Starting phenix.real_space_refine on Wed Mar 4 12:58:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572.map" model { file = "/net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2j_20572/03_2026/6q2j_20572_neut.cif" } resolution = 4.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 132 5.16 5 C 8612 2.51 5 N 2426 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13796 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1477 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 183} Chain: "E" Number of atoms: 4493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4493 Classifications: {'peptide': 571} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 535} Chain breaks: 5 Chain: "E" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Restraints were copied for chains: B, D, F Time building chain proxies: 3.41, per 1000 atoms: 0.25 Number of scatterers: 13796 At special positions: 0 Unit cell: (129.47, 172.27, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 132 16.00 O 2618 8.00 N 2426 7.00 C 8612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 274 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 305 " distance=2.01 Simple disulfide: pdb=" SG CYS A 244 " - pdb=" SG CYS A 307 " distance=2.02 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 167 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 210 " distance=2.03 Simple disulfide: pdb=" SG CYS C 191 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 233 " distance=2.03 Simple disulfide: pdb=" SG CYS C 244 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 304 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 243 " distance=2.03 Simple disulfide: pdb=" SG CYS E 426 " - pdb=" SG CYS E 430 " distance=2.03 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 478 " distance=2.03 Simple disulfide: pdb=" SG CYS E 515 " - pdb=" SG CYS E 531 " distance=2.03 Simple disulfide: pdb=" SG CYS E 519 " - pdb=" SG CYS E 541 " distance=2.03 Simple disulfide: pdb=" SG CYS E 528 " - pdb=" SG CYS E 558 " distance=2.03 Simple disulfide: pdb=" SG CYS E 565 " - pdb=" SG CYS E 581 " distance=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 585 " distance=2.03 Simple disulfide: pdb=" SG CYS E 609 " - pdb=" SG CYS E 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 611 " - pdb=" SG CYS E 618 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 210 " distance=2.03 Simple disulfide: pdb=" SG CYS B 211 " - pdb=" SG CYS B 274 " distance=2.04 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 305 " distance=2.01 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 307 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 167 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 220 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 233 " distance=2.03 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 304 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 142 " distance=2.03 Simple disulfide: pdb=" SG CYS F 157 " - pdb=" SG CYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 243 " distance=2.03 Simple disulfide: pdb=" SG CYS F 426 " - pdb=" SG CYS F 430 " distance=2.03 Simple disulfide: pdb=" SG CYS F 449 " - pdb=" SG CYS F 478 " distance=2.03 Simple disulfide: pdb=" SG CYS F 515 " - pdb=" SG CYS F 531 " distance=2.03 Simple disulfide: pdb=" SG CYS F 519 " - pdb=" SG CYS F 541 " distance=2.03 Simple disulfide: pdb=" SG CYS F 528 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 565 " - pdb=" SG CYS F 581 " distance=2.03 Simple disulfide: pdb=" SG CYS F 570 " - pdb=" SG CYS F 585 " distance=2.03 Simple disulfide: pdb=" SG CYS F 609 " - pdb=" SG CYS F 620 " distance=2.03 Simple disulfide: pdb=" SG CYS F 611 " - pdb=" SG CYS F 618 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 701 " - " ASN E 361 " " NAG E 702 " - " ASN E 336 " " NAG E 703 " - " ASN E 377 " " NAG E 704 " - " ASN E 394 " " NAG E 705 " - " ASN E 468 " " NAG E 706 " - " ASN E 367 " " NAG E 707 " - " ASN E 98 " " NAG F 701 " - " ASN F 361 " " NAG F 702 " - " ASN F 336 " " NAG F 703 " - " ASN F 377 " " NAG F 704 " - " ASN F 394 " " NAG F 705 " - " ASN F 468 " " NAG F 706 " - " ASN F 367 " " NAG F 707 " - " ASN F 98 " Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 665.0 milliseconds 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 34 sheets defined 23.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 252 through 265 removed outlier: 3.759A pdb=" N GLN A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 155 Processing helix chain 'C' and resid 163 through 177 removed outlier: 3.657A pdb=" N GLN C 176 " --> pdb=" O ARG C 172 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 255 through 260 Processing helix chain 'C' and resid 272 through 283 Processing helix chain 'C' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN C 288 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 161 through 165 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 327' Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.891A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 433 " --> pdb=" O CYS E 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 433' Processing helix chain 'E' and resid 475 through 478 removed outlier: 3.510A pdb=" N CYS E 478 " --> pdb=" O ARG E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 475 through 478' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.582A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'B' and resid 252 through 265 removed outlier: 3.760A pdb=" N GLN B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 139 removed outlier: 3.603A pdb=" N VAL D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.658A pdb=" N GLN D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 177 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.594A pdb=" N PHE D 188 " --> pdb=" O GLN D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.566A pdb=" N GLN D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 229 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 255 through 260 Processing helix chain 'D' and resid 272 through 283 Processing helix chain 'D' and resid 285 through 289 removed outlier: 3.564A pdb=" N GLN D 288 " --> pdb=" O THR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.620A pdb=" N CYS D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.748A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 322 through 327 removed outlier: 4.038A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN F 327 " --> pdb=" O THR F 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 327' Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.890A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE F 433 " --> pdb=" O CYS F 430 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 433' Processing helix chain 'F' and resid 475 through 478 removed outlier: 3.509A pdb=" N CYS F 478 " --> pdb=" O ARG F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 475 through 478' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.581A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG A 212 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 241 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS A 274 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 307 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS A 305 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 278 " --> pdb=" O LYS A 303 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N MET A 282 " --> pdb=" O ASP A 299 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP A 299 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 284 " --> pdb=" O TYR A 297 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N TYR A 297 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN A 286 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN A 295 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR A 288 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 293 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR E 30 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU E 40 " --> pdb=" O PHE E 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR E 152 " --> pdb=" O LEU E 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.293A pdb=" N LEU E 97 " --> pdb=" O PRO E 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU E 94 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.954A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE E 174 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N TYR E 263 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE E 176 " --> pdb=" O TYR E 263 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL E 223 " --> pdb=" O PHE E 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU E 222 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 217 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 278 through 283 removed outlier: 3.859A pdb=" N ALA E 279 " --> pdb=" O HIS E 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 394 " --> pdb=" O ALA E 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 396 " --> pdb=" O ALA E 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL E 292 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU E 358 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 removed outlier: 6.900A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 421 through 425 removed outlier: 7.155A pdb=" N GLN E 421 " --> pdb=" O VAL E 467 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL E 467 " --> pdb=" O GLN E 421 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY E 423 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU E 465 " --> pdb=" O GLY E 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER E 462 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AB7, first strand: chain 'E' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER E 589 " --> pdb=" O CYS E 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS E 620 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 591 " --> pdb=" O CYS E 620 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AB9, first strand: chain 'B' and resid 212 through 219 removed outlier: 4.075A pdb=" N ARG B 212 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 241 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 288 removed outlier: 6.702A pdb=" N CYS B 274 " --> pdb=" O CYS B 307 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS B 307 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N CYS B 305 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER B 278 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 282 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP B 299 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 