Starting phenix.real_space_refine on Wed Mar 4 02:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfs_30346/03_2026/7cfs_30346.map" } resolution = 3.56 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 81 5.16 5 Na 1 4.78 5 C 6402 2.51 5 N 1631 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9974 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3249 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 11, 'TYR:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3267 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 2, 'TYR:plan': 2, 'ASP:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3268 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 189 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'TYR:plan': 1, 'ASP:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' NA': 1, 'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.21, per 1000 atoms: 0.22 Number of scatterers: 9974 At special positions: 0 Unit cell: (97.344, 96.33, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 Na 1 11.00 O 1859 8.00 N 1631 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 314 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 345 " distance=2.03 Simple disulfide: pdb=" SG CYS A 325 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 314 " - pdb=" SG CYS B 361 " distance=2.33 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 345 " distance=2.03 Simple disulfide: pdb=" SG CYS B 325 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 367 " distance=2.02 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 314 " - pdb=" SG CYS C 361 " distance=2.33 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 345 " distance=2.03 Simple disulfide: pdb=" SG CYS C 325 " - pdb=" SG CYS C 337 " 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 A 601 " - " ASN A 395 " " NAG A 602 " - " ASN A 368 " " NAG B 601 " - " ASN B 395 " " NAG B 602 " - " ASN B 368 " " NAG C 601 " - " ASN C 395 " " NAG C 602 " - " ASN C 368 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 416.6 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 15 sheets defined 35.2% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 45 through 61 removed outlier: 4.264A pdb=" N LEU A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.511A pdb=" N HIS A 70 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.706A pdb=" N ARG A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP A 183 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR A 229 " --> pdb=" O GLN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE A 352 " --> pdb=" O PRO A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY A 402 " --> pdb=" O GLU A 398 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.509A pdb=" N HIS B 70 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL B 103 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 removed outlier: 3.542A pdb=" N HIS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.582A pdb=" N ILE B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.582A pdb=" N ASP B 183 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.810A pdb=" N TYR B 229 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.559A pdb=" N TYR B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.784A pdb=" N LYS B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.548A pdb=" N PHE B 352 " --> pdb=" O PRO B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.012A pdb=" N GLY B 433 " --> pdb=" O ALA B 429 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 4.263A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.510A pdb=" N HIS C 70 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.830A pdb=" N VAL C 103 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.543A pdb=" N HIS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.581A pdb=" N ILE C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 138 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.707A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.583A pdb=" N ASP C 183 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 184 " --> pdb=" O ALA C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 184' Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.811A pdb=" N TYR C 229 " --> pdb=" O GLN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.560A pdb=" N TYR C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.783A pdb=" N LYS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 removed outlier: 3.547A pdb=" N PHE C 352 " --> pdb=" O PRO C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 394 removed outlier: 3.620A pdb=" N ALA C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.513A pdb=" N GLY C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 403 " --> pdb=" O GLN C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 4.013A