Starting phenix.real_space_refine on Sun Oct 25 00:40:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2o_20576/10_2026/6q2o_20576.map" } resolution = 3.65 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= 0.003 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 138 5.16 5 C 9434 2.51 5 N 2738 2.21 5 O 2878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15196 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 789 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "C" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2222 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 12, 'TRANS': 267} Chain breaks: 3 Chain: "E" Number of atoms: 4499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4499 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 537} Chain breaks: 4 Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: B, D, F Time building chain proxies: 5.57, per 1000 atoms: 0.37 Number of scatterers: 15196 At special positions: 0 Unit cell: (128.4, 200.09, 102.72, 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 138 16.00 O 2878 8.00 N 2738 7.00 C 9434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=53, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 194 " distance=2.02 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 40 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 105 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 222 " distance=2.02 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 174 " distance=2.02 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 224 " - pdb=" SG CYS C 229 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 258 " - pdb=" SG CYS C 264 " distance=2.04 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 285 " - pdb=" SG CYS C 347 " 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=2.02 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 D 40 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 222 " distance=2.02 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 224 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 258 " - pdb=" SG CYS D 264 " distance=2.04 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 285 " - pdb=" SG CYS D 347 " 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=2.02 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 E2005 " - " ASN E 377 " " NAG E2006 " - " ASN E 394 " " NAG E2007 " - " ASN E 468 " " NAG E2008 " - " ASN E 367 " " NAG E2009 " - " ASN E 336 " " NAG E2010 " - " ASN E 361 " " NAG F2005 " - " ASN F 377 " " NAG F2006 " - " ASN F 394 " " NAG F2007 " - " ASN F 468 " " NAG F2008 " - " ASN F 367 " " NAG F2009 " - " ASN F 336 " " NAG F2010 " - " ASN F 361 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 638.8 milliseconds 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 36 sheets defined 26.8% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 113 through 116 removed outlier: 3.695A pdb=" N GLY A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 113 through 116' Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.695A pdb=" N GLY B 116 " --> pdb=" O SER B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 101 through 110 removed outlier: 3.547A pdb=" N CYS C 105 " --> pdb=" O LYS C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 196 through 208 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.623A pdb=" N THR C 216 " --> pdb=" O PRO C 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR C 217 " --> pdb=" O SER C 213 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 219 " --> pdb=" O TYR C 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 220 " --> pdb=" O THR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.738A pdb=" N ALA C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.659A pdb=" N ASP C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 275 removed outlier: 3.655A pdb=" N ASN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 288 Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.592A pdb=" N CYS C 293 " --> pdb=" O ASN C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 344 removed outlier: 3.863A pdb=" N ASP C 341 " --> pdb=" O LYS C 337 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.508A pdb=" N TRP E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 112 " --> pdb=" O LYS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 167 removed outlier: 3.924A pdb=" N PHE E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 309 through 313 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.595A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 433 removed outlier: 3.764A pdb=" N ALA E 432 " --> pdb=" O ASN E 429 " (cutoff:3.500A) removed outlier: 3.869A 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 470 through 475 removed outlier: 3.640A pdb=" N ARG E 475 " --> pdb=" O LYS E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 530 Processing helix chain 'E' and resid 564 through 568 removed outlier: 3.963A pdb=" N ASP E 567 " --> pdb=" O THR E 564 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY E 568 " --> pdb=" O CYS E 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 564 through 568' Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.580A pdb=" N ASP E 584 " --> pdb=" O CYS E 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 51 through 65 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 101 through 110 removed outlier: 3.546A pdb=" N CYS D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 173 through 186 Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.623A pdb=" N THR D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 217 " --> pdb=" O SER D 213 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET D 219 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 220 