Starting phenix.real_space_refine on Thu Sep 18 08:13:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_20576_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_20576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_20576.map" model { file = "/net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_20576_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6q2o_20576/09_2025/6q2o_20576_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.18, per 1000 atoms: 0.34 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=8, 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=" CB CYS B 103 " - pdb=" SG CYS B 103 " distance=1.82 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 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: 0.98 Conformation dependent library (CDL) restraints added in 750.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.62 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: 2.68 Time building geometry restraints manager: 1.36 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: 153 Bond restraints: 15503 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 15498 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 - 14.86: 9197 14.86 - 29.71: 315 29.71 - 44.57: 60 44.57 - 59.43: 14 59.43 - 74.28: 6 Dihedral angle restraints: 9592 sinusoidal: 4038 harmonic: 5554 Sorted by residual: dihedral pdb=" CB CYS B 134 " pdb=" SG CYS B 134 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.48 -57.48 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 134 " pdb=" SG CYS A 134 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.46 -57.46 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CA VAL E 427 " pdb=" C VAL E 427 " pdb=" N GLU E 428 " pdb=" CA GLU E 428 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9589 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: 58 2.21 - 2.88: 5253 2.88 - 3.55: 18433 3.55 - 4.23: 32802 4.23 - 4.90: 55680 Nonbonded interactions: 112226 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 112221 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: 0.03 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: 1.450 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.310 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2309 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 : 0.005 0.213 15523 Z= 0.217 Angle : 1.068 104.200 21048 Z= 0.557 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 aren 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 covalent geometry : bond 0.00421 (15503) covalent geometry : angle 0.78507 (20996) SS BOND : bond 0.07546 ( 8) SS BOND : angle 26.09761 ( 16) hydrogen bonds : bond 0.14516 ( 486) hydrogen bonds : angle 6.63338 ( 1350) link_NAG-ASN : bond 0.00307 ( 12) link_NAG-ASN : angle 2.09284 ( 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 : 0.614 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: 0.1677 time to fit residues: 83.8171 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 : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN C 160 HIS C 272 HIS C 274 ASN C 308 ASN E 103 HIS ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 246 HIS ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN F 54 HIS F 103 HIS F 114 HIS F 187 GLN ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN F 421 GLN F 482 HIS ** 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 = 0.4919 r_free = 0.4919 target = 0.187033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.170404 restraints weight = 51250.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.171750 restraints weight = 33101.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.172019 restraints weight = 23570.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.172334 restraints weight = 21727.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.172435 restraints weight = 21009.120| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4657 moved from start: 0.6383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15523 Z= 0.249 Angle : 1.134 104.200 21048 Z= 0.572 Chirality : 0.050 0.254 2324 Planarity : 0.008 0.070 2750 Dihedral : 6.178 58.495 2378 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.19 % Allowed : 8.97 % Favored : 87.85 % 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 aren not related in a simple way. whole: -2.77 (0.17), residues: 1860 helix: -1.44 (0.22), residues: 424 sheet: -1.07 (0.23), residues: 456 loop : -2.44 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 175 TYR 0.030 0.003 TYR C 181 PHE 0.030 0.003 PHE D 207 TRP 0.030 0.003 TRP E 85 HIS 0.013 0.002 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00540 (15503) covalent geometry : angle 0.87322 (20996) SS BOND : bond 0.02240 ( 8) SS BOND : angle 26.17261 ( 16) hydrogen bonds : bond 0.05033 ( 486) hydrogen bonds : angle 6.16165 ( 1350) link_NAG-ASN : bond 0.00910 ( 12) link_NAG-ASN : angle 1.81535 ( 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 286 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.6904 (t80) cc_final: 0.6305 (t80) REVERT: C 199 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5729 (tppt) REVERT: E 465 LEU cc_start: 0.5280 (tt) cc_final: 0.4893 (tp) REVERT: E 529 GLU cc_start: 0.5100 (mm-30) cc_final: 0.4190 (pt0) REVERT: F 101 LEU cc_start: 0.1940 (mt) cc_final: 0.0922 (mp) REVERT: F 314 TYR cc_start: 0.2412 (OUTLIER) cc_final: 0.1127 (t80) REVERT: F 437 ASN cc_start: 0.7352 (m-40) cc_final: 0.7120 (m-40) outliers start: 53 outliers final: 27 residues processed: 269 average time/residue: 0.1580 time to fit residues: 58.6690 Evaluate side-chains 159 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 153 ARG 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 222 CYS 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 E residue 127 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 460 ASP Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 222 CYS Chi-restraints excluded: chain D residue 248 LYS 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 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: chunk 180 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 46 optimal weight: 0.0020 chunk 187 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN C 250 ASN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 GLN E 579 ASN F 246 HIS ** F 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.184424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.167048 restraints weight = 51272.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.167076 restraints weight = 36516.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.167300 restraints weight = 29209.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.167555 restraints weight = 24605.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.167708 restraints weight = 21751.246| |-----------------------------------------------------------------------------| r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4973 moved from start: 0.7623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15523 Z= 0.138 Angle : 0.948 104.200 21048 Z= 0.469 Chirality : 0.044 0.243 2324 Planarity : 0.005 0.047 2750 Dihedral : 5.092 61.282 2378 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.59 % Allowed : 11.79 % Favored : 85.62 % 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 aren not related in a simple way. whole: -2.06 (0.18), residues: 1860 helix: -0.46 (0.24), residues: 446 sheet: -0.77 (0.24), residues: 448 loop : -2.13 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 340 TYR 0.028 0.002 TYR C 181 PHE 0.014 0.001 PHE A 127 TRP 0.016 0.002 TRP F 334 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00294 (15503) covalent geometry : angle 0.61551 (20996) SS BOND : bond 0.00506 ( 8) SS BOND : angle 26.07627 ( 16) hydrogen bonds : bond 0.03364 ( 486) hydrogen bonds : angle 5.31129 ( 1350) link_NAG-ASN : bond 0.00536 ( 12) link_NAG-ASN : angle 1.65532 ( 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 206 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 529 GLU cc_start: 0.5496 (mm-30) cc_final: 0.4258 (pt0) REVERT: D 181 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5089 (t80) REVERT: D 248 LYS cc_start: 0.4647 (OUTLIER) cc_final: 0.3852 (ptpt) REVERT: F 314 TYR cc_start: 0.3170 (OUTLIER) cc_final: 0.2224 (t80) REVERT: F 528 CYS cc_start: 0.1774 (OUTLIER) cc_final: 0.1104 (t) outliers start: 43 outliers final: 24 residues processed: 194 average time/residue: 0.1434 time to fit residues: 40.2258 Evaluate side-chains 150 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 196 CYS 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 C residue 317 ILE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS 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 404 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 150 optimal weight: 2.9990 chunk 71 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 27 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 0.0870 chunk 42 optimal weight: 0.6980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN C 250 ASN C 262 HIS E 114 HIS E 371 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.182737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.164193 restraints weight = 50692.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.164904 restraints weight = 38051.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.165145 restraints weight = 27399.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.165143 restraints weight = 26537.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.165317 restraints weight = 23247.034| |-----------------------------------------------------------------------------| r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.8560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15523 Z= 0.113 Angle : 0.910 104.200 21048 Z= 0.447 Chirality : 0.042 0.209 2324 Planarity : 0.004 0.051 2750 Dihedral : 4.564 60.402 2378 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.47 % Allowed : 12.82 % Favored : 84.72 % 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 aren not related in a simple way. whole: -1.55 (0.19), residues: 1860 helix: 0.04 (0.25), residues: 448 sheet: -0.49 (0.25), residues: 434 loop : -1.83 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 163 TYR 0.019 0.002 TYR C 181 PHE 0.012 0.001 PHE F 188 TRP 0.014 0.001 TRP F 334 HIS 0.004 0.001 HIS E 114 Details of bonding type rmsd covalent geometry : bond 0.00248 (15503) covalent geometry : angle 0.55702 (20996) SS BOND : bond 0.00381 ( 8) SS BOND : angle 26.06712 ( 16) hydrogen bonds : bond 0.03077 ( 486) hydrogen bonds : angle 5.01045 ( 1350) link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.22098 ( 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 207 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 CYS cc_start: 0.7683 (t) cc_final: 0.7461 (p) REVERT: C 332 GLU cc_start: 