pdb=" N GLY C 433 " --> pdb=" O ALA C 429 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 3.822A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS C 462 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 274 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 276 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 278 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE A 269 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE A 410 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR A 271 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE A 412 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL A 273 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL A 414 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS A 275 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 416 " --> pdb=" O CYS A 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 277 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 189 removed outlier: 7.261A pdb=" N LYS A 193 " --> pdb=" O ASN A 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN A 94 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS A 250 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 274 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN B 276 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 278 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE B 269 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE B 410 " --> pdb=" O PHE B 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR B 271 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE B 412 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N VAL B 273 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL B 414 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS B 275 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 416 " --> pdb=" O CYS B 275 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 277 " --> pdb=" O ASN B 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS B 193 " --> pdb=" O ASN B 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN B 94 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS B 250 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB2, first strand: chain 'C' and resid 73 through 81 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 274 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN C 276 " --> pdb=" O GLY C 373 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 278 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 removed outlier: 10.264A pdb=" N PHE C 269 " --> pdb=" O LEU C 408 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N ILE C 410 " --> pdb=" O PHE C 269 " (cutoff:3.500A) removed outlier: 10.376A pdb=" N THR C 271 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N PHE C 412 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N VAL C 273 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL C 414 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N CYS C 275 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 416 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU C 277 " --> pdb=" O ASN C 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'C' and resid 185 through 189 removed outlier: 7.262A pdb=" N LYS C 193 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASN C 94 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 250 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 174 303 hydrogen bonds defined for protein. 810 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: 1.35 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3154 1.34 - 1.45: 1745 1.45 - 1.57: 5202 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 10209 Sorted by residual: bond pdb=" CAI Y01 B 603 " pdb=" CAK Y01 B 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAK Y01 C 603 " ideal model delta sigma weight residual 1.492 1.386 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" CAI Y01 A 603 " pdb=" CAK Y01 A 603 " ideal model delta sigma weight residual 1.492 1.387 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CAI Y01 C 603 " pdb=" CAZ Y01 C 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " ideal model delta sigma weight residual 1.332 1.380 -0.048 2.00e-02 2.50e+03 5.78e+00 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 13283 1.94 - 3.88: 492 3.88 - 5.82: 65 5.82 - 7.76: 21 7.76 - 9.70: 21 Bond angle restraints: 13882 Sorted by residual: angle pdb=" N ILE A 381 " pdb=" CA ILE A 381 " pdb=" C ILE A 381 " ideal model delta sigma weight residual 108.88 117.02 -8.14 2.16e+00 2.14e-01 1.42e+01 angle pdb=" N ILE C 381 " pdb=" CA ILE C 381 " pdb=" C ILE C 381 " ideal model delta sigma weight residual 108.88 116.98 -8.10 2.16e+00 2.14e-01 1.41e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 108.88 116.97 -8.09 2.16e+00 2.14e-01 1.40e+01 