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 235 removed outlier: 3.738A pdb=" N ALA D 230 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.659A pdb=" N ASP D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 275 removed outlier: 3.655A pdb=" N ASN D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS D 275 " --> pdb=" O PHE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 288 Processing helix chain 'D' and resid 289 through 299 removed outlier: 3.592A pdb=" N CYS D 293 " --> pdb=" O ASN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.864A pdb=" N ASP D 341 " --> pdb=" O LYS D 337 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 357 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.507A pdb=" N TRP F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 167 removed outlier: 3.925A pdb=" N PHE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.596A pdb=" N GLN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.764A pdb=" N ALA F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) removed outlier: 3.869A 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 470 through 475 removed outlier: 3.640A pdb=" N ARG F 475 " --> pdb=" O LYS F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 530 Processing helix chain 'F' and resid 564 through 568 removed outlier: 3.963A pdb=" N ASP F 567 " --> pdb=" O THR F 564 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY F 568 " --> pdb=" O CYS F 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 564 through 568' Processing helix chain 'F' and resid 581 through 585 removed outlier: 3.580A pdb=" N ASP F 584 " --> pdb=" O CYS F 581 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 111 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.646A pdb=" N ARG A 166 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 195 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU A 193 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR A 170 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA A 191 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 176 Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 111 Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.645A pdb=" N ARG B 166 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 195 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU B 193 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR B 170 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 191 " --> pdb=" O TYR B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 176 Processing sheet with id=AA7, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AA8, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AA9, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.210A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 35 through 36 removed outlier: 6.210A pdb=" N TYR E 36 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER E 148 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.226A pdb=" N LEU E 97 " --> pdb=" O PRO E 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 72 through 73 removed outlier: 3.994A pdb=" N HIS E 81 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 174 through 177 removed outlier: 6.268A pdb=" N PHE E 174 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR E 263 " --> pdb=" O PHE E 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 176 " --> pdb=" O TYR E 263 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 187 removed outlier: 6.498A pdb=" N THR E 184 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR E 225 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS E 186 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 278 through 283 Processing sheet with id=AB7, first strand: chain 'E' and resid 292 through 300 removed outlier: 7.053A pdb=" N VAL E 292 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU E 358 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 294 " --> pdb=" O LEU E 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 407 through 413 removed outlier: 6.132A pdb=" N TYR E 408 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR E 503 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 410 " --> pdb=" O THR E 503 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU E 505 " --> pdb=" O LEU E 410 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 412 " --> pdb=" O GLU E 505 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 421 through 425 removed outlier: 6.711A pdb=" N LEU E 465 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS E 424 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY E 463 " --> pdb=" O LYS E 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL E 455 " --> pdb=" O ILE E 464 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 542 through 544 Processing sheet with id=AC2, first strand: chain 'E' and resid 589 through 591 Processing sheet with id=AC3, first strand: chain 'E' and resid 594 through 596 Processing sheet with id=AC4, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC5, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AC6, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.211A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 35 through 36 removed outlier: 6.211A pdb=" N TYR F 36 " --> pdb=" O TYR F 146 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER F 148 " --> pdb=" O TYR F 36 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.226A pdb=" N LEU F 97 " --> pdb=" O PRO F 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.994A pdb=" N HIS F 81 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 174 through 177 removed outlier: 6.268A pdb=" N PHE F 174 " --> pdb=" O THR F 261 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TYR F 263 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 176 " --> pdb=" O TYR