284 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR B 297 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN B 286 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLN B 295 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 288 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 293 " --> pdb=" O THR B 288 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.749A pdb=" N TYR F 30 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 40 " --> pdb=" O PHE F 150 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR F 152 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.438A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.292A pdb=" N LEU F 97 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU F 94 " --> pdb=" O GLN F 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 71 through 72 removed outlier: 3.953A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.510A pdb=" N PHE F 174 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N TYR F 263 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 176 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.739A pdb=" N VAL F 223 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU F 222 " --> pdb=" O ALA F 217 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA F 217 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 278 through 283 removed outlier: 3.858A pdb=" N ALA F 279 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 394 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER F 396 " --> pdb=" O ALA F 281 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 292 through 300 removed outlier: 7.120A pdb=" N VAL F 292 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU F 358 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 407 through 408 removed outlier: 6.899A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 421 through 425 removed outlier: 7.154A pdb=" N GLN F 421 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 467 " --> pdb=" O GLN F 421 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY F 423 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU F 465 " --> pdb=" O GLY F 423 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER F 462 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD6, first strand: chain 'F' and resid 589 through 591 removed outlier: 6.910A pdb=" N SER F 589 " --> pdb=" O CYS F 618 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N CYS F 620 " --> pdb=" O SER F 589 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 591 " --> pdb=" O CYS F 620 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 594 through 596 424 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4577 1.34 - 1.47: 3332 1.47 - 1.59: 6031 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 14090 Sorted by residual: bond pdb=" C1 NAG E 707 " pdb=" O5 NAG E 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG F 707 " pdb=" O5 NAG F 707 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.46e+00 bond pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.27e+00 bond pdb=" C1 NAG E 703 " pdb=" O5 NAG E 703 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 14085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 18382 2.19 - 4.37: 647 4.37 - 6.56: 75 6.56 - 8.75: 26 8.75 - 10.94: 10 Bond angle restraints: 19140 Sorted by residual: angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 120.24 125.00 -4.76 6.30e-01 2.52e+00 5.71e+01 angle pdb=" C CYS C 252 " pdb=" N HIS C 253 " pdb=" CA HIS C 253 " ideal model delta sigma weight residual 121.54 132.37 -10.83 1.91e+00 2.74e-01 3.21e+01 angle pdb=" C CYS D 252 " pdb=" N HIS D 253 " pdb=" CA HIS D 253 " ideal model delta sigma weight residual 121.54 132.36 -10.82 1.91e+00 2.74e-01 3.21e+01 angle pdb=" N ASP E 584 " pdb=" CA ASP E 584 " pdb=" C ASP E 584 " ideal model delta sigma weight residual 114.09 106.53 7.56 1.55e+00 4.16e-01 2.38e+01 ... (remaining 19135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 8472 16.65 - 33.29: 305 33.29 - 49.94: 68 49.94 - 66.59: 8 66.59 - 83.23: 8 Dihedral angle restraints: 8861 sinusoidal: 3789 harmonic: 5072 Sorted by residual: dihedral pdb=" CB CYS F 426 " pdb=" SG CYS F 426 " pdb=" SG CYS F 430 " pdb=" CB CYS F 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.23 83.23 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS E 426 " pdb=" SG CYS E 426 " pdb=" SG CYS E 430 " pdb=" CB CYS E 430 " ideal model delta sinusoidal sigma weight residual -86.00 -169.21 83.21 1 1.00e+01 1.00e-02 8.47e+01 dihedral pdb=" CB CYS C 191 " pdb=" SG CYS C 191 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual -86.00 -168.97 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 8858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1984 0.097 - 0.194: 194 0.194 - 0.292: 2 0.292 - 0.389: 0 0.389 - 0.486: 6 Chirality restraints: 2186 Sorted by residual: chirality pdb=" C1 NAG E 706 " pdb=" ND2 ASN E 367 " pdb=" C2 NAG E 706 " pdb=" O5 NAG E 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG F 706 " pdb=" ND2 ASN F 367 " pdb=" C2 NAG F 706 " pdb=" O5 NAG F 706 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" C1 NAG E 705 " pdb=" ND2 ASN E 468 " pdb=" C2 NAG E 705 " pdb=" O5 NAG E 705 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.86e+00 ... (remaining 2183 not shown) Planarity restraints: 