291 removed outlier: 6.502A pdb=" N ILE H 317 " --> pdb=" O ILE H 358 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU H 360 " --> pdb=" O ILE H 317 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE H 319 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 9.923A pdb=" N GLN H 362 " --> pdb=" O ILE H 319 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE H 206 " --> pdb=" O ALA H 359 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER H 361 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL H 208 " --> pdb=" O SER H 361 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU H 205 " --> pdb=" O ILE H 392 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA H 394 " --> pdb=" O LEU H 205 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE H 207 " --> pdb=" O ALA H 394 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU H 396 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ALA H 209 " --> pdb=" O LEU H 396 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ARG H 398 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL H 393 " --> pdb=" O ALA H 417 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 288 through 291 removed outlier: 3.650A pdb=" N ALA F 210 " --> pdb=" O SER F 361 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU F 205 " --> pdb=" O ILE F 392 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA F 394 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE F 207 " --> pdb=" O ALA F 394 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU F 396 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA F 209 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N ARG F 398 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL F 393 " --> pdb=" O ALA F 417 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1683 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: 2.25 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3950 1.33 - 1.45: 1510 1.45 - 1.57: 7476 1.57 - 1.69: 40 1.69 - 1.81: 139 Bond restraints: 13115 Sorted by residual: bond pdb=" O3A TYD C 502 " pdb=" PB TYD C 502 " ideal model delta sigma weight residual 1.714 1.600 0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" O3A TYD A 502 " pdb=" PB TYD A 502 " ideal model delta sigma weight residual 1.714 1.600 0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" O3A TYD H 502 " pdb=" PB TYD H 502 " ideal model delta sigma weight residual 1.714 1.600 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" O3A TYD D 502 " pdb=" PB TYD D 502 " ideal model delta sigma weight residual 1.714 1.600 0.114 2.00e-02 2.50e+03 3.25e+01 bond pdb=" O3A TYD F 502 " pdb=" PB TYD F 502 " ideal model delta sigma weight residual 1.714 1.600 0.114 2.00e-02 2.50e+03 3.23e+01 ... (remaining 13110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.25: 17694 14.25 - 28.51: 20 28.51 - 42.76: 0 42.76 - 57.01: 0 57.01 - 71.26: 10 Bond angle restraints: 17724 Sorted by residual: angle pdb=" F1 ALF F 503 " pdb="AL ALF F 503 " pdb=" F2 ALF F 503 " ideal model delta sigma weight residual 108.68 179.94 -71.26 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F1 ALF D 503 " pdb="AL ALF D 503 " pdb=" F2 ALF D 503 " ideal model delta sigma weight residual 108.68 179.89 -71.21 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F1 ALF H 503 " pdb="AL ALF H 503 " pdb=" F2 ALF H 503 " ideal model delta sigma weight residual 108.68 179.87 -71.19 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F1 ALF A 503 " pdb="AL ALF A 503 " pdb=" F2 ALF A 503 " ideal model delta sigma weight residual 108.68 179.83 -71.15 3.00e+00 1.11e-01 5.63e+02 angle pdb=" F1 ALF B 501 " pdb="AL ALF B 501 " pdb=" F2 ALF B 501 " ideal model delta sigma weight residual 108.68 179.74 -71.06 3.00e+00 1.11e-01 5.61e+02 ... (remaining 17719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7755 17.90 - 35.79: 308 35.79 - 53.69: 94 53.69 - 71.58: 32 71.58 - 89.48: 5 Dihedral angle restraints: 8194 sinusoidal: 3558 harmonic: 4636 Sorted by residual: dihedral pdb=" O5' TYD D 502 " pdb=" O3A TYD D 502 " pdb=" PA TYD D 502 " pdb=" PB TYD D 502 " ideal model delta sinusoidal sigma weight residual 86.64 176.12 -89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA LYS A 216 " pdb=" CB LYS A 216 " pdb=" CG LYS A 216 " pdb=" CD LYS