F 263 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 6.499A pdb=" N THR F 184 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR F 225 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS F 186 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 278 through 283 Processing sheet with id=AD4, first strand: chain 'F' and resid 292 through 300 removed outlier: 7.052A pdb=" N VAL F 292 " --> pdb=" O LEU F 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU F 358 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 294 " --> pdb=" O LEU F 356 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 407 through 413 removed outlier: 6.133A pdb=" N TYR F 408 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N THR F 503 " --> pdb=" O TYR F 408 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 410 " --> pdb=" O THR F 503 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLU F 505 " --> pdb=" O LEU F 410 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL F 412 " --> pdb=" O GLU F 505 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 421 through 425 removed outlier: 6.710A pdb=" N LEU F 465 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LYS F 424 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY F 463 " --> pdb=" O LYS F 424 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 455 " --> pdb=" O ILE F 464 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AD8, first strand: chain 'F' and resid 589 through 591 Processing sheet with id=AD9, first strand: chain 'F' and resid 594 through 596 486 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5136 1.35 - 1.47: 3653 1.47 - 1.59: 6561 1.59 - 1.71: 0 1.71 - 1.84: 154 Bond restraints: 15504 Sorted by residual: bond pdb=" C1 NAG E2006 " pdb=" O5 NAG E2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG F2006 " pdb=" O5 NAG F2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C1 NAG E2008 " pdb=" O5 NAG E2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C1 NAG F2008 " pdb=" O5 NAG F2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG F2005 " pdb=" O5 NAG F2005 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 15499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 20286 1.90 - 3.81: 626 3.81 - 5.71: 48 5.71 - 7.62: 30 7.62 - 9.52: 6 Bond angle restraints: 20996 Sorted by residual: angle pdb=" N ASN E 579 " pdb=" CA ASN E 579 " pdb=" C ASN E 579 " ideal model delta sigma weight residual 114.64 107.57 7.07 1.52e+00 4.33e-01 2.16e+01 angle pdb=" N ASN F 579 " pdb=" CA ASN F 579 " pdb=" C ASN F 579 " ideal model delta sigma weight residual 114.64 107.58 7.06 1.52e+00 4.33e-01 2.16e+01 angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 122.13 128.77 -6.64 1.85e+00 2.92e-01 1.29e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 122.13 128.76 -6.63 1.85e+00 2.92e-01 1.28e+01 angle pdb=" CA TYR C 181 " pdb=" CB TYR C 181 " pdb=" CG TYR C 181 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.19e+01 ... (remaining 20991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 9353 16.11 - 32.22: 296 32.22 - 48.34: 58 48.34 - 64.45: 10 64.45 - 80.56: 10 Dihedral angle restraints: 9727 sinusoidal: 4173 harmonic: 5554 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 -166.56 80.56 1 1.00e+01 1.00e-02 8.03e+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 -166.54 80.54 1 1.00e+01 1.00e-02 8.02e+01 dihedral pdb=" CB CYS E 515 " pdb=" SG CYS E 515 " pdb=" SG CYS E 531 " pdb=" CB CYS E 531 " ideal model delta sinusoidal sigma weight residual 93.00 168.71 -75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 9724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1446 0.040 - 0.079: 625 0.079 - 0.119: 205 0.119 - 0.159: 46 0.159 - 0.199: 2 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA ASP E 378 " pdb=" N ASP E 378 " pdb=" C ASP E 378 " pdb=" CB ASP E 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA ASP F 378 " pdb=" N ASP F 378 " pdb=" C ASP F 378 " pdb=" CB ASP F 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA VAL E 425 " pdb=" N VAL E 425 " pdb=" C VAL E 425 " pdb=" CB VAL E 425 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 2321 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 334 " 0.024 2.00e-02 2.50e+03 1.56e-02 6.05e+00 pdb=" CG TRP F 334 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP F 334 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP F 334 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP F 334 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 334 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 334 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 334 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP F 334 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 334 " -0.024 2.00e-02 2.50e+03 1.54e-02 5.91e+00 pdb=" CG TRP E 334 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 334 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 334 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 334 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 334 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 334 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 334 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER C 190 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 191 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.031 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 12 2.21 - 2.88: 5253 2.88 - 3.55: 18341 3.55 - 4.23: 32802 4.23 - 4.90: 55680 Nonbonded interactions: 112088 Sorted by model distance: nonbonded pdb=" OD2 ASP F 300 " pdb=" OH TYR F 314 " model vdw 1.534 3.040 nonbonded pdb=" OD2 ASP E 300 " pdb=" OH TYR E 314 " model vdw 1.534 3.040 nonbonded pdb=" OD1 ASP F 230 " pdb=" OE1 GLU F 232 " model vdw 1.615 3.040 nonbonded pdb=" OD1 ASP