angle pdb=" CA ILE C 381 " pdb=" C ILE C 381 " pdb=" N PRO C 382 " ideal model delta sigma weight residual 118.88 124.19 -5.31 1.54e+00 4.22e-01 1.19e+01 angle pdb=" CA ILE B 381 " pdb=" C ILE B 381 " pdb=" N PRO B 382 " ideal model delta sigma weight residual 118.88 124.17 -5.29 1.54e+00 4.22e-01 1.18e+01 ... (remaining 13877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 5486 16.89 - 33.78: 656 33.78 - 50.68: 141 50.68 - 67.57: 39 67.57 - 84.46: 21 Dihedral angle restraints: 6343 sinusoidal: 2607 harmonic: 3736 Sorted by residual: dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 345 " pdb=" CB CYS C 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.46 84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS B 323 " pdb=" SG CYS B 323 " pdb=" SG CYS B 345 " pdb=" CB CYS B 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 323 " pdb=" SG CYS A 323 " pdb=" SG CYS A 345 " pdb=" CB CYS A 345 " ideal model delta sinusoidal sigma weight residual -86.00 -170.45 84.45 1 1.00e+01 1.00e-02 8.67e+01 ... (remaining 6340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1248 0.067 - 0.135: 270 0.135 - 0.202: 33 0.202 - 0.270: 0 0.270 - 0.337: 6 Chirality restraints: 1557 Sorted by residual: chirality pdb=" CBG Y01 C 603 " pdb=" CAQ Y01 C 603 " pdb=" CBD Y01 C 603 " pdb=" CBI Y01 C 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CBG Y01 B 603 " pdb=" CAQ Y01 B 603 " pdb=" CBD Y01 B 603 " pdb=" CBI Y01 B 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.66 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 1554 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO B 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 338 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 339 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 338 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO C 339 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 339 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 339 " -0.026 5.00e-02 4.00e+02 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 25 2.45 - 3.06: 5484 3.06 - 3.67: 14301 3.67 - 4.29: 20002 4.29 - 4.90: 33905 Nonbonded interactions: 73717 Sorted by model distance: nonbonded pdb=" CE1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.835 3.260 nonbonded pdb=" ND1 HIS C 73 " pdb=" OE1 GLN C 422 " model vdw 1.971 3.120 nonbonded pdb=" CD2 HIS A 73 " pdb=" OE1 GLN A 422 " model vdw 1.990 3.260 nonbonded pdb=" CD2 HIS B 73 " pdb=" OE1 GLN B 422 " model vdw 2.116 3.260 nonbonded pdb=" OD1 ASP A 434 " pdb="NA NA A 604 " model vdw 2.251 2.470 ... (remaining 73712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 198 or (resid 199 and ( \ name N or name CA or name C or name O or name CB )) or resid 200 through 290 or \ (resid 291 through 300 and (name N or name CA or name C or name O or name CB )) \ or resid 301 through 452 or (resid 453 through 455 and (name N or name CA or nam \ e C or name O or name CB )) or resid 456 through 464 or (resid 465 and (name N o \ r name CA or name C or name O or name CB )) or resid 601 through 603)) selection = (chain 'B' and (resid 40 through 42 or (resid 43 through 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 290 or (resid 291 through 300 and (name N or name CA or nam \ e C or name O or name CB )) or resid 301 through 314 or (resid 315 and (name N o \ r name CA or name C or name O or name CB )) or resid 316 through 363 or (resid 3 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 365 through \ 452 or (resid 453 through 455 and (name N or name CA or name C or name O or nam \ e CB )) or resid 456 through 603)) selection = (chain 'C' and (resid 40 through 87 or (resid 88 through 89 and (name N or name \ CA or name C or name O or name CB )) or resid 90 through 146 or (resid 147 throu \ gh 148 and (name N or name CA or name C or name O or name CB )) or resid 149 thr \ ough 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) \ or resid 183 through 198 or (resid 199 and (name N or name CA or name C or name \ O or name CB )) or resid 200 through 234 or (resid 235 and (name N or name CA or \ name C or name O or name CB )) or resid 236 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 363 or (res \ id 364 and (name N or name CA or name C or name O or name CB )) or resid 365 thr \ ough 457 or (resid 458 through 459 and (name N or name CA or name C or name O or \ name CB )) or resid 460 through 603)) } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.299 10236 Z= 0.426 Angle : 1.090 34.509 13942 Z= 0.548 Chirality : 0.058 0.337 1557 Planarity : 0.005 0.047 1789 Dihedral : 15.513 84.427 3880 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.60 % Allowed : 8.97 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -5.35 (0.18), residues: 1272 helix: -4.61 (0.10), residues: 342 sheet: -3.63 (0.23), residues: 300 loop : -2.77 (0.21), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 371 TYR 0.016 0.001 TYR C 426 PHE 0.018 0.002 PHE B 263 TRP 0.004 0.001 TRP C 46 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00761 (10209) covalent geometry : angle 0.93645 (13882) SS BOND : bond 0.11288 ( 21) SS BOND : angle 9.99785 ( 42) hydrogen bonds : bond 0.30271 ( 294) hydrogen bonds : angle 10.91542 ( 810) link_NAG-ASN : bond 0.00236 ( 6) link_NAG-ASN : angle 3.27069 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.370 Fit side-chains REVERT: A 50 PHE cc_start: 0.8789 (t80) cc_final: 0.8562 (t80) REVERT: A 219 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 313 ASP cc_start: 0.8171 (t70) cc_final: 0.7847 (t0) REVERT: A 327 MET cc_start: 0.8442 (mtp) cc_final: 0.8143 (mtm) REVERT: A 330 MET cc_start: 0.9331 (mtt) cc_final: 0.8540 (mtt) REVERT: A 342 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7047 (t80) REVERT: A 351 ASP cc_start: 0.8245 (t0) cc_final: 0.7927 (t0) REVERT: B 291 LYS cc_start: 0.8194 (tppt) cc_final: 0.7774 (tttp) REVERT: B 313 ASP cc_start: 0.8265 (t70) cc_final: 0.8019 (t0) REVERT: B 330 MET cc_start: 0.9270 (mtt) cc_final: 0.8499 (mtt) REVERT: B 342 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8499 (t80) REVERT: C 63 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7203 (tm-30) REVERT: C 313 ASP cc_start: 0.8246 (t70) cc_final: 0.7826 (t0) REVERT: C 330 MET cc_start: 0.9240 (mtt) cc_final: 0.8684 (mtt) REVERT: C 342 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7070 (t80) outliers start: 6 outliers final: 0 residues processed: 188 average time/residue: 0.1147 time to fit residues: 28.8750 Evaluate side-chains 134 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain C residue 342 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 73 HIS A 276 GLN A 329 HIS A 438 GLN B 66 GLN B 73 HIS B 276 GLN B 438 GLN C 276 GLN C 329 HIS C 438 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114770 restraints weight = 13255.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.118335 restraints weight = 7456.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.120545 restraints weight = 5487.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121567 restraints weight = 4669.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122246 restraints weight = 4313.784| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10236 Z= 0.118 Angle : 0.575 7.420 13942 Z= 0.293 Chirality : 0.041 0.129 1557 Planarity : 0.004 0.035 1789 Dihedral : 6.746 57.749 1727 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.92 % Allowed : 14.82 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.20), residues: 1272 helix: -2.78 (0.20), residues: 369 sheet: -3.40 (0.25), residues: 279 loop : -2.03 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 201 TYR 0.019 0.001 TYR C 67 PHE 0.017 0.001 PHE B 50 TRP 0.005 0.001 TRP B 46 HIS 0.005 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00277 (10209) covalent geometry : angle 0.56578 (13882) SS BOND : bond 0.00144 ( 21) SS BOND : angle 1.35726 ( 42) hydrogen bonds : bond 0.03582 ( 294) hydrogen bonds : angle 5.95935 ( 810) link_NAG-ASN : bond 0.00065 ( 6) link_NAG-ASN : angle 2.19606 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.362 Fit side-chains REVERT: A 63 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7528 (tm-30) REVERT: A 313 ASP cc_start: 0.7543 (t70) cc_final: 0.7256 (t0) REVERT: A 330 MET cc_start: 0.9378 (mtt) cc_final: 0.8684 (mtt) REVERT: A 342 TYR cc_start: 0.9021 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 351 ASP cc_start: 0.7851 (t0) cc_final: 0.7556 (t0) REVERT: B 291 LYS cc_start: 0.8262 (tppt) cc_final: 0.7834 (tttp) REVERT: B 313 ASP cc_start: 0.7543 (t70) cc_final: 0.7114 (t0) REVERT: B 330 MET cc_start: 0.9347 (mtt) cc_final: 0.8612 (mtt) REVERT: B 342 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8603 (t80) REVERT: C 211 LYS cc_start: 0.8319 (mtmt) cc_final: 0.8022 (mtpp) REVERT: C 233 TRP cc_start: 0.8009 (p90) cc_final: 0.7720 (p90) REVERT: C 313 ASP cc_start: 0.7453 (t70) cc_final: 0.7102 (t0) REVERT: C 330 MET cc_start: 0.9301 (mtt) cc_final: 0.8759 (mtt) REVERT: C 342 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.7155 (t80) REVERT: C 351 ASP cc_start: 0.7939 (t0) cc_final: 0.7720 (t0) REVERT: C 421 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7583 (tt0) outliers start: 19 outliers final: 8 residues processed: 171 average time/residue: 0.0879 time to fit residues: 22.0578 Evaluate side-chains 136 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 423 LYS Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS C 66 GLN C 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117005 restraints weight = 13225.