0.5640 (tt0) cc_final: 0.5168 (tt0) REVERT: E 163 ARG cc_start: 0.6501 (tpp80) cc_final: 0.6077 (mtm180) REVERT: E 529 GLU cc_start: 0.5654 (mm-30) cc_final: 0.4484 (pt0) REVERT: D 181 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5285 (t80) REVERT: D 248 LYS cc_start: 0.4916 (OUTLIER) cc_final: 0.3950 (ptpt) REVERT: F 314 TYR cc_start: 0.3249 (OUTLIER) cc_final: 0.2577 (t80) REVERT: F 528 CYS cc_start: 0.1975 (OUTLIER) cc_final: 0.1164 (t) outliers start: 41 outliers final: 27 residues processed: 195 average time/residue: 0.1377 time to fit residues: 39.6634 Evaluate side-chains 168 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 154 LEU 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 186 ASN Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 346 PHE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS 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 314 TYR Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 502 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 589 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 164 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 0.3980 chunk 136 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS C 44 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 250 ASN C 262 HIS E 114 HIS E 576 GLN D 272 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN F 437 ASN F 482 HIS ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 499 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.171630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.151816 restraints weight = 47706.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.151552 restraints weight = 38157.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.152601 restraints weight = 32794.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.152639 restraints weight = 23804.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.152822 restraints weight = 23737.023| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 1.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 15523 Z= 0.207 Angle : 1.047 104.200 21048 Z= 0.520 Chirality : 0.047 0.274 2324 Planarity : 0.006 0.058 2750 Dihedral : 5.719 76.880 2378 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.33 % Allowed : 11.49 % Favored : 84.18 % 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 aren not related in a simple way. whole: -1.99 (0.19), residues: 1860 helix: -0.78 (0.23), residues: 440 sheet: -0.60 (0.26), residues: 424 loop : -1.92 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 232 TYR 0.027 0.003 TYR F 73 PHE 0.024 0.002 PHE C 342 TRP 0.022 0.002 TRP F 334 HIS 0.050 0.002 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00461 (15503) covalent geometry : angle 0.75620 (20996) SS BOND : bond 0.00788 ( 8) SS BOND : angle 26.10176 ( 16) hydrogen bonds : bond 0.04275 ( 486) hydrogen bonds : angle 5.97673 ( 1350) link_NAG-ASN : bond 0.00420 ( 12) link_NAG-ASN : angle 2.10819 ( 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 253 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 181 time to evaluate : 0.619 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 125 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7884 (m) REVERT: C 195 CYS cc_start: 0.8144 (t) cc_final: 0.7690 (p) REVERT: C 262 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.2774 (m-70) REVERT: C 332 GLU cc_start: 0.6609 (tt0) cc_final: 0.6376 (tt0) REVERT: E 188 PHE cc_start: 0.4717 (m-80) cc_final: 0.4430 (m-10) REVERT: E 284 GLU cc_start: 0.4707 (tp30) cc_final: 0.4408 (tp30) REVERT: E 529 GLU cc_start: 0.5871 (mm-30) cc_final: 0.4637 (pt0) REVERT: D 248 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.4412 (mttt) REVERT: F 314 TYR cc_start: 0.2478 (OUTLIER) cc_final: 0.1085 (t80) REVERT: F 402 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6036 (pt) REVERT: F 528 CYS cc_start: 0.3485 (OUTLIER) cc_final: 0.2677 (t) outliers start: 72 outliers final: 41 residues processed: 232 average time/residue: 0.1471 time to fit residues: 49.0091 Evaluate side-chains 169 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 183 TYR 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 B residue 186 VAL Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 528 CYS 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 176 LYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 146 TYR 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 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 402 LEU Chi-restraints excluded: chain F residue 404 LEU Chi-restraints excluded: chain F residue 437 ASN 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 536 SER Chi-restraints excluded: chain F residue 551 ILE 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: chunk 40 optimal weight: 0.8980 chunk 75 optimal weight: 0.0870 chunk 84 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 146 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 ASN C 262 HIS E 54 HIS E 114 HIS E 179 ASN ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN F 437 ASN F 569 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.169226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.150008 restraints weight = 48225.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.148827 restraints weight = 40671.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.149903 restraints weight = 37275.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.150042 restraints weight = 26562.