2492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 275 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO B 276 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 275 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 276 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 598 " 0.039 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO F 599 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 599 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 599 " 0.034 5.00e-02 4.00e+02 ... (remaining 2489 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 24 2.32 - 2.97: 6014 2.97 - 3.61: 18089 3.61 - 4.26: 29216 4.26 - 4.90: 48607 Nonbonded interactions: 101950 Sorted by model distance: nonbonded pdb=" OD1 ASP E 230 " pdb=" OE1 GLU E 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 230 " pdb=" OE1 GLU F 232 " model vdw 1.677 3.040 nonbonded pdb=" OD1 ASP F 567 " pdb=" OD2 ASP F 584 " model vdw 1.917 3.040 nonbonded pdb=" OD1 ASP E 567 " pdb=" OD2 ASP E 584 " model vdw 1.918 3.040 nonbonded pdb=" O HIS F 569 " pdb=" OD2 ASP F 584 " model vdw 2.111 3.040 ... (remaining 101945 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2844 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 0.061 14159 Z= 0.273 Angle : 1.014 12.448 19292 Z= 0.560 Chirality : 0.059 0.486 2186 Planarity : 0.007 0.061 2478 Dihedral : 9.003 70.338 5396 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.04 % Favored : 94.84 % Rotamer: Outliers : 0.13 % Allowed : 1.70 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -3.22 (0.18), residues: 1706 helix: -2.97 (0.19), residues: 346 sheet: -1.09 (0.24), residues: 436 loop : -2.35 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 355 TYR 0.032 0.003 TYR E 263 PHE 0.025 0.003 PHE F 258 TRP 0.033 0.004 TRP E 334 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00581 (14090) covalent geometry : angle 0.97772 (19140) SS BOND : bond 0.00519 ( 55) SS BOND : angle 1.43915 ( 110) hydrogen bonds : bond 0.15524 ( 424) hydrogen bonds : angle 7.39444 ( 1176) link_NAG-ASN : bond 0.00982 ( 14) link_NAG-ASN : angle 5.57578 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 299 SER cc_start: 0.7256 (p) cc_final: 0.5982 (t) REVERT: D 310 MET cc_start: -0.0991 (mtm) cc_final: -0.2766 (mmp) REVERT: F 255 MET cc_start: -0.2474 (ptp) cc_final: -0.4323 (mtm) outliers start: 2 outliers final: 0 residues processed: 326 average time/residue: 0.1462 time to fit residues: 64.9685 Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 286 GLN C 184 GLN C 200 GLN C 206 HIS C 228 GLN C 229 ASN E 84 ASN E 187 GLN E 495 GLN B 286 GLN B 306 HIS ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 206 HIS D 228 GLN D 318 ASN F 187 GLN F 333 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.198498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.178714 restraints weight = 43935.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.179719 restraints weight = 36129.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.182224 restraints weight = 26634.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.182468 restraints weight = 20175.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.182448 restraints weight = 18217.994| |-----------------------------------------------------------------------------| r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3671 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 14159 Z= 0.146 Angle : 0.724 11.585 19292 Z= 0.362 Chirality : 0.049 0.395 2186 Planarity : 0.006 0.063 2478 Dihedral : 6.704 55.707 2182 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.26 % Allowed : 2.28 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.41 (0.19), residues: 1706 helix: -1.72 (0.24), residues: 360 sheet: -1.04 (0.24), residues: 462 loop : -1.82 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 217 TYR 0.014 0.002 TYR E 263 PHE 0.022 0.002 PHE F 31 TRP 0.019 0.002 TRP E 334 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00316 (14090) covalent geometry : angle 0.69550 (19140) SS BOND : bond 0.00453 ( 55) SS BOND : angle 1.38341 ( 110) hydrogen bonds : bond 0.04330 ( 424) hydrogen bonds : angle 6.07702 ( 1176) link_NAG-ASN : bond 0.00756 ( 14) link_NAG-ASN : angle 3.92674 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.5821 (mtp) cc_final: 0.5293 (mmm) REVERT: C 299 SER cc_start: 0.8224 (p) cc_final: 0.7411 (m) REVERT: E 43 ASP cc_start: 0.6909 (t70) cc_final: 0.6653 (t0) REVERT: E 500 LEU cc_start: 0.6963 (tp) cc_final: 0.6446 (tp) REVERT: D 310 MET cc_start: -0.1209 (mtm) cc_final: -0.2803 (mmp) REVERT: F 255 MET cc_start: -0.3419 (ptp) cc_final: -0.5215 (mtt) outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.1076 time to fit residues: 32.5026 Evaluate side-chains 136 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 104 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS C 206 HIS E 187 GLN D 318 ASN F 187 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.195597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.173725 restraints weight = 43805.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.176187 restraints weight = 31819.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.177535 restraints weight = 22666.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.178414 restraints weight = 18257.