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120645 restraints weight = 7698.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121752 restraints weight = 5218.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122023 restraints weight = 4840.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122150 restraints weight = 4755.555| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10236 Z= 0.107 Angle : 0.532 7.063 13942 Z= 0.272 Chirality : 0.040 0.129 1557 Planarity : 0.003 0.032 1789 Dihedral : 6.119 58.803 1727 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.42 % Allowed : 17.44 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.22), residues: 1272 helix: -1.73 (0.24), residues: 375 sheet: -2.95 (0.27), residues: 282 loop : -1.62 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 160 TYR 0.017 0.001 TYR C 67 PHE 0.010 0.001 PHE C 301 TRP 0.007 0.001 TRP A 46 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00248 (10209) covalent geometry : angle 0.52192 (13882) SS BOND : bond 0.00170 ( 21) SS BOND : angle 1.50820 ( 42) hydrogen bonds : bond 0.02745 ( 294) hydrogen bonds : angle 5.41011 ( 810) link_NAG-ASN : bond 0.00082 ( 6) link_NAG-ASN : angle 2.00257 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9301 (mtt) cc_final: 0.8388 (mtt) REVERT: A 342 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.7243 (t80) REVERT: A 351 ASP cc_start: 0.8043 (t0) cc_final: 0.7802 (t0) REVERT: B 291 LYS cc_start: 0.8254 (tppt) cc_final: 0.8022 (ttmt) REVERT: B 327 MET cc_start: 0.8470 (mtp) cc_final: 0.8184 (mtp) REVERT: B 330 MET cc_start: 0.9365 (mtt) cc_final: 0.8552 (mtt) REVERT: B 342 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8631 (t80) REVERT: B 399 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 211 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8019 (mtpp) REVERT: C 313 ASP cc_start: 0.7407 (t70) cc_final: 0.7135 (t0) REVERT: C 342 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7099 (t80) REVERT: C 351 ASP cc_start: 0.8199 (t0) cc_final: 0.7921 (t0) REVERT: C 421 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7648 (tt0) outliers start: 24 outliers final: 7 residues processed: 160 average time/residue: 0.0772 time to fit residues: 18.9310 Evaluate side-chains 144 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112964 restraints weight = 13230.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116439 restraints weight = 7508.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118534 restraints weight = 5562.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119336 restraints weight = 4761.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120211 restraints weight = 4439.547| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10236 Z= 0.161 Angle : 0.565 8.627 13942 Z= 0.287 Chirality : 0.041 0.128 1557 Planarity : 0.003 0.036 1789 Dihedral : 6.043 59.183 1727 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.83 % Allowed : 18.15 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.23), residues: 1272 helix: -0.97 (0.27), residues: 375 sheet: -2.70 (0.27), residues: 300 loop : -1.62 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.011 0.001 TYR B 400 PHE 0.011 0.001 PHE C 442 TRP 0.006 0.001 TRP A 46 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00384 (10209) covalent geometry : angle 0.55385 (13882) SS BOND : bond 0.00364 ( 21) SS BOND : angle 1.59910 ( 42) hydrogen bonds : bond 0.02762 ( 294) hydrogen bonds : angle 5.23521 ( 810) link_NAG-ASN : bond 0.00028 ( 6) link_NAG-ASN : angle 2.14301 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.9379 (mtt) cc_final: 0.8479 (mtt) REVERT: A 342 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.7200 (t80) REVERT: A 351 ASP cc_start: 0.7974 (t0) cc_final: 0.7756 (t0) REVERT: B 179 CYS cc_start: 0.6346 (OUTLIER) cc_final: 0.5981 (m) REVERT: B 291 LYS cc_start: 0.8232 (tppt) cc_final: 0.8017 (ttmt) REVERT: B 327 MET cc_start: 0.8506 (mtp) cc_final: 0.8243 (mtp) REVERT: B 330 MET cc_start: 0.9366 (mtt) cc_final: 0.8569 (mtt) REVERT: B 342 TYR cc_start: 0.9062 (OUTLIER) cc_final: 0.8606 (t80) REVERT: B 345 CYS cc_start: 0.5408 (m) cc_final: 0.5107 (m) REVERT: B 351 ASP cc_start: 0.7804 (t0) cc_final: 0.7571 (t0) REVERT: B 399 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 211 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8053 (mtpp) REVERT: C 313 ASP cc_start: 0.7450 (t70) cc_final: 0.7168 (t0) REVERT: C 330 MET cc_start: 0.9437 (mtt) cc_final: 0.8723 (mtt) REVERT: C 342 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.6952 (t80) REVERT: C 351 ASP cc_start: 0.8075 (t0) cc_final: 0.7832 (t0) outliers start: 38 outliers final: 22 residues processed: 161 average time/residue: 0.0770 time to fit residues: 19.0245 Evaluate side-chains 154 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.2980 chunk 10 optimal weight: 0.0370 chunk 101 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.160369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116995 restraints weight = 13211.