Starting phenix.real_space_refine on Fri Sep 27 06:49:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_20576_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_20576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_20576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_20576_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q2o_20576/09_2024/6q2o_20576_neut.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: F, B, D Time building chain proxies: 11.98, per 1000 atoms: 0.79 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=3, 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 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: 3.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.66 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: 4.89 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5136 1.35 - 1.47: 3653 1.47 - 1.59: 6561 1.59 - 1.71: 0 1.71 - 1.84: 154 Bond restraints: 15504 Sorted by residual: bond pdb=" C1 NAG E2006 " pdb=" O5 NAG E2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.51e+00 bond pdb=" C1 NAG F2006 " pdb=" O5 NAG F2006 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 bond pdb=" C1 NAG E2008 " pdb=" O5 NAG E2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C1 NAG F2008 " pdb=" O5 NAG F2008 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG F2005 " pdb=" O5 NAG F2005 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 15499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 20286 1.90 - 3.81: 626 3.81 - 5.71: 48 5.71 - 7.62: 30 7.62 - 9.52: 6 Bond angle restraints: 20996 Sorted by residual: angle pdb=" N ASN E 579 " pdb=" CA ASN E 579 " pdb=" C ASN E 579 " ideal model delta sigma weight residual 114.64 107.57 7.07 1.52e+00 4.33e-01 2.16e+01 angle pdb=" N ASN F 579 " pdb=" CA ASN F 579 " pdb=" C ASN F 579 " ideal model delta sigma weight residual 114.64 107.58 7.06 1.52e+00 4.33e-01 2.16e+01 angle pdb=" C VAL F 303 " pdb=" N VAL F 304 " pdb=" CA VAL F 304 " ideal model delta sigma weight residual 122.13 128.77 -6.64 1.85e+00 2.92e-01 1.29e+01 angle pdb=" C VAL E 303 " pdb=" N VAL E 304 " pdb=" CA VAL E 304 " ideal model delta sigma weight residual 122.13 128.76 -6.63 1.85e+00 2.92e-01 1.28e+01 angle pdb=" CA TYR C 181 " pdb=" CB TYR C 181 " pdb=" CG TYR C 181 " ideal model delta sigma weight residual 113.90 120.12 -6.22 1.80e+00 3.09e-01 1.19e+01 ... (remaining 20991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 9194 14.86 - 29.71: 305 29.71 - 44.57: 59 44.57 - 59.43: 13 59.43 - 74.28: 6 Dihedral angle restraints: 9577 sinusoidal: 4023 harmonic: 5554 Sorted by residual: 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 dihedral pdb=" CA VAL F 427 " pdb=" C VAL F 427 " pdb=" N GLU F 428 " pdb=" CA GLU F 428 " ideal model delta harmonic sigma weight residual -180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9574 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: 62 2.21 - 2.88: 5253 2.88 - 3.55: 18441 3.55 - 4.23: 32802 4.23 - 4.90: 55680 Nonbonded interactions: 112238 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 112233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.410 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- 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 : 0.004 0.051 15504 Z= 0.285 Angle : 0.785 9.523 20996 Z= 0.439 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.040 0.003 TRP F 334 HIS 0.004 0.001 HIS E 246 PHE 0.022 0.002 PHE F 188 TYR 0.020 0.002 TYR C 181 ARG 0.011 0.001 ARG E 544 *********************** 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 fitting. rotamer outliers: 2 poor density : 368 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 PHE cc_start: 0.2945 (m-80) cc_final: 0.1656 (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: 0.5468 (m) REVERT: F 410 LEU cc_start: 0.3601 (pp) cc_final: 0.3384 (pt) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.3414 time to fit residues: 170.7277 Evaluate side-chains 158 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 0.0470 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 44 ASN C 250 ASN C 272 HIS 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 D 225 GLN F 187 GLN F 246 HIS ** F 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN F 421 GLN F 482 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3087 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 15504 Z= 0.192 Angle : 0.618 9.165 20996 Z= 0.318 Chirality : 0.043 0.175 2324 Planarity : 0.005 0.049 2750 Dihedral : 5.374 44.017 2378 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.35 % Allowed : 8.97 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.18), residues: 1860 helix: -0.99 (0.22), residues: 450 sheet: -0.94 (0.23), residues: 472 loop : -2.34 (0.18), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 334 HIS 0.014 0.001 HIS E 114 PHE 0.012 0.001 PHE F 188 