Starting phenix.real_space_refine on Mon Aug 10 03:43:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.map" model { file = "/net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ri_75407/08_2026/10ri_75407.cif" } resolution = 3.6 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= 0.002 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 132 5.16 5 C 12834 2.51 5 N 3496 2.21 5 O 3858 1.98 5 H 19760 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40084 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2285 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 9389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 9389 Classifications: {'peptide': 604} Link IDs: {'PCIS': 6, 'PTRANS': 25, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 8324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 8324 Classifications: {'peptide': 537} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 503} Chain breaks: 3 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, D, F Time building chain proxies: 23.39, per 1000 atoms: 0.58 Number of scatterers: 40084 At special positions: 0 Unit cell: (135, 180.36, 238.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 132 16.00 O 3858 8.00 N 3496 7.00 C 12834 6.00 H 19760 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 93 " distance=2.02 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS B 85 " distance=2.03 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS B 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 93 " distance=2.02 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 171 " - pdb=" SG CYS B 185 " 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 C 801 " - " ASN C 247 " " NAG C 802 " - " ASN C 397 " " NAG D 801 " - " ASN D 247 " " NAG D 802 " - " ASN D 397 " " NAG E 901 " - " ASN E 150 " " NAG F 901 " - " ASN F 150 " Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 64 sheets defined 5.4% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.700A pdb=" N PHE A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.699A pdb=" N PHE B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 300 through 304 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.659A pdb=" N ALA C 395 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 298 through 307 removed outlier: 7.191A pdb=" N VAL E 303 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU E 304 " --> pdb=" O TRP E 301 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG E 307 " --> pdb=" O GLU E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 463 removed outlier: 3.794A pdb=" N ILE E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 463 " --> pdb=" O PRO E 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 458 through 463' Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 298 through 307 removed outlier: 7.192A pdb=" N VAL F 303 " --> pdb=" O ASN F 300 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU F 304 " --> pdb=" O TRP F 301 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG F 307 " --> pdb=" O GLU F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 463 removed outlier: 3.794A pdb=" N ILE F 462 " --> pdb=" O MET F 458 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG F 463 " --> pdb=" O PRO F 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 458 through 463' Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 391 through 395 removed outlier: 3.659A pdb=" N ALA D 395 " --> pdb=" O GLU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.707A pdb=" N GLN B 104 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.707A pdb=" N GLN B 104 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 91 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 93 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 129 " --> pdb=" O CYS B 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS B 127 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER B 97 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 58 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 73 removed outlier: 6.547A pdb=" N LEU A 91 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS A 93 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS A 129 " --> pdb=" O CYS A 93 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS A 127 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER A 97 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 removed outlier: 9.802A pdb=" N ILE B 40 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR A 102 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 176 through 178 removed outlier: 4.018A pdb=" N LYS A 187 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 58 Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.018A pdb=" N LYS B 187 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.701A pdb=" N GLY C 136 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 219 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL C 138 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 135 through 139 removed outlier: 6.701A pdb=" N GLY C 136 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 219 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL C 138 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 147 through 150 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 231 removed outlier: 5.294A pdb=" N ASP C 227 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG C 251 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 250 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET C 289 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 236 through 239 removed outlier: 6.414A pdb=" N ILE C 236 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS C 327 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 238 " --> pdb=" O HIS C 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 331 through 334 removed outlier: 3.552A