E 230 " pdb=" OE1 GLU E 232 " model vdw 1.615 3.040 nonbonded pdb=" OD1 ASP F 266 " pdb=" OD2 ASP F 302 " model vdw 1.689 3.040 ... (remaining 112083 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: 0.02 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.230 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2303 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 : 0.004 0.051 15569 Z= 0.200 Angle : 0.793 9.523 21138 Z= 0.440 Chirality : 0.049 0.199 2324 Planarity : 0.006 0.056 2750 Dihedral : 8.536 74.283 5968 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.12 % Allowed : 1.68 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -3.75 (0.16), residues: 1860 helix: -3.14 (0.14), residues: 454 sheet: -1.38 (0.22), residues: 490 loop : -2.77 (0.17), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 544 TYR 0.020 0.002 TYR C 181 PHE 0.022 0.002 PHE F 188 TRP 0.040 0.003 TRP F 334 HIS 0.004 0.001 HIS E 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (15504) covalent geometry : angle 0.78507 / 0.44 (20996) SS BOND : bond 0.00579 / 0.41 ( 53) SS BOND : angle 1.38902 / 0.93 ( 106) hydrogen bonds : bond 0.14516 / 9.95 ( 486) hydrogen bonds : angle 6.63338 / 4.59 ( 1350) link_NAG-ASN : bond 0.00307 / 0.16 ( 12) link_NAG-ASN : angle 2.09284 / 1.49 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 368 time to evaluate : 0.636 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 221 PHE cc_start: 0.2945 (m-80) cc_final: 0.1655 (m-10) REVERT: E 264 ASP cc_start: 0.0252 (t0) cc_final: -0.0423 (t0) REVERT: E 291 THR cc_start: 0.5853 (m) cc_final: 0.5469 (m) REVERT: F 410 LEU cc_start: 0.3601 (pp) cc_final: 0.3385 (pt) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.1533 time to fit residues: 77.7776 Evaluate side-chains 157 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 HIS C 160 HIS C 201 HIS C 272 HIS C 308 ASN E 103 HIS ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 HIS ** E 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 114 HIS F 246 HIS F 359 ASN F 437 ASN F 443 HIS F 482 HIS F 499 GLN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.182589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.164245 restraints weight = 51258.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.165641 restraints weight = 33335.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.166068 restraints weight = 24547.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.166062 restraints weight = 21822.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.166290 restraints weight = 21644.586| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 0.8544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 15569 Z= 0.330 Angle : 1.094 12.404 21138 Z= 0.569 Chirality : 0.058 0.310 2324 Planarity : 0.010 0.080 2750 Dihedral : 7.258 75.253 2378 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.15 % Favored : 92.80 % Rotamer: Outliers : 3.85 % Allowed : 9.03 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.36 (0.17), residues: 1860 helix: -2.33 (0.19), residues: 458 sheet: -1.40 (0.23), residues: 444 loop : -2.60 (0.18), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 232 TYR 0.039 0.004 TYR D 181 PHE 0.031 0.003 PHE F 188 TRP 0.052 0.004 TRP E 85 HIS 0.011 0.002 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.33 (15504) covalent geometry : angle 1.08425 / 0.57 (20996) SS BOND : bond 0.00830 / 0.48 ( 53) SS BOND : angle 1.89172 / 1.26 ( 106) hydrogen bonds : bond 0.06293 / 4.37 ( 486) hydrogen bonds : angle 7.12090 / 5.00 ( 1350) link_NAG-ASN : bond 0.00991 / 0.65 ( 12) link_NAG-ASN : angle 2.49924 / 1.64 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 246 time to evaluate : 0.579 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 199 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6786 (tppt) REVERT: E 205 ARG cc_start: 0.6278 (ptt90) cc_final: 0.6065 (tpp-160) REVERT: E 354 TYR cc_start: 0.4336 (OUTLIER) cc_final: 0.2935 (m-80) REVERT: E 465 LEU cc_start: 0.5773 (tt) cc_final: 0.5308 (tp) REVERT: D 245 ASP cc_start: 0.2509 (m-30) cc_final: 0.2266 (m-30) REVERT: D 248 LYS cc_start: 0.4579 (OUTLIER) cc_final: 0.3921 (mttt) REVERT: D 331 MET cc_start: 0.4798 (OUTLIER) cc_final: 0.4249 (tpt) REVERT: F 101 LEU cc_start: 0.1949 (mt) cc_final: 0.1293 (mp) REVERT: F 314 TYR cc_start: 0.2395 (OUTLIER) cc_final: 0.0970 (t80) outliers start: 64 outliers final: 32 residues processed: 294 average time/residue: 0.1406 time to fit residues: 58.4788 Evaluate side-chains 179 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 354 TYR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 536 SER Chi-restraints excluded: chain F residue 538 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [180, 174, 161, 4, 74, 172, 46, 187, 79, 160, 111] chunk 180 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 46 optimal weight: 0.0370 chunk 187 optimal weight: 0.0010 chunk 79 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 171 ASN C 186 ASN C 262 HIS E 114 HIS E 187 GLN E 429 ASN E 579 ASN D 274 ASN F 84 ASN ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.183956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.165549 restraints weight = 51179.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.166486 restraints weight = 32066.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.166711 restraints weight = 25158.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.166813 restraints weight = 21519.