A 216 " ideal model delta sinusoidal sigma weight residual 180.00 120.68 59.32 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA GLU D 174 " pdb=" CB GLU D 174 " pdb=" CG GLU D 174 " pdb=" CD GLU D 174 " ideal model delta sinusoidal sigma weight residual 180.00 121.84 58.16 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1367 0.036 - 0.072: 439 0.072 - 0.108: 130 0.108 - 0.144: 95 0.144 - 0.180: 5 Chirality restraints: 2036 Sorted by residual: chirality pdb=" C3' TYD H 502 " pdb=" C2' TYD H 502 " pdb=" C4' TYD H 502 " pdb=" O3' TYD H 502 " both_signs ideal model delta sigma weight residual False -2.50 -2.68 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" C3' TYD C 502 " pdb=" C2' TYD C 502 " pdb=" C4' TYD C 502 " pdb=" O3' TYD C 502 " both_signs ideal model delta sigma weight residual False -2.50 -2.67 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C3' TYD D 502 " pdb=" C2' TYD D 502 " pdb=" C4' TYD D 502 " pdb=" O3' TYD D 502 " both_signs ideal model delta sigma weight residual False -2.50 -2.67 0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 2033 not shown) Planarity restraints: 2256 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 422 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO D 423 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO D 423 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 423 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 422 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO F 423 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 423 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO F 423 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY H 422 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.00e+00 pdb=" N PRO H 423 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 423 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 423 " 0.019 5.00e-02 4.00e+02 ... (remaining 2253 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 130 2.61 - 3.19: 10577 3.19 - 3.76: 17230 3.76 - 4.33: 23833 4.33 - 4.90: 41713 Nonbonded interactions: 93483 Sorted by model distance: nonbonded pdb=" OG1 THR H 217 " pdb="MG MG H 501 " model vdw 2.042 2.170 nonbonded pdb=" NZ LYS F 418 " pdb=" F1 ALF A 503 " model vdw 2.052 3.070 nonbonded pdb="MG MG H 501 " pdb=" O1B TYD H 502 " model vdw 2.075 2.170 nonbonded pdb="MG MG D 501 " pdb=" O1B TYD D 502 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR F 217 " pdb="MG MG F 501 " model vdw 2.101 2.170 ... (remaining 93478 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 183 through 328 or resid 333 through 502)) selection = (chain 'C' and (resid 183 through 328 or resid 333 through 502)) selection = (chain 'D' and resid 183 through 502) selection = (chain 'F' and (resid 183 through 328 or resid 333 through 502)) selection = (chain 'H' and (resid 183 through 328 or resid 333 through 502)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.500 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.006 0.114 13120 Z= 0.308 Angle : 1.869 71.265 17724 Z= 0.673 Chirality : 0.045 0.180 2036 Planarity : 0.003 0.037 2256 Dihedral : 11.441 89.479 5182 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 0.58 % Allowed : 4.18 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.46 (0.22), residues: 1574 helix: 1.96 (0.22), residues: 602 sheet: 2.14 (0.27), residues: 366 loop : -0.88 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 398 TYR 0.007 0.001 TYR C 401 PHE 0.011 0.001 PHE C 219 TRP 0.005 0.001 TRP A 273 HIS 0.001 0.001 HIS F 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.29 (13115) covalent geometry : angle 1.86866 / 0.67 (17724) hydrogen bonds : bond 0.23910 / 16.40 ( 593) hydrogen bonds : angle 6.63258 / 4.65 ( 1683) Misc. bond : bond 0.05617 / 2.75 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 314 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 432 ILE cc_start: 0.7305 (mt) cc_final: 0.6958 (pt) REVERT: A 433 LYS cc_start: 0.8679 (mttp) cc_final: 0.7970 (mmtt) REVERT: B 161 ASN cc_start: 0.6673 (m-40) cc_final: 0.6436 (m-40) REVERT: B 165 ILE cc_start: 0.8484 (mt) cc_final: 0.8027 (mm) REVERT: B 368 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6730 (mp0) REVERT: B 440 ASN cc_start: 0.5623 (m-40) cc_final: 0.5318 (m-40) REVERT: C 437 LYS cc_start: 0.8499 (tttm) cc_final: 0.8254 (ttpt) REVERT: D 433 LYS cc_start: 0.8261 (mttp) cc_final: 0.7653 (mttm) REVERT: H 361 SER cc_start: 0.8304 (t) cc_final: 0.8016 (p) outliers start: 8 outliers final: 5 residues processed: 322 average time/residue: 0.1366 time to fit residues: 59.8417 Evaluate side-chains 159 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 392 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 GLN A 261 GLN A 371 GLN A 408 ASN A 419 GLN A 436 ASN B 168 GLN B 201 GLN B 222 ASN B 362 GLN B 419 GLN C 172 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN C 408 ASN C 419 GLN C 428 GLN D 225 GLN D 419 GLN H 336 GLN H 362 GLN H 419 GLN H 428 GLN F 419 GLN F 428 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.149802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.111990 restraints weight = 17611.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.116643 restraints weight = 10396.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118379 restraints weight = 6958.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118828 restraints weight = 5618.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119187 restraints weight = 5467.375| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13120 Z= 0.144 Angle : 0.912 34.262 17724 Z= 0.387 Chirality : 0.046 0.157 2036 Planarity : 0.004 0.069 2256 Dihedral : 11.824 114.779 2020 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.43 % Favored : 96.51 % Rotamer: Outliers : 2.74 % Allowed : 10.46 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.62 (0.22), residues: 1574 helix: 2.29 (0.21), residues: 629 sheet: 1.70 (0.27), residues: 371 loop : -0.81 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 398 TYR 0.014 0.001 TYR F 170 PHE 0.011 0.001 PHE C 219 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (13115) covalent geometry : angle 0.91157 / 0.39 (17724) hydrogen bonds : bond 0.05813 / 3.99 ( 593) hydrogen bonds : angle 5.01320 / 3.53 ( 1683) Misc. bond : bond 0.00358 / 0.18 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.398 Fit side-chains REVERT: A 433 LYS cc_start: 0.8480 (mttp) cc_final: 0.7890 (mmtt) REVERT: B 165 ILE cc_start: 0.8069 (mt) cc_final: 0.7769 (mm) REVERT: B 346 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7104 (mp) REVERT: B 362 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6378 (mp10) REVERT: C 233 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: C 437 LYS cc_start: 0.8290 (tttm) cc_final: 0.7882 (ttpt) REVERT: D 433 LYS cc_start: 0.8197 (mttp) cc_final: 0.7612 (mttm) REVERT: F 377 MET cc_start: 0.8552 (mtp) cc_final: 0.8286 (ttm) outliers start: 38 outliers final: 19 residues processed: 188 average time/residue: 0.1166 time to fit residues: 30.5674 Evaluate side-chains 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 362 GLN Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 233 GLU Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN B 222 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.149066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110904 restraints weight = 17759.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115666 restraints weight = 10654.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117352 restraints weight = 7295.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117960 restraints weight = 5521.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118314 restraints weight = 5432.919| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13120 Z= 0.122 Angle : 0.860 30.844 17724 Z= 0.356 Chirality : 0.046 0.167 2036 Planarity : 0.003 0.050 2256 Dihedral : 11.560 116.619 2016 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer: Outliers : 2.45 % Allowed : 12.41 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.62 (0.22), residues: 1574 helix: 2.44 (0.21), residues: 627 sheet: 1.59 (0.27), residues: 362 loop : -0.84 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 398 TYR 0.017 0.001 TYR F 170 PHE 0.012 0.001 PHE H 219 TRP 0.004 0.001 TRP A 273 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13115) covalent geometry : angle 0.85967 / 0.36 (17724) hydrogen bonds : bond 0.04546 / 3.10 ( 593) hydrogen bonds : angle 4.56125 / 3.23 ( 1683) Misc. bond : bond 0.00121 / 0.06 