pdb=" N PHE C 331 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 341 through 345 removed outlier: 6.645A pdb=" N VAL C 342 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN C 420 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C 344 " --> pdb=" O ASN C 420 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 450 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 425 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 448 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA C 451 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN C 509 " --> pdb=" O ALA C 451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 371 through 372 removed outlier: 3.558A pdb=" N ASP C 363 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR C 450 " --> pdb=" O PRO C 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE C 425 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 448 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA C 451 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN C 509 " --> pdb=" O ALA C 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 350 through 353 Processing sheet with id=AC2, first strand: chain 'C' and resid 437 through 438 removed outlier: 6.026A pdb=" N TYR C 437 " --> pdb=" O ILE C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 484 through 485 Processing sheet with id=AC4, first strand: chain 'C' and resid 468 through 470 Processing sheet with id=AC5, first strand: chain 'C' and resid 550 through 554 Processing sheet with id=AC6, first strand: chain 'C' and resid 608 through 610 removed outlier: 3.563A pdb=" N TRP C 608 " --> pdb=" O LYS C 583 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP C 581 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 578 " --> pdb=" O GLN C 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 674 through 677 removed outlier: 3.822A pdb=" N GLN C 674 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 753 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 681 through 685 Processing sheet with id=AC9, first strand: chain 'E' and resid 29 through 32 Processing sheet with id=AD1, first strand: chain 'E' and resid 37 through 40 Processing sheet with id=AD2, first strand: chain 'E' and resid 149 through 151 removed outlier: 6.472A pdb=" N LEU E 211 " --> pdb=" O ARG E 226 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG E 226 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 213 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.754A pdb=" N GLY E 257 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 192 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER E 259 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 277 through 278 removed outlier: 6.812A pdb=" N CYS E 424 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL E 336 " --> pdb=" O CYS E 424 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N ILE E 326 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL E 409 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N VAL E 328 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS E 407 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU E 330 " --> pdb=" O ARG E 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG E 405 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU E 332 " --> pdb=" O PHE E 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE E 403 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 338 " --> pdb=" O LYS E 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS E 397 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N GLY E 340 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE E 395 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 291 through 293 removed outlier: 12.656A pdb=" N ILE E 326 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N VAL E 409 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 12.614A pdb=" N VAL E 328 " --> pdb=" O LYS E 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS E 407 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU E 330 " --> pdb=" O ARG E 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG E 405 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N LEU E 332 " --> pdb=" O PHE E 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE E 403 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA E 338 " --> pdb=" O LYS E 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS E 397 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N GLY E 340 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE E 395 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 344 through 345 Processing sheet with id=AD7, first strand: chain 'E' and resid 373 through 374 removed outlier: 3.803A pdb=" N LYS E 377 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 447 through 449 removed outlier: 12.281A pdb=" N LEU E 485 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 11.291A pdb=" N GLU E 567 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 12.549A pdb=" N VAL E 487 " --> pdb=" O TYR E 565 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N TYR E 565 " --> pdb=" O VAL E 487 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N LEU E 489 " --> pdb=" O ARG E 563 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N ARG E 563 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N ASP E 491 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N PHE E 561 " --> pdb=" O ASP E 491 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS E 514 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA E 569 " --> pdb=" O MET E 512 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N MET E 512 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 471 through 473 removed outlier: 6.663A pdb=" N ARG E 577 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE E 500 " --> pdb=" O ARG E 577 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU E 579 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL E 498 " --> pdb=" O GLU E 579 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 581 " --> pdb=" O ARG E 496 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 503 through 505 Processing sheet with id=AE2, first strand: chain 'F' and resid 29 through 32 Processing sheet with id=AE3, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AE4, first strand: chain 'F' and resid 149 through 151 removed outlier: 6.472A pdb=" N LEU F 211 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG F 226 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE F 213 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 155 through 159 removed outlier: 6.754A pdb=" N GLY F 257 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE F 192 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER F 259 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 277 through 278 removed outlier: 6.812A pdb=" N CYS F 424 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL F 336 " --> pdb=" O CYS F 424 " (cutoff:3.500A) removed outlier: 12.656A pdb=" N ILE F 326 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N VAL F 409 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 12.613A pdb=" N VAL F 328 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS F 407 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU F 330 " --> pdb=" O ARG F 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG F 405 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N LEU F 332 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 403 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA F 338 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS F 397 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N GLY F 340 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE F 395 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 291 through 293 removed outlier: 12.656A pdb=" N ILE F 326 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N VAL F 409 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 12.613A pdb=" N VAL F 328 " --> pdb=" O LYS F 407 " (cutoff:3.500A) removed outlier: 11.565A pdb=" N LYS F 407 " --> pdb=" O VAL F 328 " (cutoff:3.500A) removed outlier: 11.707A pdb=" N LEU F 330 " --> pdb=" O ARG F 405 " (cutoff:3.500A) removed outlier: 12.514A pdb=" N ARG F 405 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.632A pdb=" N LEU F 332 " --> pdb=" O PHE F 403 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE F 403 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA F 338 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N LYS F 397 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N GLY F 340 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N PHE F 395 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 344 through 345 Processing sheet with id=AE9, first strand: chain 'F' and resid 373 through 374 removed outlier: 3.802A pdb=" N LYS F 377 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 447 through 449 removed outlier: 12.281A pdb=" N LEU F 485 " --> pdb=" O GLU F 567 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N GLU F 567 " --> pdb=" O LEU F 485 " (cutoff:3.500A) removed outlier: 12.548A pdb=" N VAL F 487 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 11.410A pdb=" N TYR F 565 " --> pdb=" O VAL F 487 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N LEU F 489 " --> pdb=" O ARG F 563 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N ARG F 563 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ASP F 491 " --> pdb=" O PHE F 561 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N PHE F 561 " --> pdb=" O ASP F 491 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS F 514 " --> pdb=" O GLU F 567 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA F 569 " --> pdb=" O MET F 512 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N MET F 512 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 471 through 473 removed outlier: 6.662A pdb=" N ARG F 577 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE F 500 " --> pdb=" O ARG F 577 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU F 579 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL F 498 " --> pdb=" O GLU F 579 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU F 581 " --> pdb=" O ARG F 496 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 503 through 505 Processing sheet with id=AF4, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.702A pdb=" N GLY D 136 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL D 219 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 138 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.702A pdb=" N GLY D 136 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL D 219 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N VAL D 138 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 147 through 150 Processing sheet with id=AF7, first strand: chain 'D' and resid 225 through 231 removed outlier: 5.295A pdb=" N ASP D 227 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 251 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 250 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N MET D 289 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 236 through 239 removed outlier: 6.413A pdb=" N ILE D 236 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N HIS D 327 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 238 " --> pdb=" O HIS D 327 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.552A pdb=" N PHE D 331 " --> pdb=" O TYR D 359 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 341 through 345 removed outlier: 6.644A pdb=" N VAL D 342 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASN D 420 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA D 344 