TYR 0.032 0.002 TYR C 181 ARG 0.007 0.001 ARG C 234 *********************** 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 223 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 184 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 PHE cc_start: 0.4790 (m-80) cc_final: 0.2978 (m-10) REVERT: E 264 ASP cc_start: -0.0041 (t0) cc_final: -0.0394 (t0) REVERT: F 314 TYR cc_start: 0.2501 (OUTLIER) cc_final: 0.2205 (t80) outliers start: 39 outliers final: 20 residues processed: 210 average time/residue: 0.3150 time to fit residues: 94.0001 Evaluate side-chains 144 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain B residue 168 THR 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 165 LEU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 222 CYS 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 538 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 152 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 HIS ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 HIS C 201 HIS C 250 ASN ** C 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN E 44 GLN E 187 GLN E 499 GLN E 576 GLN E 579 ASN ** E 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN F 114 HIS F 187 GLN F 343 ASN F 443 HIS ** F 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.9898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 15504 Z= 0.473 Angle : 1.037 13.811 20996 Z= 0.540 Chirality : 0.056 0.420 2324 Planarity : 0.009 0.089 2750 Dihedral : 7.056 55.034 2378 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 3.73 % Allowed : 9.63 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.17), residues: 1860 helix: -1.47 (0.22), residues: 436 sheet: -1.47 (0.23), residues: 468 loop : -2.48 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP F 334 HIS 0.014 0.002 HIS F 71 PHE 0.033 0.003 PHE D 207 TYR 0.047 0.004 TYR D 215 ARG 0.019 0.001 ARG A 139 *********************** 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 289 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 227 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 CYS cc_start: 0.3302 (OUTLIER) cc_final: 0.2931 (m) REVERT: E 80 LEU cc_start: 0.3911 (mt) cc_final: 0.3604 (tt) REVERT: D 248 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4863 (mttt) REVERT: D 300 MET cc_start: -0.0131 (mmm) cc_final: -0.1787 (ttp) REVERT: F 314 TYR cc_start: 0.2042 (OUTLIER) cc_final: 0.0879 (t80) REVERT: F 528 CYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2120 (t) REVERT: F 608 THR cc_start: 0.6882 (p) cc_final: 0.6624 (t) outliers start: 62 outliers final: 31 residues processed: 276 average time/residue: 0.3033 time to fit residues: 118.3837 Evaluate side-chains 168 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 114 GLU 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 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 105 CYS Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 580 ILE 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 D residue 251 CYS 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 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 538 THR Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 186 ASN C 250 ASN E 44 GLN E 54 HIS E 186 HIS E 429 ASN D 201 HIS D 272 HIS ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 HIS F 341 GLN F 576 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 1.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15504 Z= 0.274 Angle : 0.687 11.384 20996 Z= 0.356 Chirality : 0.046 0.284 2324 Planarity : 0.005 0.052 2750 Dihedral : 5.560 51.328 2378 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 12.82 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 1860 helix: -0.74 (0.24), residues: 426 sheet: -1.00 (0.24), residues: 428 loop : -2.15 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 334 HIS 0.007 0.001 HIS A 180 PHE 0.018 0.002 PHE E 299 TYR 0.019 0.002 TYR E 237 ARG 0.026 0.001 ARG C 94 *********************** 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 245 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 180 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 186 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8057 (t0) REVERT: C 251 CYS cc_start: 0.6410 (m) cc_final: 0.6122 (p) REVERT: C 339 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7915 (mm) REVERT: E 304 VAL cc_start: 0.4023 (t) cc_final: 0.3762 (m) REVERT: D 181 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5117 (t80) REVERT: F 314 TYR cc_start: 0.2750 (OUTLIER) cc_final: 0.1818 (t80) REVERT: F 402 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5697 (pt) REVERT: F 528 CYS cc_start: 0.2863 (OUTLIER) cc_final: 0.1914 (t) REVERT: F 562 THR cc_start: 0.7566 (t) cc_final: 0.7270 (m) outliers start: 65 outliers final: 32 residues processed: 227 average time/residue: 0.2820 time to fit residues: 93.2344 Evaluate side-chains 166 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 128 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 186 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 297 ARG Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 163 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 262 HIS ** E 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5454 moved from start: 1.