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119684 restraints weight = 7599.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121006 restraints weight = 6011.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122215 restraints weight = 4935.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.122296 restraints weight = 4927.605| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10236 Z= 0.094 Angle : 0.515 7.275 13942 Z= 0.258 Chirality : 0.039 0.128 1557 Planarity : 0.003 0.041 1789 Dihedral : 5.697 59.578 1727 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.33 % Allowed : 19.35 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.24), residues: 1272 helix: -0.75 (0.27), residues: 393 sheet: -2.75 (0.28), residues: 297 loop : -1.20 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.011 0.001 TYR C 417 PHE 0.011 0.001 PHE C 442 TRP 0.005 0.001 TRP A 46 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00222 (10209) covalent geometry : angle 0.50767 (13882) SS BOND : bond 0.00223 ( 21) SS BOND : angle 1.23460 ( 42) hydrogen bonds : bond 0.02234 ( 294) hydrogen bonds : angle 5.10550 ( 810) link_NAG-ASN : bond 0.00069 ( 6) link_NAG-ASN : angle 1.86954 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6223 (OUTLIER) cc_final: 0.5707 (m) REVERT: A 330 MET cc_start: 0.9407 (mtt) cc_final: 0.8458 (mtt) REVERT: A 342 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.7157 (t80) REVERT: A 351 ASP cc_start: 0.8179 (t0) cc_final: 0.7884 (t0) REVERT: B 291 LYS cc_start: 0.8265 (tppt) cc_final: 0.8037 (ttmt) REVERT: B 327 MET cc_start: 0.8439 (mtp) cc_final: 0.8081 (mtp) REVERT: B 330 MET cc_start: 0.9384 (mtt) cc_final: 0.8491 (mtt) REVERT: B 342 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8535 (t80) REVERT: B 351 ASP cc_start: 0.8054 (t0) cc_final: 0.7819 (t0) REVERT: B 399 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7709 (tm-30) REVERT: C 211 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8047 (mtpp) REVERT: C 313 ASP cc_start: 0.7420 (t70) cc_final: 0.7192 (t0) REVERT: C 330 MET cc_start: 0.9439 (mtt) cc_final: 0.8766 (mtt) REVERT: C 342 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.6899 (t80) REVERT: C 351 ASP cc_start: 0.8222 (t0) cc_final: 0.7960 (t0) REVERT: C 421 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7723 (tt0) outliers start: 33 outliers final: 22 residues processed: 172 average time/residue: 0.0728 time to fit residues: 19.7135 Evaluate side-chains 161 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115853 restraints weight = 13208.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119373 restraints weight = 7355.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121551 restraints weight = 5388.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.122580 restraints weight = 4587.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123016 restraints weight = 4235.705| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10236 Z= 0.112 Angle : 0.521 7.352 13942 Z= 0.263 Chirality : 0.041 0.204 1557 Planarity : 0.003 0.031 1789 Dihedral : 5.645 59.391 1727 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.43 % Allowed : 20.56 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.24), residues: 1272 helix: -0.77 (0.27), residues: 414 sheet: -2.72 (0.29), residues: 279 loop : -1.02 (0.28), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.011 0.001 TYR A 417 PHE 0.010 0.001 PHE C 442 TRP 0.005 0.001 TRP A 46 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00275 (10209) covalent geometry : angle 0.51041 (13882) SS BOND : bond 0.00217 ( 21) SS BOND : angle 1.51441 ( 42) hydrogen bonds : bond 0.02317 ( 294) hydrogen bonds : angle 5.04645 ( 810) link_NAG-ASN : bond 0.00061 ( 6) link_NAG-ASN : angle 1.90058 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6068 (OUTLIER) cc_final: 0.5617 (m) REVERT: A 330 MET cc_start: 0.9378 (mtt) cc_final: 0.8480 (mtt) REVERT: A 342 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 400 TYR cc_start: 0.8396 (t80) cc_final: 0.8092 (t80) REVERT: B 46 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.7407 (m100) REVERT: B 327 MET cc_start: 0.8444 (mtp) cc_final: 0.8156 (mtp) REVERT: B 330 MET cc_start: 0.9326 (mtt) cc_final: 0.8504 (mtt) REVERT: B 342 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8672 (t80) REVERT: B 399 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7686 (tm-30) REVERT: C 211 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8067 (mtpp) REVERT: C 313 ASP cc_start: 0.7257 (t70) cc_final: 0.7047 (t0) REVERT: C 330 MET cc_start: 0.9371 (mtt) cc_final: 0.8766 (mtt) REVERT: C 342 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.6889 (t80) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.0705 time to fit residues: 19.0619 Evaluate side-chains 163 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 0.3980 chunk 90 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120388 restraints weight = 13099.