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.166944 restraints weight = 21138.189| |-----------------------------------------------------------------------------| r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.8869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15569 Z= 0.125 Angle : 0.628 9.557 21138 Z= 0.324 Chirality : 0.044 0.339 2324 Planarity : 0.005 0.057 2750 Dihedral : 5.309 63.340 2378 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.41 % Allowed : 12.64 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -2.25 (0.18), residues: 1860 helix: -0.94 (0.23), residues: 438 sheet: -0.76 (0.25), residues: 436 loop : -2.14 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 600 TYR 0.022 0.002 TYR C 181 PHE 0.018 0.001 PHE E 299 TRP 0.020 0.002 TRP E 106 HIS 0.006 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15504) covalent geometry : angle 0.62013 / 0.32 (20996) SS BOND : bond 0.00378 / 0.23 ( 53) SS BOND : angle 1.26372 / 0.76 ( 106) hydrogen bonds : bond 0.03438 / 2.35 ( 486) hydrogen bonds : angle 5.50274 / 3.84 ( 1350) link_NAG-ASN : bond 0.00319 / 0.19 ( 12) link_NAG-ASN : angle 1.58878 / 1.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.554 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: C 199 LYS cc_start: 0.7090 (tppt) cc_final: 0.6785 (tppt) REVERT: E 205 ARG cc_start: 0.6342 (ptt90) cc_final: 0.6114 (tpp-160) REVERT: E 215 ARG cc_start: 0.4239 (OUTLIER) cc_final: 0.0568 (ptm-80) REVERT: D 181 TYR cc_start: 0.6591 (OUTLIER) cc_final: 0.4826 (t80) REVERT: D 248 LYS cc_start: 0.4820 (OUTLIER) cc_final: 0.3779 (mttt) REVERT: D 300 MET cc_start: -0.0455 (mmm) cc_final: -0.0955 (ttp) REVERT: F 314 TYR cc_start: 0.2524 (OUTLIER) cc_final: 0.1208 (t80) outliers start: 40 outliers final: 23 residues processed: 202 average time/residue: 0.1235 time to fit residues: 37.2867 Evaluate side-chains 158 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 504 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [150, 71, 67, 140, 181, 31, 27, 126, 148, 117, 42] chunk 150 optimal weight: 0.0670 chunk 71 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS E 114 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.181891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.161840 restraints weight = 50449.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.162632 restraints weight = 34343.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.163244 restraints weight = 25435.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.163328 restraints weight = 20737.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.163506 restraints weight = 21231.257| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5451 moved from start: 0.9327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15569 Z= 0.110 Angle : 0.578 8.458 21138 Z= 0.295 Chirality : 0.042 0.196 2324 Planarity : 0.004 0.042 2750 Dihedral : 4.849 61.467 2378 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.59 % Allowed : 13.12 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.79 (0.19), residues: 1860 helix: -0.31 (0.25), residues: 438 sheet: -0.62 (0.24), residues: 448 loop : -1.91 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 TYR 0.022 0.002 TYR C 181 PHE 0.011 0.001 PHE A 127 TRP 0.014 0.001 TRP E 334 HIS 0.018 0.001 HIS C 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15504) covalent geometry : angle 0.57107 / 0.29 (20996) SS BOND : bond 0.00412 / 0.21 ( 53) SS BOND : angle 1.15554 / 0.72 ( 106) hydrogen bonds : bond 0.03011 / 2.10 ( 486) hydrogen bonds : angle 5.22676 / 3.61 ( 1350) link_NAG-ASN : bond 0.00239 / 0.14 ( 12) link_NAG-ASN : angle 1.40868 / 0.87 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 205 ARG cc_start: 0.6377 (ptt90) cc_final: 0.6162 (tpp-160) REVERT: E 215 ARG cc_start: 0.3977 (OUTLIER) cc_final: 0.0940 (ptm-80) REVERT: D 181 TYR cc_start: 0.6713 (OUTLIER) cc_final: 0.4789 (t80) REVERT: D 248 LYS cc_start: 0.4970 (OUTLIER) cc_final: 0.4376 (ptpt) REVERT: D 300 MET cc_start: -0.0243 (mmm) cc_final: -0.0917 (ttp) REVERT: F 71 HIS cc_start: 0.4247 (p90) cc_final: 0.3838 (p90) REVERT: F 314 TYR cc_start: 0.2735 (OUTLIER) cc_final: 0.1686 (t80) outliers start: 43 outliers final: 28 residues processed: 176 average time/residue: 0.1130 time to fit residues: 30.1172 Evaluate side-chains 157 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [164, 52, 137, 123, 119, 136, 74, 55, 29, 107, 184] chunk 164 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 29 optimal weight: 0.0470 chunk 107 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN E 70 GLN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN D 227 GLN D 272 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 403 HIS F 482 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.171175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.151995 restraints weight = 48495.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.151240 restraints weight = 42197.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.152263 restraints weight = 36457.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.152394 restraints weight = 25939.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.153028 restraints weight = 24686.504| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 1.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15569 Z= 0.199 Angle : 0.777 14.347 21138 Z= 0.395 Chirality : 0.047 0.227 2324 Planarity : 0.006 0.060 2750 Dihedral : 5.868 80.848 2378 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.73 % Allowed : 13.48 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.01 (0.19), residues: 1860 helix: -0.68 (0.24), residues: 437 sheet: -0.83 (0.25), residues: 450 loop : -1.91 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 139 TYR 0.030 0.003 TYR C 181 PHE 0.022 0.002 PHE C 342 TRP 0.022 0.002 TRP F 334 HIS 0.009 0.001 HIS F 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (15504) covalent geometry : angle 0.76597 / 0.39 (20996) SS BOND : bond 0.00539 / 0.33 ( 53) SS BOND : angle 1.58316 / 1.02 ( 106) hydrogen bonds : bond 0.04207 / 2.87 ( 486) hydrogen bonds : angle 6.13528 / 4.27 ( 1350) link_NAG-ASN : bond 0.00393 / 0.21 ( 12) link_NAG-ASN : angle 2.13475 / 1.