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 433 LYS cc_start: 0.8413 (mttp) cc_final: 0.7862 (mmtt) REVERT: B 165 ILE cc_start: 0.8208 (mt) cc_final: 0.7950 (mm) REVERT: B 346 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7024 (mp) REVERT: C 233 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: C 437 LYS cc_start: 0.8302 (tttm) cc_final: 0.7920 (ttpt) REVERT: D 302 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7739 (ttt-90) REVERT: D 433 LYS cc_start: 0.8178 (mttp) cc_final: 0.7580 (mttm) REVERT: H 326 GLN cc_start: 0.8149 (mt0) cc_final: 0.7934 (tt0) REVERT: F 377 MET cc_start: 0.8560 (mtp) cc_final: 0.8358 (ttm) outliers start: 34 outliers final: 22 residues processed: 167 average time/residue: 0.1098 time to fit residues: 25.9310 Evaluate side-chains 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 120 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.149988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112251 restraints weight = 17678.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116347 restraints weight = 10580.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118685 restraints weight = 6763.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118743 restraints weight = 5644.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118868 restraints weight = 5457.646| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13120 Z= 0.102 Angle : 0.843 30.309 17724 Z= 0.343 Chirality : 0.045 0.164 2036 Planarity : 0.003 0.044 2256 Dihedral : 11.518 114.160 2014 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 2.96 % Allowed : 12.27 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.75 (0.22), residues: 1574 helix: 2.66 (0.21), residues: 619 sheet: 1.59 (0.27), residues: 360 loop : -0.82 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.018 0.001 TYR F 170 PHE 0.013 0.001 PHE B 219 TRP 0.004 0.001 TRP A 273 HIS 0.001 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13115) covalent geometry : angle 0.84297 / 0.34 (17724) hydrogen bonds : bond 0.03784 / 2.60 ( 593) hydrogen bonds : angle 4.31351 / 3.06 ( 1683) Misc. bond : bond 0.00057 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 141 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 433 LYS cc_start: 0.8409 (mttp) cc_final: 0.7845 (mmtt) REVERT: B 165 ILE cc_start: 0.8259 (mt) cc_final: 0.8046 (mm) REVERT: B 346 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7146 (mp) REVERT: C 233 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8054 (mm-30) REVERT: C 249 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8243 (tpp) REVERT: C 437 LYS cc_start: 0.8268 (tttm) cc_final: 0.7824 (ttpt) REVERT: D 280 MET cc_start: 0.8572 (mtm) cc_final: 0.8350 (mtp) REVERT: D 433 LYS cc_start: 0.8171 (mttp) cc_final: 0.7567 (mttm) REVERT: F 307 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7558 (ttm110) outliers start: 41 outliers final: 24 residues processed: 171 average time/residue: 0.1118 time to fit residues: 27.0883 Evaluate side-chains 157 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 321 TYR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 436 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 GLN H 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.147297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109400 restraints weight = 17983.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.112725 restraints weight = 11304.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115317 restraints weight = 7463.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115249 restraints weight = 6090.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115617 restraints weight = 5916.605| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13120 Z= 0.132 Angle : 0.851 30.373 17724 Z= 0.350 Chirality : 0.045 0.160 2036 Planarity : 0.003 0.043 2256 Dihedral : 11.447 110.672 2014 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 2.67 % Allowed : 13.06 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.22), residues: 1574 helix: 2.66 (0.21), residues: 619 sheet: 1.37 (0.27), residues: 360 loop : -0.85 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.018 0.001 TYR F 170 PHE 0.011 0.001 PHE H 219 TRP 0.005 0.001 TRP D 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13115) covalent