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15504 Z= 0.240 Angle : 0.656 8.157 20996 Z= 0.341 Chirality : 0.044 0.197 2324 Planarity : 0.005 0.050 2750 Dihedral : 5.282 52.894 2378 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.73 % Allowed : 13.78 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 1860 helix: -0.57 (0.25), residues: 436 sheet: -0.88 (0.24), residues: 444 loop : -1.98 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 334 HIS 0.009 0.001 HIS F 71 PHE 0.017 0.002 PHE E 299 TYR 0.023 0.002 TYR A 129 ARG 0.012 0.001 ARG E 287 *********************** 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 212 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 150 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 MET cc_start: 0.4671 (ttm) cc_final: 0.4370 (ttt) REVERT: C 262 HIS cc_start: 0.3584 (OUTLIER) cc_final: 0.2549 (m90) REVERT: C 314 PRO cc_start: 0.6470 (Cg_exo) cc_final: 0.6265 (Cg_endo) REVERT: E 491 GLN cc_start: 0.2415 (OUTLIER) cc_final: 0.1407 (pp30) REVERT: D 248 LYS cc_start: 0.4885 (OUTLIER) cc_final: 0.3984 (mttt) REVERT: F 314 TYR cc_start: 0.3268 (OUTLIER) cc_final: 0.2788 (t80) REVERT: F 528 CYS cc_start: 0.3381 (OUTLIER) cc_final: 0.2482 (t) outliers start: 62 outliers final: 39 residues processed: 198 average time/residue: 0.2822 time to fit residues: 82.4256 Evaluate side-chains 161 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 117 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 491 GLN Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE 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 121 VAL 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 354 TYR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 60 optimal weight: 0.0870 chunk 95 optimal weight: 5.9990 overall best weight: 3.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 371 GLN D 201 HIS D 274 ASN F 44 GLN F 437 ASN ** F 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 1.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 15504 Z= 0.363 Angle : 0.819 9.670 20996 Z= 0.426 Chirality : 0.049 0.253 2324 Planarity : 0.006 0.066 2750 Dihedral : 6.378 73.221 2378 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.21 % Allowed : 14.62 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.18), residues: 1860 helix: -1.19 (0.23), residues: 459 sheet: -1.15 (0.25), residues: 422 loop : -2.01 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 139 HIS 0.058 0.002 HIS C 262 PHE 0.044 0.003 PHE E 185 TYR 0.028 0.003 TYR D 309 ARG 0.012 0.001 ARG C 259 *********************** 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 229 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 159 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7075 (mm) cc_final: 0.6590 (mm) REVERT: A 158 ARG cc_start: 0.5518 (tpm170) cc_final: 0.4987 (mmp-170) REVERT: E 354 TYR cc_start: 0.4300 (OUTLIER) cc_final: 0.3449 (m-80) REVERT: E 483 TYR cc_start: 0.4119 (OUTLIER) cc_final: 0.1280 (m-80) REVERT: D 248 LYS cc_start: 0.5443 (OUTLIER) cc_final: 0.4627 (mttt) REVERT: F 314 TYR cc_start: 0.3011 (OUTLIER) cc_final: 0.2560 (t80) REVERT: F 402 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6057 (pt) REVERT: F 528 CYS cc_start: 0.4342 (OUTLIER) cc_final: 0.3590 (t) outliers start: 70 outliers final: 45 residues processed: 212 average time/residue: 0.2629 time to fit residues: 82.5039 Evaluate side-chains 164 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 113 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 291 THR Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 354 TYR Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 396 SER Chi-restraints excluded: chain E residue 483 TYR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE 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 121 VAL 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 357 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 437 ASN Chi-restraints excluded: chain F residue 451 THR Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 83 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS F 44 GLN F 84 ASN F 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 moved from start: 1.