Starting phenix.real_space_refine on Tue Jul 7 01:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ri_75407/07_2026/10ri_75407.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ri_75407/07_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_75407/07_2026/10ri_75407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ri_75407/07_2026/10ri_75407.map" model { file = "/net/cci-nas-00/data/ceres_data/10ri_75407/07_2026/10ri_75407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ri_75407/07_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-dev-6108/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, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 21.25, per 1000 atoms: 0.53 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: 3.41 Conformation dependent library (CDL) restraints added in 1.2 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: 1.13 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: 11.26 Time building geometry restraints manager: 4.87 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: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 53.260 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.240 ------------------------------------------------------------------------------- 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 : 1.090 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: 0.3040 time to fit residues: 48.7342 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 : 1.101 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.127878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.079736 restraints weight = 186438.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081795 restraints weight = 75871.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082278 restraints weight = 50051.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.082586 restraints weight = 46217.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.082731 restraints weight = 42693.014| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.1083 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= 0.185 Angle : 0.557 4.681 28246 Z= 0.299 Chirality : 0.048 0.151 3106 Planarity : 0.004 0.045 3642 Dihedral : 5.045 23.869 2946 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.49 % Allowed : 8.59 % 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 (0.58), 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 0.00414 / 0.18 (20790) covalent geometry : angle 0.55467 / 0.30 (28196) SS BOND : bond 0.00217 / 0.15 ( 16) SS BOND : angle 1.16435 / 0.77 ( 32) hydrogen bonds : bond 0.04308 / 2.86 ( 679) hydrogen bonds : angle 7.23017 / 5.04 ( 1809) link_NAG-ASN : bond 0.00488 / 0.28 ( 6) link_NAG-ASN : angle 1.71173 / 1.10 ( 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 117 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.107 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: 0.8836 (ttt) cc_final: 0.8608 (ttm) outliers start: 11 outliers final: 7 residues processed: 115 average time/residue: 0.2679 time to fit residues: 51.7239 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 : 1.004 ------------------------------------------------------------------------------- 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: 1.9990 chunk 187 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 245 optimal weight: 30.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.128437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080178 restraints weight = 187220.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.083292 restraints weight = 85094.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.083665 restraints weight = 48984.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.083920 restraints weight = 42939.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.084054 restraints weight = 43035.397| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20812 Z= 0.133 Angle : 0.499 4.886 28246 Z= 0.264 Chirality : 0.047 0.145 3106 Planarity : 0.004 0.042 3642 Dihedral : 4.680 20.949 2932 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.89 % Allowed : 8.27 % Favored : 90.83 % 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: -0.34 (0.17), residues: 2538 helix: -2.13 (0.66), residues: 50 sheet: 0.60 (0.16), residues: 1034 loop : -0.77 (0.16), residues: 1454 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 0.009 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 0.00296 / 0.13 (20790) covalent geometry : angle 0.49732 / 0.26 (28196) SS BOND : bond 0.00164 / 0.10 ( 16) SS BOND : angle 1.01015 / 0.66 ( 32) hydrogen bonds : bond 0.03261 / 2.15 ( 679) hydrogen bonds : angle 6.17929 / 4.30 ( 1809) link_NAG-ASN : bond 0.00195 / 0.11 ( 6) link_NAG-ASN : angle 1.48103 / 0.95 ( 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 123 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.900 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: D 185 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6696 (pp) outliers start: 20 outliers final: 14 residues processed: 120 average time/residue: 0.2469 time to fit residues: 50.0277 Evaluate side-chains 113 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 218 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 480 CYS 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 378 THR 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: 20.0000 chunk 203 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 244 optimal weight: 20.0000 chunk 175 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN C 207 ASN C 501 GLN ** C 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.127084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078283 restraints weight = 186200.