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.150234 restraints weight = 25824.008| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 1.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15523 Z= 0.172 Angle : 0.997 104.200 21048 Z= 0.491 Chirality : 0.045 0.270 2324 Planarity : 0.005 0.046 2750 Dihedral : 5.299 82.129 2378 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.15 % Allowed : 13.30 % Favored : 82.55 % 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 aren not related in a simple way. whole: -1.84 (0.19), residues: 1860 helix: -0.39 (0.25), residues: 440 sheet: -0.66 (0.26), residues: 420 loop : -1.88 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 94 TYR 0.017 0.002 TYR D 243 PHE 0.015 0.002 PHE D 355 TRP 0.016 0.002 TRP F 334 HIS 0.042 0.002 HIS C 262 Details of bonding type rmsd covalent geometry : bond 0.00389 (15503) covalent geometry : angle 0.68786 (20996) SS BOND : bond 0.00695 ( 8) SS BOND : angle 26.08043 ( 16) hydrogen bonds : bond 0.03621 ( 486) hydrogen bonds : angle 5.54361 ( 1350) link_NAG-ASN : bond 0.00481 ( 12) link_NAG-ASN : angle 1.79857 ( 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 219 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 262 HIS cc_start: 0.4075 (OUTLIER) cc_final: 0.3817 (m-70) REVERT: E 171 ARG cc_start: 0.3517 (ptm160) cc_final: 0.3009 (mmm160) REVERT: D 248 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.4574 (mttt) REVERT: D 305 MET cc_start: 0.3172 (mmt) cc_final: 0.2448 (tpp) REVERT: F 314 TYR cc_start: 0.2861 (OUTLIER) cc_final: 0.2461 (t80) REVERT: F 528 CYS cc_start: 0.3996 (OUTLIER) cc_final: 0.3257 (t) REVERT: F 562 THR cc_start: 0.7875 (t) cc_final: 0.7669 (m) outliers start: 69 outliers final: 45 residues processed: 202 average time/residue: 0.1348 time to fit residues: 40.5121 Evaluate side-chains 161 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 112 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 148 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 B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 351 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 189 ILE Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 73 TYR 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 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 404 LEU Chi-restraints excluded: chain F residue 437 ASN 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 544 ARG Chi-restraints excluded: chain F residue 551 ILE 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: chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 250 ASN C 262 HIS E 114 HIS ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN F 44 GLN F 333 HIS F 403 HIS F 437 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.163112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.142776 restraints weight = 45876.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.141012 restraints weight = 39772.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.142048 restraints weight = 36628.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.142248 restraints weight = 26144.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.142655 restraints weight = 24987.516| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 1.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 15523 Z= 0.207 Angle : 1.034 104.200 21048 Z= 0.512 Chirality : 0.047 0.225 2324 Planarity : 0.006 0.054 2750 Dihedral : 5.663 72.669 2378 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.73 % Allowed : 15.04 % Favored : 81.23 % 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 aren not related in a simple way. whole: -2.11 (0.19), residues: 1860 helix: -0.80 (0.23), residues: 474 sheet: -0.82 (0.25), residues: 428 loop : -2.00 (0.19), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 287 TYR 0.026 0.002 TYR C 181 PHE 0.025 0.002 PHE E 185 TRP 0.034 0.002 TRP E 139 HIS 0.042 0.002 HIS C 262 Details of bonding type rmsd covalent geometry : bond 0.00456 (15503) covalent geometry : angle 0.73908 (20996) SS BOND : bond 0.02578 ( 8) SS BOND : angle 26.10693 ( 16) hydrogen bonds : bond 0.04132 ( 486) hydrogen bonds : angle 6.15745 ( 1350) link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 1.98131 ( 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 215 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 195 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7873 (p) REVERT: C 314 PRO cc_start: 0.7907 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: E 88 ILE cc_start: 0.3595 (OUTLIER) cc_final: 0.2745 (pt) REVERT: E 171 ARG cc_start: 0.4256 (ptm160) cc_final: 0.3513 (mmm160) REVERT: E 264 ASP cc_start: 0.1703 (t0) cc_final: 0.1375 (p0) REVERT: D 248 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5112 (mttt) REVERT: F 314 TYR cc_start: 0.2813 (OUTLIER) cc_final: 0.2214 (t80) REVERT: F 528 CYS cc_start: 0.4288 (OUTLIER) cc_final: 0.3856 (t) REVERT: F 553 ARG cc_start: 0.6850 (tmm160) cc_final: 0.6643 (tpt90) outliers start: 62 outliers final: 39 residues processed: 201 average time/residue: 0.1341 time to fit residues: 39.7656 Evaluate side-chains 160 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 154 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 B residue 168 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain C residue 195 CYS Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 528 CYS 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 248 LYS Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 84 ASN 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 404 LEU Chi-restraints excluded: chain F residue 437 ASN 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 544 ARG Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 124 optimal weight: 0.0870 chunk 64 optimal weight: 20.0000 chunk 173 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 140 optimal weight: 0.0870 chunk 49 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS D 227 GLN D 274 ASN D 345 ASN F 44 GLN F 84 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.167897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.149211 restraints weight = 48511.