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR D 450 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 425 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 448 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA D 451 " --> pdb=" O ASN D 509 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN D 509 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 371 through 372 removed outlier: 3.559A pdb=" N ASP D 363 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TYR D 450 " --> pdb=" O PRO D 423 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE D 425 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 448 " --> pdb=" O ILE D 425 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA D 451 " --> pdb=" O ASN D 509 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN D 509 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 350 through 353 Processing sheet with id=AG4, first strand: chain 'D' and resid 437 through 438 removed outlier: 6.026A pdb=" N TYR D 437 " --> pdb=" O ILE D 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'D' and resid 484 through 485 Processing sheet with id=AG6, first strand: chain 'D' and resid 468 through 470 Processing sheet with id=AG7, first strand: chain 'D' and resid 550 through 554 Processing sheet with id=AG8, first strand: chain 'D' and resid 608 through 610 removed outlier: 3.562A pdb=" N TRP D 608 " --> pdb=" O LYS D 583 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TRP D 581 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 578 " --> pdb=" O GLN D 643 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 674 through 677 removed outlier: 3.822A pdb=" N GLN D 674 " --> pdb=" O LEU D 749 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 753 " --> pdb=" O THR D 676 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 681 through 685 730 hydrogen bonds defined for protein. 1809 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: 10.80 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19756 1.02 - 1.22: 12 1.22 - 1.42: 8740 1.42 - 1.62: 11864 1.62 - 1.82: 178 Bond restraints: 40550 Sorted by residual: bond pdb=" CB ASN B 87 " pdb=" CG ASN B 87 " ideal model delta sigma weight residual 1.516 1.642 -0.126 2.50e-02 1.60e+03 2.54e+01 bond pdb=" CB ASN A 87 " pdb=" CG ASN A 87 " ideal model delta sigma weight residual 1.516 1.641 -0.125 2.50e-02 1.60e+03 2.50e+01 bond pdb=" CG PRO A 110 " pdb=" CD PRO A 110 " ideal model delta sigma weight residual 1.503 1.411 0.092 3.40e-02 8.65e+02 7.34e+00 bond pdb=" CG PRO B 110 " pdb=" CD PRO B 110 " ideal model delta sigma weight residual 1.503 1.412 0.091 3.40e-02 8.65e+02 7.16e+00 bond pdb=" CA PHE B 153 " pdb=" CB PHE B 153 " ideal model delta sigma weight residual 1.535 1.489 0.046 2.09e-02 2.29e+03 4.90e+00 ... (remaining 40545 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 72509 3.79 - 7.58: 536 7.58 - 11.37: 74 11.37 - 15.16: 21 15.16 - 18.95: 4 Bond angle restraints: 73144 Sorted by residual: angle pdb=" CG ASP A 186 " pdb=" CB ASP A 186 " pdb=" HB3 ASP A 186 " ideal model delta sigma weight residual 108.00 126.95 -18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" CG ASP B 186 " pdb=" CB ASP B 186 " pdb=" HB3 ASP B 186 " ideal model delta sigma weight residual 108.00 126.90 -18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" CG ASP B 186 " pdb=" CB ASP B 186 " pdb=" HB2 ASP B 186 " ideal model delta sigma weight residual 108.00 90.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CG ASP A 186 " pdb=" CB ASP A 186 " pdb=" HB2 ASP A 186 " ideal model delta sigma weight residual 108.00 90.37 17.63 3.00e+00 1.11e-01 3.45e+01 angle pdb=" CD LYS A 132 " pdb=" CG LYS A 132 " pdb=" HG2 LYS A 132 " ideal model delta sigma weight residual 108.00 93.13 14.87 3.00e+00 1.11e-01 2.46e+01 ... (remaining 73139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 17392 17.66 - 35.31: 1355 35.31 - 52.97: 399 52.97 - 70.63: 128 70.63 - 88.29: 40 Dihedral angle restraints: 19314 sinusoidal: 10540 harmonic: 8774 Sorted by residual: dihedral pdb=" CA LYS B 109 " pdb=" C LYS B 109 " pdb=" N PRO B 110 " pdb=" CA PRO B 110 " ideal model delta harmonic sigma weight residual -180.00 -155.44 -24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta harmonic sigma weight residual -180.00 -155.47 -24.53 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER C 375 " pdb=" C SER C 375 " pdb=" N ASN C 376 " pdb=" CA ASN C 376 " ideal model delta harmonic sigma weight residual 180.00 161.24 18.76 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 19311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2446 0.054 - 0.108: 465 0.108 - 0.162: 176 0.162 - 0.215: 15 0.215 - 0.269: 4 Chirality restraints: 3106 Sorted by residual: chirality pdb=" CB VAL C 400 " pdb=" CA VAL C 400 " pdb=" CG1 VAL C 400 " pdb=" CG2 VAL C 400 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB VAL D 400 " pdb=" CA VAL D 400 " pdb=" CG1 VAL D 400 " pdb=" CG2 VAL D 400 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL D 200 " pdb=" N VAL D 200 " pdb=" C VAL D 200 " pdb=" CB VAL D 200 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3103 not shown) Planarity restraints: 6056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 181 " 0.018 9.50e-02 1.11e+02 6.00e-02 8.03e+01 pdb=" NE ARG A 181 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 181 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 181 " 0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG A 181 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 181 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 181 " -0.092 2.00e-02 2.50e+03 pdb="HH21 ARG A 181 " -0.090 2.00e-02 2.50e+03 pdb="HH22 ARG A 181 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 181 " -0.017 9.50e-02 1.11e+02 6.00e-02 8.02e+01 pdb=" NE ARG B 181 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 