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.178601 restraints weight = 17420.017| |-----------------------------------------------------------------------------| r_work (final): 0.4731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4024 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14159 Z= 0.147 Angle : 0.673 14.156 19292 Z= 0.336 Chirality : 0.048 0.350 2186 Planarity : 0.005 0.051 2478 Dihedral : 6.058 57.711 2182 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.13 % Allowed : 2.35 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.98 (0.20), residues: 1706 helix: -1.14 (0.25), residues: 368 sheet: -0.85 (0.23), residues: 472 loop : -1.62 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 250 TYR 0.034 0.002 TYR E 263 PHE 0.019 0.001 PHE E 174 TRP 0.024 0.002 TRP B 225 HIS 0.013 0.001 HIS F 333 Details of bonding type rmsd covalent geometry : bond 0.00291 (14090) covalent geometry : angle 0.64683 (19140) SS BOND : bond 0.00946 ( 55) SS BOND : angle 1.23707 ( 110) hydrogen bonds : bond 0.03880 ( 424) hydrogen bonds : angle 5.78745 ( 1176) link_NAG-ASN : bond 0.00724 ( 14) link_NAG-ASN : angle 3.66489 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.5602 (mtp) cc_final: 0.5160 (mmm) REVERT: C 299 SER cc_start: 0.7986 (p) cc_final: 0.7343 (m) REVERT: E 43 ASP cc_start: 0.7396 (t70) cc_final: 0.7107 (t0) REVERT: E 313 ARG cc_start: 0.6807 (mmm160) cc_final: 0.6246 (mmm160) REVERT: E 408 TYR cc_start: 0.4730 (m-80) cc_final: 0.4509 (m-80) REVERT: D 310 MET cc_start: -0.0331 (mtm) cc_final: -0.1728 (mmt) REVERT: F 240 VAL cc_start: 0.1039 (t) cc_final: 0.0605 (t) REVERT: F 255 MET cc_start: -0.4069 (ptp) cc_final: -0.5143 (mtt) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.1107 time to fit residues: 32.3314 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 11 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN E 333 HIS E 359 ASN E 429 ASN ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 GLN D 206 HIS D 236 HIS ** D 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 HIS F 187 GLN F 429 ASN F 594 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.187038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.166267 restraints weight = 42454.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.168237 restraints weight = 33131.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.169602 restraints weight = 23447.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.169524 restraints weight = 18590.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.169846 restraints weight = 17453.118| |-----------------------------------------------------------------------------| r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4884 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 14159 Z= 0.186 Angle : 0.794 16.495 19292 Z= 0.398 Chirality : 0.051 0.357 2186 Planarity : 0.006 0.051 2478 Dihedral : 6.153 58.822 2182 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.13 % Allowed : 3.72 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.94 (0.19), residues: 1706 helix: -1.15 (0.25), residues: 362 sheet: -0.81 (0.24), residues: 462 loop : -1.57 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 175 TYR 0.040 0.003 TYR F 606 PHE 0.030 0.002 PHE C 307 TRP 0.029 0.003 TRP E 334 HIS 0.016 0.002 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00411 (14090) covalent geometry : angle 0.76845 (19140) SS BOND : bond 0.00452 ( 55) SS BOND : angle 1.84827 ( 110) hydrogen bonds : bond 0.04045 ( 424) hydrogen bonds : angle 6.04447 ( 1176) link_NAG-ASN : bond 0.00665 ( 14) link_NAG-ASN : angle 3.39729 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.2732 (mt) cc_final: 0.1946 (pt) REVERT: C 185 MET cc_start: 0.6376 (mtp) cc_final: 0.5819 (mmm) REVERT: C 281 ASP cc_start: 0.8140 (t0) cc_final: 0.7891 (p0) REVERT: C 299 SER cc_start: 0.7858 (p) cc_final: 0.7007 (m) REVERT: E 43 ASP cc_start: 0.7117 (t70) cc_final: 0.6904 (t0) REVERT: B 253 MET cc_start: 0.6138 (ptt) cc_final: 0.5538 (ptp) REVERT: D 310 MET cc_start: 0.1128 (mtm) cc_final: -0.0185 (mmp) REVERT: F 237 TYR cc_start: 0.1921 (m-80) cc_final: 0.1557 (m-80) REVERT: F 255 MET cc_start: -0.3564 (ptp) cc_final: -0.5137 (mtt) REVERT: F 346 PHE cc_start: 0.5322 (m-80) cc_final: 0.5076 (m-10) REVERT: F 579 ASN cc_start: 0.6778 (p0) cc_final: 0.6439 (m-40) outliers start: 2 outliers final: 1 residues processed: 199 average time/residue: 0.1224 time to fit residues: 35.6856 Evaluate side-chains 135 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 166 optimal weight: 0.0970 chunk 142 optimal weight: 0.0670 chunk 124 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 151 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 44 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS D 147 GLN D 184 GLN D 265 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.186352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.164953 restraints weight = 42400.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.166352 restraints weight = 33849.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.167964 restraints weight = 24091.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.168097 restraints weight = 17932.