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081194 restraints weight = 89275.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081073 restraints weight = 55851.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081662 restraints weight = 52252.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.081931 restraints weight = 47657.003| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20812 Z= 0.216 Angle : 0.539 4.938 28246 Z= 0.285 Chirality : 0.047 0.149 3106 Planarity : 0.004 0.045 3642 Dihedral : 4.826 24.588 2932 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.16 % Allowed : 9.66 % Favored : 89.18 % 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: -0.45 (0.17), residues: 2538 helix: -2.02 (0.67), residues: 50 sheet: 0.46 (0.16), residues: 1044 loop : -0.81 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 226 TYR 0.018 0.001 TYR D 359 PHE 0.011 0.001 PHE E 247 TRP 0.007 0.001 TRP D 460 HIS 0.006 0.001 HIS C 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (20790) covalent geometry : angle 0.53610 / 0.28 (28196) SS BOND : bond 0.00232 / 0.12 ( 16) SS BOND : angle 1.14597 / 0.72 ( 32) hydrogen bonds : bond 0.03162 / 2.08 ( 679) hydrogen bonds : angle 5.93470 / 4.13 ( 1809) link_NAG-ASN : bond 0.00418 / 0.24 ( 6) link_NAG-ASN : angle 1.99599 / 1.33 ( 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: 26 poor density : 100 time to evaluate : 0.743 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: D 185 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6805 (pp) REVERT: D 199 MET cc_start: 0.5838 (ttt) cc_final: 0.5393 (ttt) outliers start: 26 outliers final: 20 residues processed: 117 average time/residue: 0.2537 time to fit residues: 50.1090 Evaluate side-chains 118 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 130 HIS Chi-restraints excluded: chain F residue 130 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 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 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: 3.9990 chunk 253 optimal weight: 9.9990 chunk 72 optimal weight: 40.0000 chunk 138 optimal weight: 8.9990 chunk 247 optimal weight: 40.0000 chunk 41 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 51 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4370 r_free = 0.4370 target = 0.127129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.078051 restraints weight = 187462.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082046 restraints weight = 79010.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.081922 restraints weight = 46453.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.082223 restraints weight = 41877.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082350 restraints weight = 39795.996| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20812 Z= 0.171 Angle : 0.505 5.366 28246 Z= 0.266 Chirality : 0.046 0.147 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.693 21.996 2932 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.94 % Allowed : 10.06 % Favored : 89.00 % 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: -0.49 (0.17), residues: 2538 helix: -1.59 (0.74), residues: 50 sheet: 0.30 (0.16), residues: 1068 loop : -0.76 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.016 0.001 TYR D 359 PHE 0.009 0.001 PHE F 403 TRP 0.006 0.001 TRP D 460 HIS 0.006 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (20790) covalent geometry : angle 0.50083 / 0.26 (28196) SS BOND : bond 0.00337 / 0.17 ( 16) SS BOND : angle 1.40352 / 0.86 ( 32) hydrogen bonds : bond 0.02895 / 1.90 ( 679) hydrogen bonds : angle 5.76103 / 4.00 ( 1809) link_NAG-ASN : bond 0.00254 / 0.15 ( 6) link_NAG-ASN : angle 1.72928 / 1.15 ( 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 118 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.873 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: D 185 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6612 (pp) outliers start: 21 outliers final: 18 residues processed: 116 average time/residue: 0.2505 time to fit residues: 49.0226 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 : 1.089 ------------------------------------------------------------------------------- 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 218 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 101 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 133 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 40.0000 chunk 87 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 235 optimal weight: 0.6980 chunk 240 optimal weight: 8.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.126909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077187 restraints weight = 188164.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.080059 restraints weight = 76250.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.081605 restraints weight = 47913.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.082813 restraints weight = 38181.