181 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 181 " -0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG B 181 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG B 181 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 181 " 0.092 2.00e-02 2.50e+03 pdb="HH21 ARG B 181 " 0.090 2.00e-02 2.50e+03 pdb="HH22 ARG B 181 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " 0.259 9.50e-02 1.11e+02 9.12e-02 2.64e+01 pdb=" NE ARG A 107 " 0.026 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " -0.062 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG A 107 " -0.034 2.00e-02 2.50e+03 pdb="HH12 ARG A 107 " 0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 107 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 107 " -0.008 2.00e-02 2.50e+03 ... (remaining 6053 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 1347 2.13 - 2.75: 73283 2.75 - 3.37: 111057 3.37 - 3.98: 145484 3.98 - 4.60: 223130 Nonbonded interactions: 554301 Sorted by model distance: nonbonded pdb=" OE1 GLN A 47 " pdb=" HH TYR C 167 " model vdw 1.514 2.450 nonbonded pdb="HD22 ASN A 87 " pdb=" H GLY C 198 " model vdw 1.535 2.100 nonbonded pdb="HD22 ASN B 87 " pdb=" H GLY D 198 " model vdw 1.541 2.100 nonbonded pdb=" H ASP D 701 " pdb=" O LEU D 732 " model vdw 1.547 2.450 nonbonded pdb=" H ASP C 701 " pdb=" O LEU C 732 " model vdw 1.548 2.450 ... (remaining 554296 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: 0.05 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: 0.010 Normalize map: mean=0, sd=1: 2.410 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: 0.240 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 54.770 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 0.126 20812 Z= 0.179 Angle : 0.719 11.180 28246 Z= 0.390 Chirality : 0.051 0.269 3106 Planarity : 0.008 0.107 3642 Dihedral : 13.931 86.689 7796 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.65 % Favored : 95.23 % Rotamer: Outliers : 0.18 % Allowed : 8.54 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2538 helix: -4.11 (0.47), residues: 44 sheet: 0.59 (0.15), residues: 1058 loop : -1.04 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.002 ARG A 107 TYR 0.064 0.003 TYR C 216 PHE 0.029 0.002 PHE C 331 TRP 0.035 0.001 TRP D 181 HIS 0.022 0.003 HIS B 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (20790) covalent geometry : angle 0.71692 / 0.39 (28196) SS BOND : bond 0.00473 / 0.33 ( 16) SS BOND : angle 1.50404 / 1.10 ( 32) hydrogen bonds : bond 0.21587 / 14.26 ( 679) hydrogen bonds : angle 10.42042 / 7.27 ( 1809) link_NAG-ASN : bond 0.00097 / 0.05 ( 6) link_NAG-ASN : angle 1.69607 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.998 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 319 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8051 (ptp90) REVERT: D 319 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8012 (ptp90) REVERT: D 646 LYS cc_start: 0.6478 (pptt) cc_final: 0.6160 (pttm) outliers start: 4 outliers final: 2 residues processed: 101 average time/residue: 0.3203 time to fit residues: 51.9257 Evaluate side-chains 101 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain D residue 319 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 40.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN D 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.127389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.079176 restraints weight = 187262.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.081946 restraints weight = 78187.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081826 restraints weight = 46699.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082147 restraints weight = 45551.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082292 restraints weight = 41381.948| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20812 Z= 0.183 Angle : 0.556 4.674 28246 Z= 0.297 Chirality : 0.048 0.151 3106 Planarity : 0.004 0.045 3642 Dihedral : 5.046 23.828 2946 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.40 % Allowed : 8.68 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2538 helix: -2.85 (0.57), residues: 50 sheet: 0.53 (0.16), residues: 1068 loop : -0.83 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 418 TYR 0.012 0.001 TYR D 359 PHE 0.012 0.001 PHE E 419 TRP 0.008 0.001 TRP C 460 HIS 0.005 0.001 HIS C 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (20790) covalent geometry : angle 0.55286 / 0.30 (28196) SS BOND : bond 0.00252 / 0.18 ( 16) SS BOND : angle 1.19537 / 0.79 ( 32) hydrogen bonds : bond 0.04267 / 2.82 ( 679) hydrogen bonds : angle 7.19382 / 5.01 ( 1809) link_NAG-ASN : bond 0.00505 / 0.29 ( 6) link_NAG-ASN : angle 1.72605 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.8823 (ttt) cc_final: 0.8610 (ttm) outliers start: 9 outliers final: 7 residues processed: 113 average time/residue: 0.2764 time to fit residues: 52.4439 Evaluate side-chains 105 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 447 CYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 447 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 234 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 187 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 192 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 245 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079145 restraints weight = 186628.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081631 restraints weight = 81995.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.082955 restraints weight = 49549.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.083034 restraints weight = 46951.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.083141 restraints weight = 39336.402| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 20812 Z= 0.100 Angle : 0.482 4.270 28246 Z= 0.255 Chirality : 0.047 0.146 3106 Planarity : 0.003 0.040 3642 Dihedral : 4.575 18.895 2932 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.76 % Allowed : 8.23 % Favored : 91.