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.168413 restraints weight = 18432.402| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4984 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 14159 Z= 0.128 Angle : 0.673 15.120 19292 Z= 0.336 Chirality : 0.048 0.322 2186 Planarity : 0.005 0.049 2478 Dihedral : 5.580 54.024 2182 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.13 % Allowed : 2.48 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.68 (0.19), residues: 1706 helix: -0.93 (0.26), residues: 366 sheet: -0.61 (0.25), residues: 424 loop : -1.41 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 368 TYR 0.036 0.002 TYR E 354 PHE 0.019 0.002 PHE C 307 TRP 0.038 0.002 TRP B 225 HIS 0.015 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00282 (14090) covalent geometry : angle 0.64694 (19140) SS BOND : bond 0.00503 ( 55) SS BOND : angle 1.74748 ( 110) hydrogen bonds : bond 0.03450 ( 424) hydrogen bonds : angle 5.75522 ( 1176) link_NAG-ASN : bond 0.00565 ( 14) link_NAG-ASN : angle 3.09371 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.3158 (mt) cc_final: 0.2238 (pt) REVERT: C 185 MET cc_start: 0.6352 (mtp) cc_final: 0.5886 (mmm) REVERT: C 200 GLN cc_start: 0.7692 (mp10) cc_final: 0.7321 (mp10) REVERT: C 299 SER cc_start: 0.7922 (p) cc_final: 0.7508 (m) REVERT: C 301 GLU cc_start: 0.6525 (tm-30) cc_final: 0.6087 (tp30) REVERT: E 408 TYR cc_start: 0.4887 (m-80) cc_final: 0.4548 (m-80) REVERT: E 486 VAL cc_start: 0.6226 (t) cc_final: 0.6020 (m) REVERT: B 253 MET cc_start: 0.6682 (ptt) cc_final: 0.5899 (ptp) REVERT: D 310 MET cc_start: 0.1485 (mtm) cc_final: 0.0152 (mmp) REVERT: F 237 TYR cc_start: 0.1771 (m-80) cc_final: 0.1472 (m-80) REVERT: F 255 MET cc_start: -0.3647 (ptp) cc_final: -0.4907 (mtp) REVERT: F 346 PHE cc_start: 0.5118 (m-80) cc_final: 0.4896 (m-10) REVERT: F 579 ASN cc_start: 0.6802 (p0) cc_final: 0.6365 (m-40) outliers start: 2 outliers final: 0 residues processed: 193 average time/residue: 0.1227 time to fit residues: 34.4608 Evaluate side-chains 134 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 26 optimal weight: 5.9990 chunk 134 optimal weight: 20.0000 chunk 67 optimal weight: 0.0470 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 156 optimal weight: 0.1980 chunk 59 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 246 HIS E 482 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 177 ASN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.181564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.160577 restraints weight = 41957.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.161656 restraints weight = 38277.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.162690 restraints weight = 30971.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.163206 restraints weight = 24954.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.163441 restraints weight = 24940.620| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5328 moved from start: 0.7767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 14159 Z= 0.174 Angle : 0.725 17.955 19292 Z= 0.364 Chirality : 0.048 0.331 2186 Planarity : 0.005 0.049 2478 Dihedral : 5.463 42.640 2182 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.80 (0.20), residues: 1706 helix: -1.26 (0.25), residues: 388 sheet: -0.59 (0.25), residues: 418 loop : -1.43 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 234 TYR 0.020 0.002 TYR F 606 PHE 0.018 0.002 PHE F 258 TRP 0.032 0.002 TRP E 334 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00375 (14090) covalent geometry : angle 0.70349 (19140) SS BOND : bond 0.00539 ( 55) SS BOND : angle 1.68050 ( 110) hydrogen bonds : bond 0.03749 ( 424) hydrogen bonds : angle 5.95695 ( 1176) link_NAG-ASN : bond 0.00496 ( 14) link_NAG-ASN : angle 2.96150 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LEU cc_start: 0.4300 (mt) cc_final: 0.2883 (pt) REVERT: C 185 MET cc_start: 0.6656 (mtp) cc_final: 0.6212 (mmm) REVERT: C 299 SER cc_start: 0.7707 (p) cc_final: 0.7463 (m) REVERT: C 301 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6496 (tp30) REVERT: C 305 LYS cc_start: 0.7746 (mtpt) cc_final: 0.7295 (mtmt) REVERT: E 39 LYS cc_start: 0.6595 (mttt) cc_final: 0.5739 (mmtt) REVERT: E 408 TYR cc_start: 0.5177 (m-80) cc_final: 0.4822 (m-80) REVERT: B 252 ASN cc_start: 0.7832 (p0) cc_final: 0.6565 (m110) REVERT: B 253 MET cc_start: 0.7374 (ptt) cc_final: 0.6504 (ptm) REVERT: D 310 MET cc_start: 0.2136 (mtm) cc_final: 0.0353 (mmp) REVERT: F 237 TYR cc_start: 0.2281 (m-80) cc_final: 0.2062 (m-80) REVERT: F 255 MET cc_start: -0.3813 (ptp) cc_final: -0.4716 (mtp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.1116 time to fit residues: 33.5415 Evaluate side-chains 133 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 HIS D 147 GLN D 228 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 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 = 0.4808 r_free = 0.4808 target = 0.180659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.160722 restraints weight = 41620.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.160524 restraints weight = 46680.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.161522 restraints weight = 41259.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.162393 restraints weight = 29896.