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15504 Z= 0.220 Angle : 0.647 11.476 20996 Z= 0.334 Chirality : 0.044 0.278 2324 Planarity : 0.005 0.055 2750 Dihedral : 5.525 59.559 2378 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.13 % Allowed : 17.63 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.19), residues: 1860 helix: -0.79 (0.24), residues: 464 sheet: -0.99 (0.25), residues: 430 loop : -1.87 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 106 HIS 0.003 0.001 HIS A 184 PHE 0.026 0.002 PHE E 299 TYR 0.019 0.002 TYR C 181 ARG 0.005 0.001 ARG F 553 *********************** 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 200 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 148 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 354 TYR cc_start: 0.4084 (OUTLIER) cc_final: 0.3615 (m-80) REVERT: D 248 LYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4521 (mttt) REVERT: F 314 TYR cc_start: 0.3197 (OUTLIER) cc_final: 0.1995 (t80) REVERT: F 528 CYS cc_start: 0.4121 (OUTLIER) cc_final: 0.3687 (t) outliers start: 52 outliers final: 35 residues processed: 184 average time/residue: 0.2671 time to fit residues: 72.6865 Evaluate side-chains 162 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 354 TYR Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE 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 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 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 456 THR Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 578 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 112 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 108 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN C 44 ASN ** C 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 576 GLN F 371 GLN F 403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 1.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15504 Z= 0.168 Angle : 0.601 10.390 20996 Z= 0.307 Chirality : 0.043 0.208 2324 Planarity : 0.004 0.050 2750 Dihedral : 4.888 51.994 2378 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.53 % Allowed : 18.59 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1860 helix: -0.35 (0.24), residues: 461 sheet: -0.88 (0.25), residues: 440 loop : -1.64 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 106 HIS 0.003 0.001 HIS F 352 PHE 0.025 0.001 PHE E 299 TYR 0.017 0.001 TYR C 181 ARG 0.008 0.001 ARG D 210 *********************** 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 187 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 145 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6671 (mm-30) REVERT: A 148 LEU cc_start: 0.7254 (mm) cc_final: 0.7049 (mm) REVERT: B 109 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6614 (mm-30) REVERT: C 300 MET cc_start: 0.8248 (mmm) cc_final: 0.7377 (mmm) REVERT: E 88 ILE cc_start: 0.3737 (tp) cc_final: 0.2976 (pt) REVERT: E 147 PHE cc_start: 0.3195 (OUTLIER) cc_final: 0.2622 (m-10) REVERT: E 171 ARG cc_start: 0.4172 (ptm160) cc_final: 0.3909 (mmm160) REVERT: E 483 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.1169 (m-80) REVERT: E 542 GLU cc_start: 0.5210 (mm-30) cc_final: 0.4951 (mm-30) REVERT: D 305 MET cc_start: 0.5873 (OUTLIER) cc_final: 0.5197 (tpt) REVERT: F 314 TYR cc_start: 0.3160 (OUTLIER) cc_final: 0.2006 (t80) REVERT: F 370 MET cc_start: 0.1822 (ptp) cc_final: 0.1615 (ptt) outliers start: 42 outliers final: 28 residues processed: 175 average time/residue: 0.2838 time to fit residues: 72.6510 Evaluate side-chains 160 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 177 LEU 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 257 VAL Chi-restraints excluded: chain E residue 147 PHE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 483 TYR Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 323 CYS 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 235 GLU Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 354 TYR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 578 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 173 optimal weight: 5.9990 chunk 158 optimal weight: 0.0030 chunk 168 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 152 optimal weight: 9.9990 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 0.2980 chunk 178 optimal weight: 6.9990 overall best weight: 2.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS E 179 ASN ** E 497 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 1.