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2538 helix: -2.09 (0.65), residues: 50 sheet: 0.63 (0.16), residues: 1042 loop : -0.73 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 418 TYR 0.010 0.001 TYR D 359 PHE 0.009 0.001 PHE F 403 TRP 0.008 0.001 TRP C 460 HIS 0.010 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (20790) covalent geometry : angle 0.48034 / 0.25 (28196) SS BOND : bond 0.00149 / 0.10 ( 16) SS BOND : angle 0.95826 / 0.64 ( 32) hydrogen bonds : bond 0.03246 / 2.14 ( 679) hydrogen bonds : angle 6.17940 / 4.30 ( 1809) link_NAG-ASN : bond 0.00148 / 0.08 ( 6) link_NAG-ASN : angle 1.30684 / 0.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.8382 (m-80) cc_final: 0.7943 (p90) REVERT: B 61 PHE cc_start: 0.8432 (m-80) cc_final: 0.7998 (p90) REVERT: B 106 MET cc_start: 0.8802 (ttt) cc_final: 0.8594 (ttm) REVERT: E 245 MET cc_start: 0.7773 (mtp) cc_final: 0.7444 (mtp) outliers start: 17 outliers final: 12 residues processed: 122 average time/residue: 0.2545 time to fit residues: 52.6636 Evaluate side-chains 115 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 447 CYS Chi-restraints excluded: chain D residue 480 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 173 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 GLN ** C 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.126016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082823 restraints weight = 187077.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.080233 restraints weight = 110237.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.080224 restraints weight = 91540.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.080842 restraints weight = 70699.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081473 restraints weight = 62325.315| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 20812 Z= 0.346 Angle : 0.632 5.924 28246 Z= 0.335 Chirality : 0.049 0.160 3106 Planarity : 0.005 0.049 3642 Dihedral : 5.205 27.017 2932 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 1.30 % Allowed : 9.66 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2538 helix: -2.18 (0.65), residues: 50 sheet: 0.28 (0.16), residues: 1060 loop : -0.94 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 226 TYR 0.019 0.002 TYR D 359 PHE 0.014 0.002 PHE C 323 TRP 0.008 0.001 TRP E 301 HIS 0.009 0.002 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00791 / 0.35 (20790) covalent geometry : angle 0.62740 / 0.33 (28196) SS BOND : bond 0.00272 / 0.14 ( 16) SS BOND : angle 1.29362 / 0.80 ( 32) hydrogen bonds : bond 0.03695 / 2.46 ( 679) hydrogen bonds : angle 6.23269 / 4.32 ( 1809) link_NAG-ASN : bond 0.00670 / 0.40 ( 6) link_NAG-ASN : angle 2.55345 / 1.74 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.7091 (pp) REVERT: D 185 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6880 (pp) REVERT: D 447 CYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7815 (m) outliers start: 29 outliers final: 21 residues processed: 118 average time/residue: 0.2802 time to fit residues: 56.0254 Evaluate side-chains 117 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 104 GLN Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 447 CYS Chi-restraints excluded: chain D residue 480 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 39 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 253 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 chunk 247 optimal weight: 50.0000 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 50.0000 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 214 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078629 restraints weight = 187505.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.081843 restraints weight = 88270.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081936 restraints weight = 50596.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.082546 restraints weight = 46733.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.082632 restraints weight = 41757.041| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20812 Z= 0.131 Angle : 0.501 4.657 28246 Z= 0.264 Chirality : 0.046 0.146 3106 Planarity : 0.004 0.043 3642 Dihedral : 4.758 20.713 2932 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.98 % Allowed : 10.24 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.17), residues: 2538 helix: -1.68 (0.73), residues: 50 sheet: 0.26 (0.15), residues: 1066 loop : -0.84 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 305 TYR 0.017 0.001 TYR D 359 PHE 0.010 0.001 PHE E 403 TRP 0.007 0.001 TRP C 460 HIS 0.006 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (20790) covalent geometry : angle 0.49854 / 0.26 (28196) SS BOND : bond 0.00190 / 0.11 ( 16) SS BOND : angle 0.98910 / 0.62 ( 32) hydrogen bonds : bond 0.02861 / 1.88 ( 679) hydrogen bonds : angle 5.78024 / 4.00 ( 1809) link_NAG-ASN : bond 0.00148 / 0.08 ( 6) link_NAG-ASN : angle 1.62949 / 1.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7141 (OUTLIER) cc_final: 0.6918 (pp) REVERT: D 185 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6607 (pp) REVERT: D 199 MET cc_start: 0.5985 (ttt) cc_final: 0.5727 (ttt) REVERT: D 447 CYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7840 (m) outliers start: 22 outliers final: 16 residues processed: 116 average time/residue: 0.2642 time to fit residues: 52.0582 Evaluate side-chains 118 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 447 CYS Chi-restraints excluded: chain D residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 87 optimal weight: 50.0000 chunk 68 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.079664 restraints weight = 188016.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.081589 restraints weight = 88328.