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.083272 restraints weight = 33840.026| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20812 Z= 0.185 Angle : 0.514 8.224 28246 Z= 0.270 Chirality : 0.046 0.144 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.777 38.713 2932 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.12 % Allowed : 10.42 % Favored : 88.46 % 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: -0.55 (0.17), residues: 2538 helix: -1.50 (0.74), residues: 50 sheet: 0.24 (0.16), residues: 1066 loop : -0.77 (0.17), residues: 1422 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 247 TRP 0.006 0.001 TRP C 460 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (20790) covalent geometry : angle 0.50886 / 0.27 (28196) SS BOND : bond 0.00254 / 0.13 ( 16) SS BOND : angle 1.78511 / 0.83 ( 32) hydrogen bonds : bond 0.02815 / 1.85 ( 679) hydrogen bonds : angle 5.59261 / 3.87 ( 1809) link_NAG-ASN : bond 0.00287 / 0.17 ( 6) link_NAG-ASN : angle 1.78490 / 1.20 ( 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 123 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.866 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: D 185 ILE cc_start: 0.6976 (OUTLIER) cc_final: 0.6687 (pp) outliers start: 25 outliers final: 23 residues processed: 119 average time/residue: 0.2482 time to fit residues: 49.7371 Evaluate side-chains 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 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 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 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 364 ILE Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 480 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 238 optimal weight: 40.0000 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 246 optimal weight: 40.0000 chunk 39 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.127543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079017 restraints weight = 187088.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082253 restraints weight = 86190.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.082477 restraints weight = 49450.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.082961 restraints weight = 43511.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.083210 restraints weight = 41426.684| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20812 Z= 0.123 Angle : 0.487 11.104 28246 Z= 0.254 Chirality : 0.046 0.144 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.542 30.127 2932 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.81 % Allowed : 10.78 % 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: -0.48 (0.17), residues: 2538 helix: -1.30 (0.78), residues: 50 sheet: 0.26 (0.16), residues: 1058 loop : -0.69 (0.17), residues: 1430 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 0.009 0.001 PHE E 403 TRP 0.007 0.001 TRP D 460 HIS 0.005 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (20790) covalent geometry : angle 0.47951 / 0.25 (28196) SS BOND : bond 0.00457 / 0.23 ( 16) SS BOND : angle 2.32444 / 1.09 ( 32) hydrogen bonds : bond 0.02552 / 1.67 ( 679) hydrogen bonds : angle 5.39667 / 3.73 ( 1809) link_NAG-ASN : bond 0.00130 / 0.07 ( 6) link_NAG-ASN : angle 1.52558 / 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 116 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.103 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: D 185 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6495 (pp) outliers start: 18 outliers final: 17 residues processed: 115 average time/residue: 0.2835 time to fit residues: 54.9836 Evaluate side-chains 114 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.5980 chunk 183 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4376 r_free = 0.4376 target = 0.127525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.078957 restraints weight = 187496.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.081972 restraints weight = 86887.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.082486 restraints weight = 50344.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.082921 restraints weight = 43056.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083091 restraints weight = 41191.125| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 20812 Z= 0.129 Angle : 0.494 10.212 28246 Z= 0.256 Chirality : 0.046 0.189 3106 Planarity : 0.003 0.043 3642 Dihedral : 4.580 46.733 2932 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.07 % Allowed : 10.55 % Favored : 88.37 % 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: -0.44 (0.17), residues: 2538 helix: -1.12 (0.79), residues: 50 sheet: 0.29 (0.16), residues: 1054 loop : -0.68 (0.17), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.016 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 0.00295 / 0.13 (20790) covalent geometry : angle 0.48495 / 0.25 (28196) SS BOND : bond 0.00343 / 0.18 ( 16) SS BOND : angle 2.56290 / 1.62 ( 32) hydrogen bonds : bond 0.02524 / 1.65 ( 679) hydrogen bonds : angle 5.28264 / 3.65 ( 1809) link_NAG-ASN : bond 0.00171 / 0.10 ( 6) link_NAG-ASN : angle 1.58020 / 1.05 ( 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 122 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.132 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: D 185 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6510 (pp) outliers start: 24 outliers final: 22 residues processed: 120 average time/residue: 0.2643 time to fit residues: 54.1837 Evaluate side-chains 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.6980 chunk 83 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.127173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078863 restraints weight = 186705.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.081416 restraints weight = 92261.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081626 restraints weight = 55684.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082091 restraints weight = 52118.