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15504 Z= 0.245 Angle : 0.668 11.124 20996 Z= 0.342 Chirality : 0.045 0.188 2324 Planarity : 0.005 0.076 2750 Dihedral : 5.275 65.944 2378 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.01 % Allowed : 18.35 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1860 helix: -0.46 (0.24), residues: 456 sheet: -0.84 (0.25), residues: 435 loop : -1.74 (0.19), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 110 HIS 0.004 0.001 HIS A 187 PHE 0.016 0.002 PHE D 338 TYR 0.024 0.002 TYR B 183 ARG 0.009 0.001 ARG D 233 *********************** 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 182 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7558 (mm) cc_final: 0.7269 (mm) REVERT: A 177 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7992 (tp) REVERT: E 483 TYR cc_start: 0.4062 (OUTLIER) cc_final: 0.1356 (m-80) REVERT: E 542 GLU cc_start: 0.5135 (mm-30) cc_final: 0.4794 (mm-30) REVERT: D 305 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6265 (tpt) REVERT: D 338 PHE cc_start: 0.6157 (t80) cc_final: 0.5916 (t80) REVERT: F 314 TYR cc_start: 0.3103 (OUTLIER) cc_final: 0.1774 (t80) REVERT: F 528 CYS cc_start: 0.4465 (OUTLIER) cc_final: 0.3837 (t) outliers start: 50 outliers final: 34 residues processed: 170 average time/residue: 0.2737 time to fit residues: 68.6402 Evaluate side-chains 151 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 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 257 VAL Chi-restraints excluded: chain C residue 262 HIS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 483 TYR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain F residue 65 SER Chi-restraints excluded: chain F residue 151 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 237 TYR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 314 TYR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 4.9990 chunk 84 optimal weight: 0.0050 chunk 124 optimal weight: 0.9990 chunk 187 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS E 443 HIS ** E 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 1.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15504 Z= 0.182 Angle : 0.599 9.715 20996 Z= 0.308 Chirality : 0.043 0.190 2324 Planarity : 0.005 0.051 2750 Dihedral : 4.919 58.742 2378 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.29 % Allowed : 19.37 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1860 helix: -0.21 (0.25), residues: 450 sheet: -0.76 (0.25), residues: 447 loop : -1.62 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 139 HIS 0.002 0.001 HIS F 352 PHE 0.012 0.001 PHE E 258 TYR 0.018 0.002 TYR C 181 ARG 0.009 0.001 ARG C 187 ********************** 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 163 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6678 (mm-30) REVERT: A 177 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7968 (tp) REVERT: B 109 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6567 (mm-30) REVERT: B 124 THR cc_start: 0.7502 (m) cc_final: 0.7280 (p) REVERT: C 300 MET cc_start: 0.8315 (mmm) cc_final: 0.7564 (mmt) REVERT: E 88 ILE cc_start: 0.3862 (tp) cc_final: 0.3148 (pt) REVERT: E 147 PHE cc_start: 0.3749 (OUTLIER) cc_final: 0.3080 (m-10) REVERT: E 483 TYR cc_start: 0.3968 (OUTLIER) cc_final: 0.1307 (m-80) REVERT: E 542 GLU cc_start: 0.4993 (mm-30) cc_final: 0.4657 (mm-30) REVERT: E 567 ASP cc_start: 0.5564 (p0) cc_final: 0.5151 (p0) REVERT: F 314 TYR cc_start: 0.2941 (OUTLIER) cc_final: 0.1810 (t80) REVERT: F 528 CYS cc_start: 0.4508 (OUTLIER) cc_final: 0.3606 (t) outliers start: 38 outliers final: 28 residues processed: 154 average time/residue: 0.2522 time to fit residues: 60.0927 Evaluate side-chains 149 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain C residue 222 CYS Chi-restraints excluded: chain E residue 147 PHE Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 347 VAL Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 483 TYR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 609 CYS Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 181 TYR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 319 VAL 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 357 VAL Chi-restraints excluded: chain F residue 400 VAL Chi-restraints excluded: chain F residue 528 CYS Chi-restraints excluded: chain F residue 580 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 HIS ** D 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.158202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.137184 restraints weight = 44255.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.136287 restraints weight = 44267.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.137068 restraints weight = 40776.156| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 1.6263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15504 Z= 0.234 Angle : 0.634 9.651 20996 Z= 0.328 Chirality : 0.044 0.189 2324 Planarity : 0.005 0.053 2750 Dihedral : 5.166 65.219 2378 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.41 % Allowed : 19.13 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.19), residues: 1860 helix: -0.31 (0.24), residues: 450 sheet: -0.71 (0.25), residues: 462 loop : -1.68 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 110 HIS 0.005 0.001 HIS F 443 PHE 0.013 0.002 PHE E 272 TYR 0.021 0.002 TYR D 181 ARG 0.013 0.001 ARG A 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2818.17 seconds wall clock time: 51 minutes 37.31 seconds (3097.31 seconds total)