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081528 restraints weight = 52751.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.082940 restraints weight = 52474.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.082451 restraints weight = 49925.151| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20812 Z= 0.146 Angle : 0.491 5.447 28246 Z= 0.257 Chirality : 0.046 0.145 3106 Planarity : 0.003 0.044 3642 Dihedral : 4.612 20.630 2932 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.12 % Allowed : 10.20 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.17), residues: 2538 helix: -1.77 (0.72), residues: 50 sheet: 0.25 (0.16), residues: 1056 loop : -0.79 (0.17), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.017 0.001 TYR D 359 PHE 0.008 0.001 PHE E 403 TRP 0.006 0.001 TRP D 181 HIS 0.006 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (20790) covalent geometry : angle 0.48764 / 0.26 (28196) SS BOND : bond 0.00246 / 0.13 ( 16) SS BOND : angle 1.15615 / 0.72 ( 32) hydrogen bonds : bond 0.02680 / 1.75 ( 679) hydrogen bonds : angle 5.53360 / 3.83 ( 1809) link_NAG-ASN : bond 0.00224 / 0.13 ( 6) link_NAG-ASN : angle 1.68205 / 1.12 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 MET cc_start: 0.8884 (mmm) cc_final: 0.8495 (mmt) REVERT: C 185 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6991 (pp) REVERT: D 185 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6695 (pp) REVERT: D 447 CYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7681 (m) outliers start: 25 outliers final: 21 residues processed: 122 average time/residue: 0.2694 time to fit residues: 56.0958 Evaluate side-chains 120 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 447 CYS Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 238 optimal weight: 50.0000 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 214 optimal weight: 1.9990 chunk 246 optimal weight: 40.0000 chunk 39 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.079014 restraints weight = 187948.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082383 restraints weight = 87659.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082409 restraints weight = 49415.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082991 restraints weight = 45713.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.083135 restraints weight = 42201.498| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20812 Z= 0.116 Angle : 0.484 9.403 28246 Z= 0.252 Chirality : 0.046 0.144 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.554 34.507 2932 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.89 % Allowed : 10.38 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2538 helix: -1.41 (0.76), residues: 50 sheet: 0.31 (0.16), residues: 1054 loop : -0.73 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.015 0.001 TYR D 359 PHE 0.008 0.001 PHE E 403 TRP 0.007 0.001 TRP D 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (20790) covalent geometry : angle 0.47736 / 0.25 (28196) SS BOND : bond 0.00253 / 0.13 ( 16) SS BOND : angle 2.06478 / 1.03 ( 32) hydrogen bonds : bond 0.02530 / 1.65 ( 679) hydrogen bonds : angle 5.37366 / 3.72 ( 1809) link_NAG-ASN : bond 0.00129 / 0.07 ( 6) link_NAG-ASN : angle 1.52546 / 1.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6851 (pp) REVERT: D 185 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6590 (pp) REVERT: D 447 CYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7578 (m) outliers start: 20 outliers final: 17 residues processed: 121 average time/residue: 0.2772 time to fit residues: 56.4780 Evaluate side-chains 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 447 CYS Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 155 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 183 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 235 optimal weight: 0.4980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.127558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.079613 restraints weight = 186893.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082770 restraints weight = 88505.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082765 restraints weight = 53197.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.083212 restraints weight = 48173.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.083377 restraints weight = 48007.685| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 20812 Z= 0.119 Angle : 0.496 12.253 28246 Z= 0.256 Chirality : 0.046 0.170 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.555 45.041 2932 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.94 % Allowed : 10.42 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.17), residues: 2538 helix: -1.22 (0.78), residues: 50 sheet: 0.31 (0.16), residues: 1054 loop : -0.69 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.015 0.001 TYR D 359 PHE 0.008 0.001 PHE E 403 TRP 0.006 0.001 TRP D 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20790) covalent geometry : angle 0.48553 / 0.25 (28196) SS BOND : bond 0.00319 / 0.16 ( 16) SS BOND : angle 2.80588 / 1.85 ( 32) hydrogen bonds : bond 0.02488 / 1.63 ( 679) hydrogen bonds : angle 5.26148 / 3.64 ( 1809) link_NAG-ASN : bond 0.00145 / 0.08 ( 6) link_NAG-ASN : angle 1.52966 / 1.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6890 (pp) REVERT: D 185 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6523 (pp) outliers start: 21 outliers final: 17 residues processed: 121 average time/residue: 0.2930 time to fit residues: 59.6487 Evaluate side-chains 117 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 11 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.127415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078955 restraints weight = 187822.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.081955 restraints weight = 89846.