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.082278 restraints weight = 49323.739| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 20812 Z= 0.197 Angle : 0.531 14.720 28246 Z= 0.276 Chirality : 0.046 0.146 3106 Planarity : 0.004 0.044 3642 Dihedral : 4.675 31.084 2932 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.16 % Allowed : 10.87 % Favored : 87.97 % 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: -0.59 (0.17), residues: 2538 helix: -1.32 (0.76), residues: 50 sheet: 0.13 (0.15), residues: 1082 loop : -0.75 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 539 TYR 0.018 0.001 TYR D 359 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 0.00451 / 0.20 (20790) covalent geometry : angle 0.51644 / 0.27 (28196) SS BOND : bond 0.00294 / 0.15 ( 16) SS BOND : angle 3.42956 / 2.32 ( 32) hydrogen bonds : bond 0.02753 / 1.80 ( 679) hydrogen bonds : angle 5.26796 / 3.63 ( 1809) link_NAG-ASN : bond 0.00325 / 0.19 ( 6) link_NAG-ASN : angle 1.90861 / 1.29 ( 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: 26 poor density : 96 time to evaluate : 0.879 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: E 195 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: D 185 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6564 (pp) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.2592 time to fit residues: 52.1381 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 : 1.106 ------------------------------------------------------------------------------- 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 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 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 C residue 651 HIS Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 195 GLU 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 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 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 166 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 255 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.130380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.087812 restraints weight = 194457.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088441 restraints weight = 90505.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087593 restraints weight = 67842.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.088133 restraints weight = 65321.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088356 restraints weight = 57525.237| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 20812 Z= 0.099 Angle : 0.488 9.637 28246 Z= 0.250 Chirality : 0.046 0.155 3106 Planarity : 0.003 0.042 3642 Dihedral : 4.441 36.815 2932 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.89 % Allowed : 11.14 % Favored : 87.97 % 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: -1.17 (0.78), residues: 50 sheet: 0.20 (0.16), residues: 1072 loop : -0.64 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 305 TYR 0.014 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 0.00228 / 0.10 (20790) covalent geometry : angle 0.48065 / 0.25 (28196) SS BOND : bond 0.00246 / 0.13 ( 16) SS BOND : angle 2.40208 / 1.60 ( 32) hydrogen bonds : bond 0.02374 / 1.55 ( 679) hydrogen bonds : angle 5.07501 / 3.52 ( 1809) link_NAG-ASN : bond 0.00082 / 0.04 ( 6) link_NAG-ASN : angle 1.42556 / 0.95 ( 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 119 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.973 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 51 CYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7170 (t) REVERT: F 425 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8814 (mtmm) REVERT: D 185 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6558 (pp) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.2708 time to fit residues: 53.4060 Evaluate side-chains 112 residues out of total 2286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 230 LEU 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 E residue 238 SER Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 480 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 254 random chunks: chunk 223 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.130234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.087872 restraints weight = 195078.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.088112 restraints weight = 91028.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087350 restraints weight = 70093.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.087907 restraints weight = 64584.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.088419 restraints weight = 57250.034| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20812 Z= 0.118 Angle : 0.487 10.694 28246 Z= 0.250 Chirality : 0.046 0.150 3106 Planarity : 0.003 0.042 3642 Dihedral : 4.373 30.249 2932 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.89 % Allowed : 11.09 % Favored : 88.01 % 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: -0.46 (0.17), residues: 2538 helix: -1.37 (0.75), residues: 50 sheet: 0.21 (0.16), residues: 1070 loop : -0.64 (0.17), residues: 1418 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 0.008 0.001 TRP C 181 HIS 0.006 0.001 HIS C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20790) covalent geometry : angle 0.47776 / 0.25 (28196) SS BOND : bond 0.00258 / 0.13 ( 16) SS BOND : angle 2.64146 / 1.76 ( 32) hydrogen bonds : bond 0.02418 / 1.57 ( 679) hydrogen bonds : angle 5.00187 / 3.46 ( 1809) link_NAG-ASN : bond 0.00138 / 0.08 ( 6) link_NAG-ASN : angle 1.53783 / 1.02 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6209.48 seconds wall clock time: 106 minutes 41.24 seconds (6401.24 seconds total)