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.148291 restraints weight = 43437.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.149378 restraints weight = 37133.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.149513 restraints weight = 25628.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.150683 restraints weight = 24184.090| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 1.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15523 Z= 0.111 Angle : 0.940 104.200 21048 Z= 0.459 Chirality : 0.043 0.223 2324 Planarity : 0.004 0.044 2750 Dihedral : 4.903 74.578 2378 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.05 % Allowed : 17.39 % Favored : 80.57 % 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 aren not related in a simple way. whole: -1.52 (0.19), residues: 1860 helix: -0.06 (0.25), residues: 451 sheet: -0.50 (0.26), residues: 430 loop : -1.73 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 149 TYR 0.019 0.001 TYR C 181 PHE 0.023 0.001 PHE E 185 TRP 0.016 0.001 TRP E 334 HIS 0.004 0.001 HIS F 443 Details of bonding type rmsd covalent geometry : bond 0.00251 (15503) covalent geometry : angle 0.60198 (20996) SS BOND : bond 0.00537 ( 8) SS BOND : angle 26.09916 ( 16) hydrogen bonds : bond 0.03057 ( 486) hydrogen bonds : angle 5.37434 ( 1350) link_NAG-ASN : bond 0.00222 ( 12) link_NAG-ASN : angle 1.55907 ( 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 179 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 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: B 109 GLU cc_start: 0.6444 (tp30) cc_final: 0.5627 (mm-30) REVERT: C 300 MET cc_start: 0.8230 (mmm) cc_final: 0.7418 (mmm) REVERT: C 314 PRO cc_start: 0.7537 (Cg_exo) cc_final: 0.7331 (Cg_endo) REVERT: E 88 ILE cc_start: 0.3456 (tp) cc_final: 0.2726 (pt) REVERT: E 171 ARG cc_start: 0.3912 (ptm160) cc_final: 0.3677 (mmm160) REVERT: D 248 LYS cc_start: 0.5025 (OUTLIER) cc_final: 0.4419 (mttt) REVERT: F 314 TYR cc_start: 0.2759 (OUTLIER) cc_final: 0.1972 (t80) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.1348 time to fit residues: 34.5372 Evaluate side-chains 140 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 262 HIS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain F residue 84 ASN 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 404 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 551 ILE 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: chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 143 optimal weight: 0.0020 chunk 1 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 576 GLN D 196 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.167466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.148772 restraints weight = 48475.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.147803 restraints weight = 42107.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.148860 restraints weight = 37321.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.149026 restraints weight = 25700.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.149424 restraints weight = 24163.433| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 1.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15523 Z= 0.113 Angle : 0.928 104.200 21048 Z= 0.453 Chirality : 0.042 0.221 2324 Planarity : 0.004 0.044 2750 Dihedral : 4.527 51.741 2378 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.62 % Allowed : 17.87 % 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 aren not related in a simple way. whole: -1.35 (0.19), residues: 1860 helix: 0.14 (0.25), residues: 450 sheet: -0.36 (0.26), residues: 432 loop : -1.68 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 287 TYR 0.018 0.001 TYR C 181 PHE 0.014 0.001 PHE E 299 TRP 0.014 0.002 TRP C 110 HIS 0.003 0.000 HIS F 392 Details of bonding type rmsd covalent geometry : bond 0.00248 (15503) covalent geometry : angle 0.58430 (20996) SS BOND : bond 0.00478 ( 8) SS BOND : angle 26.08447 ( 16) hydrogen bonds : bond 0.02968 ( 486) hydrogen bonds : angle 5.25605 ( 1350) link_NAG-ASN : bond 0.00221 ( 12) link_NAG-ASN : angle 1.51077 ( 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 157 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 MET cc_start: 0.8204 (mmm) cc_final: 0.7501 (mmm) REVERT: C 314 PRO cc_start: 0.7731 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: E 88 ILE cc_start: 0.3756 (tp) cc_final: 0.3096 (pt) REVERT: E 337 GLU cc_start: 0.6883 (mp0) cc_final: 0.6459 (tt0) REVERT: E 542 GLU cc_start: 0.5691 (mm-30) cc_final: 0.5438 (mm-30) REVERT: D 248 LYS cc_start: 0.5000 (OUTLIER) cc_final: 0.4421 (mttt) REVERT: F 314 TYR cc_start: 0.2906 (OUTLIER) cc_final: 0.2042 (t80) outliers start: 27 outliers final: 22 residues processed: 152 average time/residue: 0.1360 time to fit residues: 30.4536 Evaluate side-chains 141 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 318 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 262 VAL 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 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 404 LEU Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 544 ARG Chi-restraints excluded: chain F residue 551 ILE 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: chunk 181 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 201 HIS C 250 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** F 84 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.136424 restraints weight = 46432.