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.661 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 178 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.6648 (m-30) REVERT: E 215 ARG cc_start: 0.3800 (OUTLIER) cc_final: 0.0681 (ptm-80) REVERT: E 284 GLU cc_start: 0.5073 (tp30) cc_final: 0.4806 (tp30) REVERT: E 337 GLU cc_start: 0.7169 (mp0) cc_final: 0.6808 (mp0) REVERT: D 248 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.4981 (ptpt) REVERT: F 314 TYR cc_start: 0.2843 (OUTLIER) cc_final: 0.1949 (t80) REVERT: F 551 ILE cc_start: 0.7534 (mt) cc_final: 0.7332 (mt) outliers start: 62 outliers final: 41 residues processed: 219 average time/residue: 0.1326 time to fit residues: 42.4091 Evaluate side-chains 165 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 347 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [40, 75, 84, 184, 25, 151, 146, 28, 180, 156, 66] chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 ASN C 250 ASN E 54 HIS E 179 ASN ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.164952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.145729 restraints weight = 47641.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.144764 restraints weight = 47167.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.145766 restraints weight = 41551.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.146340 restraints weight = 28360.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.146590 restraints weight = 27121.396| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 1.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 15569 Z= 0.248 Angle : 0.816 12.912 21138 Z= 0.422 Chirality : 0.048 0.198 2324 Planarity : 0.006 0.063 2750 Dihedral : 5.946 63.444 2378 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 4.27 % Allowed : 14.86 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.26 (0.18), residues: 1860 helix: -0.90 (0.23), residues: 443 sheet: -1.01 (0.26), residues: 402 loop : -2.01 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 149 TYR 0.028 0.003 TYR D 243 PHE 0.023 0.003 PHE E 299 TRP 0.032 0.003 TRP F 106 HIS 0.006 0.002 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (15504) covalent geometry : angle 0.80334 / 0.42 (20996) SS BOND : bond 0.00689 / 0.40 ( 53) SS BOND : angle 1.88466 / 1.17 ( 106) hydrogen bonds : bond 0.04500 / 3.10 ( 486) hydrogen bonds : angle 6.47140 / 4.50 ( 1350) link_NAG-ASN : bond 0.00505 / 0.29 ( 12) link_NAG-ASN : angle 2.09271 / 1.26 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 149 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8607 (t0) REVERT: C 300 MET cc_start: 0.8482 (mmm) cc_final: 0.7845 (mmt) REVERT: E 171 ARG cc_start: 0.4148 (mtp180) cc_final: 0.3087 (tpm170) REVERT: E 215 ARG cc_start: 0.4305 (OUTLIER) cc_final: 0.0878 (ptm-80) REVERT: D 248 LYS cc_start: 0.6220 (OUTLIER) cc_final: 0.5271 (mttt) REVERT: F 314 TYR cc_start: 0.2899 (OUTLIER) cc_final: 0.2619 (t80) REVERT: F 402 LEU cc_start: 0.6963 (pp) cc_final: 0.5720 (mp) outliers start: 71 outliers final: 40 residues processed: 201 average time/residue: 0.1158 time to fit residues: 35.5192 Evaluate side-chains 163 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [53, 75, 17, 187, 65, 56, 127, 4, 5, 112, 22] chunk 53 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 56 optimal weight: 0.0040 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 22 optimal weight: 0.0870 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 44 ASN E 114 HIS E 333 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.168768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.149795 restraints weight = 47133.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.149485 restraints weight = 44500.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.150589 restraints weight = 35453.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.150767 restraints weight = 24639.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.151028 restraints weight = 24071.971| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6041 moved from start: 1.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15569 Z= 0.118 Angle : 0.643 10.887 21138 Z= 0.324 Chirality : 0.043 0.256 2324 Planarity : 0.004 0.042 2750 Dihedral : 5.200 80.629 2378 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.29 % Allowed : 17.21 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.66 (0.19), residues: 1860 helix: -0.14 (0.25), residues: 443 sheet: -0.57 (0.26), residues: 418 loop : -1.82 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 94 TYR 0.024 0.002 TYR E 122 PHE 0.021 0.001 PHE D 342 TRP 0.039 0.002 TRP F 106 HIS 0.003 0.001 HIS F 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (15504) covalent geometry : angle 0.62936 / 0.32 (20996) SS BOND : bond 0.00410 / 0.22 ( 53) SS BOND : angle 1.72850 / 1.09 ( 106) hydrogen bonds : bond 0.03299 / 2.24 ( 486) hydrogen bonds : angle 5.61362 / 3.88 ( 1350) link_NAG-ASN : bond 0.00285 / 0.17 ( 12) link_NAG-ASN : angle 1.66015 / 1.06 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8475 (t0) REVERT: C 300 MET cc_start: 0.8140 (mmm) cc_final: 0.7518 (mmt) REVERT: C 332 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6249 (mm-30) REVERT: E 66 PHE cc_start: 0.0619 (m-80) cc_final: 0.0382 (m-10) REVERT: E 215 ARG cc_start: 0.3910 (OUTLIER) cc_final: 0.0928 (ptm-80) REVERT: D 189 ILE cc_start: 0.7059 (pt) cc_final: 0.6845 (pt) REVERT: D 248 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.4839 (mttt) REVERT: F 255 MET cc_start: 0.0633 (mmt) cc_final: 0.0364 (tpt) REVERT: F 314 TYR cc_start: 0.3024 (OUTLIER) cc_final: 0.2268 (t80) outliers start: 38 outliers final: 21 residues processed: 174 average time/residue: 0.1219 time to fit residues: 31.7958 Evaluate side-chains 139 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain E residue 175 ARG Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [119, 35, 147, 124, 64, 173, 41, 125, 86, 140, 49] chunk 119 optimal weight: 0.0970 chunk 35 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN C 44 ASN E 70 GLN E 333 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.168039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.148690 restraints weight = 48213.