geometry : angle 0.85080 / 0.35 (17724) hydrogen bonds : bond 0.04304 / 2.94 ( 593) hydrogen bonds : angle 4.28615 / 3.04 ( 1683) Misc. bond : bond 0.00053 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 433 LYS cc_start: 0.8367 (mttp) cc_final: 0.7824 (mmtt) REVERT: B 346 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7014 (mp) REVERT: C 233 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: C 434 GLU cc_start: 0.8161 (mp0) cc_final: 0.7742 (pt0) REVERT: C 437 LYS cc_start: 0.8253 (tttm) cc_final: 0.7774 (ttpt) REVERT: D 280 MET cc_start: 0.8586 (mtm) cc_final: 0.8351 (mtp) REVERT: D 433 LYS cc_start: 0.8189 (mttp) cc_final: 0.7571 (mttm) outliers start: 37 outliers final: 23 residues processed: 159 average time/residue: 0.1164 time to fit residues: 26.1961 Evaluate side-chains 154 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 436 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.146453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108619 restraints weight = 17897.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112021 restraints weight = 11210.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114529 restraints weight = 7525.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114598 restraints weight = 6005.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114853 restraints weight = 5830.863| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13120 Z= 0.139 Angle : 0.857 30.135 17724 Z= 0.354 Chirality : 0.046 0.150 2036 Planarity : 0.003 0.044 2256 Dihedral : 11.227 100.290 2012 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.89 % Allowed : 13.28 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.51 (0.22), residues: 1574 helix: 2.57 (0.21), residues: 625 sheet: 1.16 (0.27), residues: 361 loop : -0.89 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.018 0.001 TYR F 170 PHE 0.011 0.001 PHE H 219 TRP 0.004 0.001 TRP D 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (13115) covalent geometry : angle 0.85694 / 0.35 (17724) hydrogen bonds : bond 0.04342 / 2.96 ( 593) hydrogen bonds : angle 4.27502 / 3.04 ( 1683) Misc. bond : bond 0.00069 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.8971 (tpp) cc_final: 0.8620 (tpp) REVERT: A 433 LYS cc_start: 0.8424 (mttp) cc_final: 0.7832 (mmtt) REVERT: B 175 MET cc_start: 0.7924 (tmm) cc_final: 0.7670 (ptm) REVERT: B 346 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7037 (mp) REVERT: C 233 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: C 434 GLU cc_start: 0.8239 (mp0) cc_final: 0.7714 (pt0) REVERT: C 437 LYS cc_start: 0.8201 (tttm) cc_final: 0.7674 (ttpt) REVERT: D 280 MET cc_start: 0.8592 (mtm) cc_final: 0.8360 (mtp) REVERT: D 433 LYS cc_start: 0.8138 (mttp) cc_final: 0.7559 (mttm) outliers start: 40 outliers final: 31 residues processed: 158 average time/residue: 0.1212 time to fit residues: 26.9576 Evaluate side-chains 163 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.107517 restraints weight = 18046.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111173 restraints weight = 12451.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112403 restraints weight = 8440.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.112576 restraints weight = 6887.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113207 restraints weight = 6500.361| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13120 Z= 0.164 Angle : 0.875 30.438 17724 Z= 0.366 Chirality : 0.047 0.155 2036 Planarity : 0.003 0.045 2256 Dihedral : 11.206 88.696 2012 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.45 % Favored : 95.49 % Rotamer: Outliers : 3.10 % Allowed : 13.78 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.32 (0.21), residues: 1574 helix: 2.51 (0.21), residues: 624 sheet: 0.90 (0.27), residues: 361 loop : -0.99 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.018 0.001 TYR F 170 PHE 0.012 0.001 PHE H 219 TRP 0.005 0.001 TRP D 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (13115) covalent geometry : angle 0.87540 / 0.37 (17724) hydrogen bonds : bond 0.04815 / 3.29 ( 593) hydrogen bonds : angle 4.36617 / 3.09 ( 1683) Misc. bond : bond 0.00087 / 0.04 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8968 (tpp) cc_final: 0.8619 (tpp) REVERT: A 433 LYS cc_start: 0.8486 (mttp) cc_final: 0.7885 (mmtt) REVERT: B 175 MET cc_start: 0.7941 (tmm) cc_final: 0.7681 (ptm) REVERT: B 372 ASP cc_start: 0.6150 (t0) cc_final: 0.5929 (t0) REVERT: C 233 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: C 249 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (tpp) REVERT: C 437 LYS cc_start: 0.8192 (tttm) cc_final: 0.7750 (ttpt) REVERT: D 280 MET cc_start: 0.8549 (mtm) cc_final: 0.8308 (mtp) REVERT: D 433 LYS cc_start: 0.8137 (mttp) cc_final: 0.7563 (mttm) outliers start: 43 outliers final: 34 residues processed: 170 average time/residue: 0.1181 time to fit residues: 28.5340 Evaluate side-chains 169 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 321 TYR Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109515 restraints weight = 17849.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112117 restraints weight = 11852.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.114494 restraints weight = 8075.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114450 restraints weight = 6567.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.114860 restraints weight = 6335.440| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13120 Z= 0.111 Angle : 0.851 30.068 17724 Z= 0.349 Chirality : 0.045 0.146 2036 Planarity : 0.003 0.042 2256 Dihedral : 11.038 88.672 2012 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.38 % Rotamer: Outliers : 2.31 % Allowed : 15.08 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.22), residues: 1574 helix: 2.69 (0.21), residues: 619 sheet: 0.99 (0.27), residues: 359 loop : -0.89 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.019 0.001 TYR F 170 PHE 0.010 0.001 PHE B 219 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (13115) covalent geometry : angle 0.85092 / 0.35 (17724) hydrogen bonds : bond 0.03748 / 2.56 ( 593) hydrogen bonds : angle 4.18552 / 2.97 ( 1683) Misc. bond : bond 0.00045 / 0.02 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.8944 (tpp) cc_final: 0.8608 (tpp) REVERT: A 433 LYS cc_start: 0.8518 (mttp) cc_final: 0.7884 (mmtt) REVERT: B 175 MET cc_start: 0.7904 (tmm) cc_final: 0.7655 (ptm) REVERT: C 233 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: C 437 LYS cc_start: 0.8227 (tttm) cc_final: 0.7782 (ttpt) REVERT: D 280 MET cc_start: 0.8594 (mtm) cc_final: 0.8363 (mtp) REVERT: D 433 LYS cc_start: 0.8120 (mttp) cc_final: 0.7545 (mttm) outliers start: 32 outliers final: 24 residues processed: 158 average time/residue: 0.1067 time to fit residues: 23.7469 Evaluate side-chains 153 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 0 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN B 326 GLN B 388 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109011 restraints weight = 18005.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113830 restraints weight = 11516.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.115006 restraints weight = 7635.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114699 restraints weight = 5969.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.115501 restraints weight = 6275.870| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13120 Z= 0.119 Angle : 0.857 30.189 17724 Z= 0.352 Chirality : 0.045 0.168 2036 Planarity : 0.003 0.041 2256 Dihedral : 11.005 88.448 2012 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.09 % Allowed : 15.37 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.22), residues: 1574 helix: 2.71 (0.21), residues: 619 sheet: 0.90 (0.27), residues: 361 loop : -0.86 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.019 0.001 TYR F 170 PHE 0.010 0.001 PHE B 219 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13115) covalent geometry : angle 0.85660 / 0.35 (17724) hydrogen bonds : bond 0.03873 / 2.65 ( 593) hydrogen bonds : angle 4.19086 / 2.97 ( 1683) Misc. bond : bond 0.00057 / 0.03 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.8940 (tpp) cc_final: 0.8615 (tpp) REVERT: A 433 LYS cc_start: 0.8519 (mttp) cc_final: 0.7898 (mmtt) REVERT: B 175 MET cc_start: 0.7915 (tmm) cc_final: 0.7585 (ptm) REVERT: C 233 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: C 437 LYS cc_start: 0.8208 (tttm) cc_final: 0.7741 (ttpt) REVERT: D 280 MET cc_start: 0.8599 (mtm) cc_final: 0.8371 (mtp) REVERT: D 433 LYS cc_start: 0.8117 (mttp) cc_final: 0.7541 (mttm) outliers start: 29 outliers final: 23 residues processed: 149 average time/residue: 0.1142 time to fit residues: 23.7611 Evaluate side-chains 151 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 119 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.144919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107177 restraints weight = 18164.