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.082056 restraints weight = 54238.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082601 restraints weight = 49254.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082720 restraints weight = 47121.714| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20812 Z= 0.164 Angle : 0.515 13.312 28246 Z= 0.266 Chirality : 0.046 0.144 3106 Planarity : 0.004 0.043 3642 Dihedral : 4.581 34.728 2932 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.07 % Allowed : 10.51 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2538 helix: -1.52 (0.73), residues: 50 sheet: 0.20 (0.15), residues: 1082 loop : -0.71 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 650 TYR 0.017 0.001 TYR D 359 PHE 0.008 0.001 PHE E 403 TRP 0.007 0.001 TRP C 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (20790) covalent geometry : angle 0.50248 / 0.26 (28196) SS BOND : bond 0.00304 / 0.15 ( 16) SS BOND : angle 3.10095 / 2.10 ( 32) hydrogen bonds : bond 0.02605 / 1.71 ( 679) hydrogen bonds : angle 5.19853 / 3.60 ( 1809) link_NAG-ASN : bond 0.00239 / 0.14 ( 6) link_NAG-ASN : angle 1.73774 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6837 (pp) REVERT: D 185 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6595 (pp) outliers start: 24 outliers final: 22 residues processed: 122 average time/residue: 0.2721 time to fit residues: 56.4417 Evaluate side-chains 118 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 166 optimal weight: 10.0000 chunk 80 optimal weight: 40.0000 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.129862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087721 restraints weight = 195081.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.087877 restraints weight = 93017.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.086982 restraints weight = 72538.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087733 restraints weight = 65983.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087789 restraints weight = 57593.425| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 20812 Z= 0.142 Angle : 0.499 10.408 28246 Z= 0.257 Chirality : 0.046 0.143 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.529 37.151 2932 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.16 % Allowed : 10.42 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2538 helix: -1.21 (0.77), residues: 50 sheet: 0.20 (0.15), residues: 1070 loop : -0.68 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 539 TYR 0.016 0.001 TYR D 359 PHE 0.009 0.001 PHE E 403 TRP 0.008 0.001 TRP C 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (20790) covalent geometry : angle 0.49040 / 0.25 (28196) SS BOND : bond 0.00280 / 0.14 ( 16) SS BOND : angle 2.59784 / 1.70 ( 32) hydrogen bonds : bond 0.02503 / 1.64 ( 679) hydrogen bonds : angle 5.11649 / 3.55 ( 1809) link_NAG-ASN : bond 0.00181 / 0.11 ( 6) link_NAG-ASN : angle 1.63045 / 1.10 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5076 Ramachandran restraints generated. 2538 Oldfield, 0 Emsley, 2538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 41 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 127 is missing expected H atoms. Skipping. Residue MET 276 is missing expected H atoms. Skipping. Residue MET 417 is missing expected H atoms. Skipping. Residue MET 458 is missing expected H atoms. Skipping. Residue TYR 192 is missing expected H atoms. Skipping. Residue MET 193 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue MET 379 is missing expected H atoms. Skipping. Residue MET 388 is missing expected H atoms. Skipping. Residue MET 434 is missing expected H atoms. Skipping. Residue MET 442 is missing expected H atoms. Skipping. Residue MET 663 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6885 (pp) REVERT: D 185 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6604 (pp) outliers start: 26 outliers final: 22 residues processed: 122 average time/residue: 0.2615 time to fit residues: 53.6026 Evaluate side-chains 120 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain B residue 51 CYS Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 480 CYS Chi-restraints excluded: chain D residue 651 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 223 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 95 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.130335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088289 restraints weight = 196484.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088558 restraints weight = 93617.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.087716 restraints weight = 72984.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088472 restraints weight = 65984.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.088575 restraints weight = 57411.393| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 20812 Z= 0.105 Angle : 0.482 9.273 28246 Z= 0.247 Chirality : 0.046 0.142 3106 Planarity : 0.003 0.042 3642 Dihedral : 4.378 34.356 2932 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.89 % Allowed : 10.60 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.17), residues: 2538 helix: -1.07 (0.80), residues: 50 sheet: 0.19 (0.15), residues: 1080 loop : -0.61 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.016 0.001 TYR C 470 PHE 0.008 0.001 PHE E 403 TRP 0.008 0.001 TRP C 181 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20790) covalent geometry : angle 0.47450 / 0.24 (28196) SS BOND : bond 0.00251 / 0.13 ( 16) SS BOND : angle 2.32557 / 1.53 ( 32) hydrogen bonds : bond 0.02358 / 1.54 ( 679) hydrogen bonds : angle 4.99414 / 3.46 ( 1809) link_NAG-ASN : bond 0.00122 / 0.07 ( 6) link_NAG-ASN : angle 1.49708 / 0.99 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6151.35 seconds wall clock time: 105 minutes 47.51 seconds (6347.51 seconds total)