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.147411 restraints weight = 43037.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.148411 restraints weight = 37240.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.148606 restraints weight = 26504.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.148821 restraints weight = 26423.581| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6140 moved from start: 1.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15569 Z= 0.117 Angle : 0.631 10.805 21138 Z= 0.319 Chirality : 0.043 0.200 2324 Planarity : 0.005 0.041 2750 Dihedral : 4.929 83.126 2378 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.07 % Allowed : 16.79 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.48 (0.19), residues: 1860 helix: -0.03 (0.24), residues: 445 sheet: -0.35 (0.26), residues: 406 loop : -1.73 (0.19), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 182 TYR 0.020 0.002 TYR A 141 PHE 0.018 0.001 PHE E 299 TRP 0.040 0.002 TRP F 106 HIS 0.017 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (15504) covalent geometry : angle 0.62115 / 0.32 (20996) SS BOND : bond 0.00468 / 0.29 ( 53) SS BOND : angle 1.43699 / 0.89 ( 106) hydrogen bonds : bond 0.03135 / 2.16 ( 486) hydrogen bonds : angle 5.48898 / 3.79 ( 1350) link_NAG-ASN : bond 0.00207 / 0.12 ( 12) link_NAG-ASN : angle 1.66035 / 1.01 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 122 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 CYS cc_start: 0.2420 (OUTLIER) cc_final: 0.1718 (m) REVERT: C 101 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7037 (mtpp) REVERT: C 186 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8482 (t0) REVERT: C 300 MET cc_start: 0.8144 (mmm) cc_final: 0.7508 (mmm) REVERT: C 314 PRO cc_start: 0.7908 (Cg_exo) cc_final: 0.7679 (Cg_endo) REVERT: C 332 GLU cc_start: 0.6687 (mm-30) cc_final: 0.6229 (mm-30) REVERT: E 171 ARG cc_start: 0.3827 (mtp180) cc_final: 0.3388 (tpm170) REVERT: E 215 ARG cc_start: 0.4477 (OUTLIER) cc_final: 0.1464 (ptm-80) REVERT: E 319 LEU cc_start: 0.4107 (mp) cc_final: 0.3819 (mt) REVERT: E 356 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6347 (mt) REVERT: E 542 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5723 (mt-10) REVERT: D 189 ILE cc_start: 0.7103 (pt) cc_final: 0.6884 (pt) REVERT: D 248 LYS cc_start: 0.5717 (OUTLIER) cc_final: 0.4941 (mttt) REVERT: F 147 PHE cc_start: 0.5836 (OUTLIER) cc_final: 0.5624 (t80) REVERT: F 255 MET cc_start: 0.0653 (mmt) cc_final: 0.0270 (tpt) REVERT: F 314 TYR cc_start: 0.2853 (OUTLIER) cc_final: 0.2039 (t80) outliers start: 51 outliers final: 34 residues processed: 162 average time/residue: 0.1046 time to fit residues: 26.4935 Evaluate side-chains 150 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 101 LYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 147 PHE Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 185 PHE Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [106, 12, 143, 1, 48, 85, 56, 77, 164, 32, 41] chunk 106 optimal weight: 0.0970 chunk 12 optimal weight: 2.9990 chunk 143 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 164 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN E 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.167184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.147729 restraints weight = 47887.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.146298 restraints weight = 43885.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.147376 restraints weight = 38172.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.147548 restraints weight = 27094.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.147764 restraints weight = 25977.587| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 1.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 15569 Z= 0.121 Angle : 0.621 10.851 21138 Z= 0.314 Chirality : 0.043 0.265 2324 Planarity : 0.005 0.079 2750 Dihedral : 4.817 82.529 2378 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.71 % Allowed : 17.57 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % 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: -1.33 (0.19), residues: 1860 helix: 0.15 (0.25), residues: 439 sheet: -0.30 (0.26), residues: 418 loop : -1.65 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.022 0.002 TYR A 141 PHE 0.017 0.001 PHE E 299 TRP 0.029 0.002 TRP F 106 HIS 0.013 0.001 HIS E 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15504) covalent geometry : angle 0.61125 / 0.31 (20996) SS BOND : bond 0.00403 / 0.22 ( 53) SS BOND : angle 1.42495 / 0.89 ( 106) hydrogen bonds : bond 0.03107 / 2.12 ( 486) hydrogen bonds : angle 5.43053 / 3.74 ( 1350) link_NAG-ASN : bond 0.00209 / 0.12 ( 12) link_NAG-ASN : angle 1.61304 / 0.