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.162663 restraints weight = 26962.413| |-----------------------------------------------------------------------------| r_work (final): 0.4552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5410 moved from start: 0.8431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14159 Z= 0.151 Angle : 0.716 17.464 19292 Z= 0.355 Chirality : 0.049 0.313 2186 Planarity : 0.005 0.072 2478 Dihedral : 5.255 39.300 2182 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.74 (0.20), residues: 1706 helix: -1.18 (0.25), residues: 392 sheet: -0.62 (0.24), residues: 440 loop : -1.36 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 212 TYR 0.018 0.002 TYR E 122 PHE 0.022 0.002 PHE C 307 TRP 0.029 0.002 TRP A 228 HIS 0.007 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00336 (14090) covalent geometry : angle 0.69614 (19140) SS BOND : bond 0.00564 ( 55) SS BOND : angle 1.56353 ( 110) hydrogen bonds : bond 0.03527 ( 424) hydrogen bonds : angle 5.76245 ( 1176) link_NAG-ASN : bond 0.00505 ( 14) link_NAG-ASN : angle 2.90904 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 ARG cc_start: 0.5206 (mmp80) cc_final: 0.4681 (mmm-85) REVERT: C 185 MET cc_start: 0.6726 (mtp) cc_final: 0.6227 (mmm) REVERT: C 214 MET cc_start: 0.7660 (mmp) cc_final: 0.6886 (mtp) REVERT: C 305 LYS cc_start: 0.7756 (mtpt) cc_final: 0.7511 (mtmt) REVERT: E 255 MET cc_start: 0.6941 (ppp) cc_final: 0.6293 (ppp) REVERT: E 256 VAL cc_start: 0.5790 (t) cc_final: 0.5583 (t) REVERT: E 408 TYR cc_start: 0.4954 (m-80) cc_final: 0.4604 (m-80) REVERT: B 252 ASN cc_start: 0.8190 (p0) cc_final: 0.7134 (m-40) REVERT: B 253 MET cc_start: 0.7199 (ptt) cc_final: 0.6640 (ptm) REVERT: D 310 MET cc_start: 0.2790 (mtm) cc_final: 0.0883 (mmp) REVERT: F 255 MET cc_start: -0.3822 (ptp) cc_final: -0.4653 (mtp) REVERT: F 422 ILE cc_start: 0.4285 (mp) cc_final: 0.4000 (mm) REVERT: F 473 LEU cc_start: 0.4207 (tp) cc_final: 0.2999 (tp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1143 time to fit residues: 34.1906 Evaluate side-chains 145 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 94 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 89 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 GLN E 359 ASN D 236 HIS D 241 GLN ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 HIS F 187 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.182973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.162472 restraints weight = 41252.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.161811 restraints weight = 43316.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.163408 restraints weight = 34137.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.164226 restraints weight = 26380.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.164551 restraints weight = 24408.026| |-----------------------------------------------------------------------------| r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5375 moved from start: 0.8590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 14159 Z= 0.111 Angle : 0.670 17.315 19292 Z= 0.326 Chirality : 0.047 0.301 2186 Planarity : 0.005 0.049 2478 Dihedral : 4.888 36.610 2182 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.43 (0.20), residues: 1706 helix: -0.79 (0.26), residues: 382 sheet: -0.49 (0.24), residues: 464 loop : -1.21 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 212 TYR 0.013 0.001 TYR E 122 PHE 0.027 0.001 PHE D 173 TRP 0.020 0.001 TRP E 334 HIS 0.009 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00247 (14090) covalent geometry : angle 0.65137 (19140) SS BOND : bond 0.00395 ( 55) SS BOND : angle 1.38469 ( 110) hydrogen bonds : bond 0.03019 ( 424) hydrogen bonds : angle 5.51716 ( 1176) link_NAG-ASN : bond 0.00530 ( 14) link_NAG-ASN : angle 2.78053 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.6641 (mtp) cc_final: 0.6240 (mmm) REVERT: C 305 LYS cc_start: 0.7617 (mtpt) cc_final: 0.7160 (mtmt) REVERT: E 408 TYR cc_start: 0.4785 (m-80) cc_final: 0.4396 (m-80) REVERT: E 500 LEU cc_start: 0.7188 (tp) cc_final: 0.6962 (tt) REVERT: E 606 TYR cc_start: 0.5255 (t80) cc_final: 0.5024 (t80) REVERT: B 299 ASP cc_start: 0.7664 (p0) cc_final: 0.7187 (p0) REVERT: D 310 MET cc_start: 0.2544 (mtm) cc_final: 0.0626 (mmp) REVERT: F 255 MET cc_start: -0.3459 (ptp) cc_final: -0.4412 (mtp) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1122 time to fit residues: 32.4779 Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 86 optimal weight: 0.0050 chunk 101 optimal weight: 0.0040 chunk 167 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 127 optimal weight: 0.0060 chunk 59 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 overall best weight: 0.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 359 ASN B 254 HIS D 147 GLN ** F 187 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 = 0.4834 r_free = 0.4834 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.161512 restraints weight = 42220.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.163612 restraints weight = 36844.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.164338 restraints weight = 28127.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.164458 restraints weight = 21468.