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.110649 restraints weight = 12520.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111956 restraints weight = 8434.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112266 restraints weight = 6897.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112678 restraints weight = 6514.948| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13120 Z= 0.160 Angle : 0.880 30.380 17724 Z= 0.367 Chirality : 0.046 0.164 2036 Planarity : 0.003 0.044 2256 Dihedral : 11.105 87.935 2012 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Rotamer: Outliers : 1.88 % Allowed : 15.51 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.31 (0.22), residues: 1574 helix: 2.59 (0.21), residues: 619 sheet: 0.67 (0.27), residues: 362 loop : -0.92 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.019 0.001 TYR F 170 PHE 0.011 0.001 PHE H 219 TRP 0.005 0.001 TRP D 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (13115) covalent geometry : angle 0.87967 / 0.37 (17724) hydrogen bonds : bond 0.04615 / 3.15 ( 593) hydrogen bonds : angle 4.33731 / 3.07 ( 1683) Misc. bond : bond 0.00087 / 0.04 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 377 MET cc_start: 0.8949 (tpp) cc_final: 0.8619 (tpp) REVERT: A 433 LYS cc_start: 0.8538 (mttp) cc_final: 0.7947 (mmtt) REVERT: B 175 MET cc_start: 0.7970 (tmm) cc_final: 0.7611 (ptm) REVERT: C 233 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: C 437 LYS cc_start: 0.8181 (tttm) cc_final: 0.7698 (ttpt) REVERT: D 280 MET cc_start: 0.8547 (mtm) cc_final: 0.8308 (mtp) REVERT: D 433 LYS cc_start: 0.8124 (mttp) cc_final: 0.7551 (mttm) outliers start: 26 outliers final: 24 residues processed: 145 average time/residue: 0.1255 time to fit residues: 25.7438 Evaluate side-chains 151 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 278 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 387 GLU Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 230 LYS Chi-restraints excluded: chain H residue 296 ILE Chi-restraints excluded: chain H residue 298 VAL Chi-restraints excluded: chain H residue 387 GLU Chi-restraints excluded: chain H residue 392 ILE Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 253 CYS Chi-restraints excluded: chain F residue 355 VAL Chi-restraints excluded: chain F residue 412 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 8 optimal weight: 0.0870 chunk 112 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110151 restraints weight = 17872.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.114697 restraints weight = 11400.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115889 restraints weight = 7499.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115992 restraints weight = 5972.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116463 restraints weight = 5867.881| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13120 Z= 0.099 Angle : 0.850 29.945 17724 Z= 0.347 Chirality : 0.045 0.168 2036 Planarity : 0.003 0.040 2256 Dihedral : 10.854 88.017 2012 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 1.73 % Allowed : 15.87 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 are not related in a simple way. whole: 1.56 (0.22), residues: 1574 helix: 2.78 (0.21), residues: 619 sheet: 0.85 (0.27), residues: 359 loop : -0.78 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 307 TYR 0.020 0.001 TYR F 170 PHE 0.010 0.001 PHE B 219 TRP 0.005 0.001 TRP A 273 HIS 0.002 0.000 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13115) covalent geometry : angle 0.84999 / 0.35 (17724) hydrogen bonds : bond 0.03328 / 2.27 ( 593) hydrogen bonds : angle 4.13075 / 2.94 ( 1683) Misc. bond : bond 0.00033 / 0.02 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1992.67 seconds wall clock time: 35 minutes 5.69 seconds (2105.69 seconds total)