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.134493 restraints weight = 51713.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.135745 restraints weight = 45848.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.136370 restraints weight = 31005.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.136635 restraints weight = 29846.176| |-----------------------------------------------------------------------------| r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 1.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 15523 Z= 0.286 Angle : 1.144 104.200 21048 Z= 0.576 Chirality : 0.051 0.218 2324 Planarity : 0.007 0.087 2750 Dihedral : 6.608 69.746 2378 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.47 % Allowed : 17.63 % Favored : 79.90 % 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 aren not related in a simple way. whole: -2.30 (0.18), residues: 1860 helix: -1.15 (0.22), residues: 456 sheet: -0.78 (0.25), residues: 443 loop : -2.10 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 233 TYR 0.028 0.003 TYR D 181 PHE 0.024 0.003 PHE E 346 TRP 0.031 0.004 TRP C 110 HIS 0.016 0.002 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00646 (15503) covalent geometry : angle 0.88396 (20996) SS BOND : bond 0.01204 ( 8) SS BOND : angle 26.16445 ( 16) hydrogen bonds : bond 0.05227 ( 486) hydrogen bonds : angle 6.85392 ( 1350) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 2.41709 ( 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 165 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ARG cc_start: 0.5745 (tpm170) cc_final: 0.5393 (mmp-170) REVERT: C 300 MET cc_start: 0.8557 (mmm) cc_final: 0.7959 (mmp) REVERT: E 88 ILE cc_start: 0.3943 (tp) cc_final: 0.3400 (pt) REVERT: E 343 ASN cc_start: 0.5899 (m-40) cc_final: 0.5683 (p0) REVERT: D 232 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7164 (mmm-85) REVERT: D 248 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.5923 (mttt) REVERT: D 338 PHE cc_start: 0.6222 (t80) cc_final: 0.5911 (m-80) REVERT: F 314 TYR cc_start: 0.2882 (OUTLIER) cc_final: 0.1729 (t80) outliers start: 41 outliers final: 27 residues processed: 154 average time/residue: 0.1495 time to fit residues: 32.9965 Evaluate side-chains 117 residues out of total 1662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU 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 318 VAL 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 200 ILE Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 608 THR Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 331 MET Chi-restraints excluded: chain D residue 349 ARG 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 504 VAL Chi-restraints excluded: chain F residue 551 ILE Chi-restraints excluded: chain F residue 572 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: chunk 40 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 64 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 GLN D 262 HIS F 44 GLN F 84 ASN ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.160884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.140159 restraints weight = 44866.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.138887 restraints weight = 42491.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.139817 restraints weight = 38562.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.140184 restraints weight = 26179.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.142097 restraints weight = 24004.766| |-----------------------------------------------------------------------------| r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 1.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15523 Z= 0.124 Angle : 0.971 104.200 21048 Z= 0.480 Chirality : 0.044 0.210 2324 Planarity : 0.005 0.050 2750 Dihedral : 5.236 48.699 2378 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.87 % Allowed : 19.13 % Favored : 79.00 % 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 aren not related in a simple way. whole: -1.65 (0.19), residues: 1860 helix: -0.23 (0.24), residues: 442 sheet: -0.62 (0.25), residues: 446 loop : -1.76 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 544 TYR 0.027 0.002 TYR E 73 PHE 0.022 0.001 PHE F 555 TRP 0.020 0.002 TRP C 110 HIS 0.003 0.001 HIS F 392 Details of bonding type rmsd covalent geometry : bond 0.00277 (15503) covalent geometry : angle 0.64806 (20996) SS BOND : bond 0.00580 ( 8) SS BOND : angle 26.12318 ( 16) hydrogen bonds : bond 0.03316 ( 486) hydrogen bonds : angle 5.69409 ( 1350) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 1.72913 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.43 seconds wall clock time: 46 minutes 26.37 seconds (2786.37 seconds total)