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.164887 restraints weight = 20440.135| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.8727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 14159 Z= 0.112 Angle : 0.684 16.770 19292 Z= 0.331 Chirality : 0.047 0.291 2186 Planarity : 0.004 0.049 2478 Dihedral : 4.690 34.082 2182 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.27 (0.20), residues: 1706 helix: -0.67 (0.27), residues: 370 sheet: -0.32 (0.25), residues: 444 loop : -1.14 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 234 TYR 0.019 0.001 TYR E 606 PHE 0.024 0.001 PHE C 307 TRP 0.030 0.002 TRP F 85 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00250 (14090) covalent geometry : angle 0.66334 (19140) SS BOND : bond 0.00380 ( 55) SS BOND : angle 1.66410 ( 110) hydrogen bonds : bond 0.03080 ( 424) hydrogen bonds : angle 5.44319 ( 1176) link_NAG-ASN : bond 0.00509 ( 14) link_NAG-ASN : angle 2.68774 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 MET cc_start: 0.6971 (mtp) cc_final: 0.6421 (mmm) REVERT: E 408 TYR cc_start: 0.4726 (m-80) cc_final: 0.4333 (m-80) REVERT: B 299 ASP cc_start: 0.7413 (p0) cc_final: 0.6477 (p0) REVERT: D 141 ASP cc_start: 0.5040 (t0) cc_final: 0.4634 (t0) REVERT: D 143 VAL cc_start: 0.7401 (t) cc_final: 0.7171 (t) REVERT: D 310 MET cc_start: 0.2521 (mtm) cc_final: 0.0785 (mmp) REVERT: F 255 MET cc_start: -0.3759 (ptp) cc_final: -0.4546 (mtp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1041 time to fit residues: 30.4419 Evaluate side-chains 140 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN E 89 GLN E 392 HIS E 482 HIS ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN D 312 HIS ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.169776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.148666 restraints weight = 41263.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.148713 restraints weight = 43447.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.149787 restraints weight = 38362.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.150340 restraints weight = 27228.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.150648 restraints weight = 27084.918| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 1.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 14159 Z= 0.295 Angle : 0.992 18.062 19292 Z= 0.504 Chirality : 0.056 0.334 2186 Planarity : 0.007 0.059 2478 Dihedral : 6.247 42.427 2182 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -2.09 (0.19), residues: 1706 helix: -1.57 (0.25), residues: 364 sheet: -0.67 (0.25), residues: 420 loop : -1.64 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 209 TYR 0.043 0.004 TYR D 279 PHE 0.035 0.003 PHE D 173 TRP 0.072 0.004 TRP A 228 HIS 0.017 0.003 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00627 (14090) covalent geometry : angle 0.96899 (19140) SS BOND : bond 0.00963 ( 55) SS BOND : angle 2.35619 ( 110) hydrogen bonds : bond 0.04881 ( 424) hydrogen bonds : angle 6.71286 ( 1176) link_NAG-ASN : bond 0.00639 ( 14) link_NAG-ASN : angle 3.04003 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3412 Ramachandran restraints generated. 1706 Oldfield, 0 Emsley, 1706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 ASP cc_start: 0.6998 (m-30) cc_final: 0.6655 (t70) REVERT: A 287 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7754 (tptm) REVERT: C 214 MET cc_start: 0.7631 (mmp) cc_final: 0.7251 (mtp) REVERT: E 606 TYR cc_start: 0.6228 (t80) cc_final: 0.5741 (t80) REVERT: B 264 LEU cc_start: 0.5676 (tp) cc_final: 0.5459 (tp) REVERT: D 292 THR cc_start: 0.5955 (p) cc_final: 0.5706 (t) REVERT: D 310 MET cc_start: 0.3618 (mtm) cc_final: 0.2429 (mmp) REVERT: F 255 MET cc_start: -0.3769 (ptp) cc_final: -0.4076 (mtt) REVERT: F 523 LYS cc_start: 0.7841 (ptmt) cc_final: 0.7565 (pttm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1103 time to fit residues: 32.2686 Evaluate side-chains 131 residues out of total 1532 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN E 44 GLN E 89 GLN D 236 HIS D 253 HIS ** D 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.174714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.154237 restraints weight = 41438.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.153834 restraints weight = 43308.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.154979 restraints weight = 36571.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.155936 restraints weight = 26092.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.155902 restraints weight = 26775.155| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 1.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 14159 Z= 0.146 Angle : 0.774 21.643 19292 Z= 0.383 Chirality : 0.049 0.318 2186 Planarity : 0.005 0.050 2478 Dihedral : 5.333 40.413 2182 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: -1.78 (0.20), residues: 1706 helix: -1.21 (0.25), residues: 372 sheet: -0.53 (0.26), residues: 402 loop : -1.44 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 144 TYR 0.026 0.002 TYR E 263 PHE 0.044 0.002 PHE C 307 TRP 0.029 0.002 TRP E 334 HIS 0.015 0.001 HIS C 236 Details of bonding type rmsd covalent geometry : bond 0.00329 (14090) covalent geometry : angle 0.74831 (19140) SS BOND : bond 0.00470 ( 55) SS BOND : angle 2.15890 ( 110) hydrogen bonds : bond 0.03534 ( 424) hydrogen bonds : angle 5.98858 ( 1176) link_NAG-ASN : bond 0.00538 ( 14) link_NAG-ASN : angle 2.75720 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.22 seconds wall clock time: 37 minutes 31.90 seconds (2251.90 seconds total)