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 ARG cc_start: 0.5191 (tpm170) cc_final: 0.4980 (mmp-170) REVERT: C 40 CYS cc_start: 0.2421 (OUTLIER) cc_final: 0.1747 (m) REVERT: C 186 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8455 (t0) REVERT: C 300 MET cc_start: 0.8152 (mmm) cc_final: 0.7487 (mmm) REVERT: E 171 ARG cc_start: 0.4276 (mtp180) cc_final: 0.4067 (tpm170) REVERT: E 215 ARG cc_start: 0.4516 (OUTLIER) cc_final: 0.1526 (ptm-80) REVERT: E 319 LEU cc_start: 0.4012 (mp) cc_final: 0.3742 (mt) REVERT: E 333 HIS cc_start: 0.1505 (OUTLIER) cc_final: 0.1172 (t-90) REVERT: E 356 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6345 (mt) REVERT: D 248 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.4914 (mttt) REVERT: F 314 TYR cc_start: 0.2912 (OUTLIER) cc_final: 0.2019 (t80) outliers start: 45 outliers final: 33 residues processed: 156 average time/residue: 0.1119 time to fit residues: 26.8510 Evaluate side-chains 149 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 333 HIS Chi-restraints excluded: chain E residue 356 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 251 CYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [181, 180, 151, 170, 95, 86, 93, 131, 72, 69, 75] chunk 181 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN C 250 ASN E 70 GLN E 179 ASN E 333 HIS E 429 ASN E 499 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.155269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.134479 restraints weight = 44509.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.132843 restraints weight = 49684.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.133767 restraints weight = 45337.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.134419 restraints weight = 30699.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.134601 restraints weight = 28392.749| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 1.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 15569 Z= 0.318 Angle : 1.011 15.445 21138 Z= 0.518 Chirality : 0.054 0.220 2324 Planarity : 0.008 0.147 2750 Dihedral : 7.061 55.046 2378 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 2.59 % Allowed : 18.11 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.44 (0.18), residues: 1860 helix: -1.13 (0.23), residues: 441 sheet: -0.92 (0.24), residues: 444 loop : -2.22 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 360 TYR 0.045 0.004 TYR D 181 PHE 0.042 0.003 PHE F 147 TRP 0.036 0.004 TRP F 37 HIS 0.010 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.32 (15504) covalent geometry : angle 0.99157 / 0.51 (20996) SS BOND : bond 0.00803 / 0.46 ( 53) SS BOND : angle 2.60141 / 1.63 ( 106) hydrogen bonds : bond 0.05491 / 3.71 ( 486) hydrogen bonds : angle 7.28449 / 5.07 ( 1350) link_NAG-ASN : bond 0.00664 / 0.43 ( 12) link_NAG-ASN : angle 2.58734 / 1.60 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3720 Ramachandran restraints generated. 1860 Oldfield, 0 Emsley, 1860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8014 (t80) REVERT: A 158 ARG cc_start: 0.5752 (tpm170) cc_final: 0.5322 (mmp-170) REVERT: A 177 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8498 (tp) REVERT: B 158 ARG cc_start: 0.5986 (tpm170) cc_final: 0.5765 (mmp-170) REVERT: C 199 LYS cc_start: 0.7998 (tppt) cc_final: 0.7492 (ttmm) REVERT: C 300 MET cc_start: 0.8512 (mmm) cc_final: 0.7759 (mmm) REVERT: E 343 ASN cc_start: 0.6345 (m-40) cc_final: 0.5603 (p0) REVERT: E 484 MET cc_start: 0.4202 (tmm) cc_final: 0.3703 (mpp) REVERT: D 231 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6527 (mm-30) REVERT: D 232 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7709 (mtp85) REVERT: D 235 GLN cc_start: 0.7997 (mp10) cc_final: 0.7736 (mp10) REVERT: D 248 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6737 (mttt) REVERT: F 314 TYR cc_start: 0.2920 (OUTLIER) cc_final: 0.1818 (t80) outliers start: 43 outliers final: 30 residues processed: 173 average time/residue: 0.1225 time to fit residues: 32.0279 Evaluate side-chains 133 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 141 TYR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 215 ARG Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain E residue 611 CYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 229 CYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: [40, 125, 9, 64, 2, 30, 17, 185, 108, 90, 169] chunk 40 optimal weight: 0.8980 chunk 125 optimal weight: 0.0970 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 333 HIS ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.155442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.134605 restraints weight = 44385.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.133064 restraints weight = 52827.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.134139 restraints weight = 46381.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.134726 restraints weight = 30925.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.134991 restraints weight = 29040.489| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 1.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.681 15569 Z= 0.401 Angle : 1.278 59.199 21138 Z= 0.665 Chirality : 0.058 0.724 2324 Planarity : 0.008 0.140 2750 Dihedral : 7.053 54.961 2378 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.53 % Allowed : 19.25 % Favored : 78.22 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.51 (0.18), residues: 1860 helix: -1.17 (0.22), residues: 440 sheet: -0.97 (0.24), residues: 444 loop : -2.26 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.001 ARG D 349 TYR 0.042 0.003 TYR D 181 PHE 0.026 0.003 PHE F 147 TRP 0.030 0.004 TRP E 334 HIS 0.011 0.002 HIS F 352 Details of bonding type rmsd/Z covalent geometry : bond 0.01093 / 0.40 (15504) covalent geometry : angle 1.18588 / 0.63 (20996) SS BOND : bond 0.01388 / 0.99 ( 53) SS BOND : angle 6.70823 / 4.28 ( 106) hydrogen bonds : bond 0.05302 / 3.59 ( 486) hydrogen bonds : angle 7.25705 / 5.05 ( 1350) link_NAG-ASN : bond 0.00613 / 0.39 ( 12) link_NAG-ASN : angle 2.59730 / 1.60 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.29 seconds wall clock time: 43 minutes 23.50 seconds (2603.50 seconds total)