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.124385 restraints weight = 7335.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126678 restraints weight = 5399.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127716 restraints weight = 4627.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127983 restraints weight = 4300.294| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10236 Z= 0.170 Angle : 0.573 6.775 13942 Z= 0.289 Chirality : 0.043 0.270 1557 Planarity : 0.004 0.058 1789 Dihedral : 5.830 59.567 1727 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.03 % Allowed : 21.17 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.25), residues: 1272 helix: -0.27 (0.28), residues: 378 sheet: -2.53 (0.28), residues: 303 loop : -1.10 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.011 0.001 TYR C 417 PHE 0.010 0.001 PHE B 442 TRP 0.006 0.001 TRP C 233 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00412 (10209) covalent geometry : angle 0.56165 (13882) SS BOND : bond 0.00310 ( 21) SS BOND : angle 1.59702 ( 42) hydrogen bonds : bond 0.02711 ( 294) hydrogen bonds : angle 5.12335 ( 810) link_NAG-ASN : bond 0.00025 ( 6) link_NAG-ASN : angle 2.15501 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 131 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9366 (mtt) cc_final: 0.8515 (mtt) REVERT: A 342 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.7236 (t80) REVERT: A 345 CYS cc_start: 0.5200 (m) cc_final: 0.4885 (m) REVERT: A 399 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7715 (tm-30) REVERT: B 46 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.7383 (m100) REVERT: B 327 MET cc_start: 0.8564 (mtp) cc_final: 0.8235 (mtp) REVERT: B 330 MET cc_start: 0.9336 (mtt) cc_final: 0.8537 (mtt) REVERT: B 342 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8564 (t80) REVERT: B 399 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 211 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8109 (mtpp) REVERT: C 313 ASP cc_start: 0.7339 (t70) cc_final: 0.7125 (t0) REVERT: C 330 MET cc_start: 0.9366 (mtt) cc_final: 0.8733 (mtt) REVERT: C 342 TYR cc_start: 0.9000 (OUTLIER) cc_final: 0.6903 (t80) REVERT: C 345 CYS cc_start: 0.5221 (m) cc_final: 0.4763 (m) outliers start: 40 outliers final: 27 residues processed: 160 average time/residue: 0.0715 time to fit residues: 17.8767 Evaluate side-chains 162 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.167465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.125849 restraints weight = 13090.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127337 restraints weight = 10255.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.128457 restraints weight = 7891.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129338 restraints weight = 5714.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.129387 restraints weight = 5371.568| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10236 Z= 0.159 Angle : 0.566 7.849 13942 Z= 0.283 Chirality : 0.043 0.276 1557 Planarity : 0.003 0.047 1789 Dihedral : 5.776 59.847 1727 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.93 % Allowed : 21.57 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1272 helix: -0.18 (0.28), residues: 378 sheet: -2.55 (0.28), residues: 303 loop : -1.04 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 371 TYR 0.011 0.001 TYR B 417 PHE 0.010 0.001 PHE B 442 TRP 0.006 0.001 TRP C 233 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00383 (10209) covalent geometry : angle 0.55595 (13882) SS BOND : bond 0.00247 ( 21) SS BOND : angle 1.43680 ( 42) hydrogen bonds : bond 0.02617 ( 294) hydrogen bonds : angle 5.11256 ( 810) link_NAG-ASN : bond 0.00031 ( 6) link_NAG-ASN : angle 2.17673 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8250 (tppt) cc_final: 0.7966 (ttpt) REVERT: A 330 MET cc_start: 0.9335 (mtt) cc_final: 0.8467 (mtt) REVERT: A 342 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7195 (t80) REVERT: A 345 CYS cc_start: 0.5098 (m) cc_final: 0.4812 (m) REVERT: B 46 TRP cc_start: 0.8088 (OUTLIER) cc_final: 0.7377 (m100) REVERT: B 327 MET cc_start: 0.8552 (mtp) cc_final: 0.8203 (mtp) REVERT: B 330 MET cc_start: 0.9313 (mtt) cc_final: 0.8512 (mtt) REVERT: B 342 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8455 (t80) REVERT: B 399 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7809 (tm-30) REVERT: C 211 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8138 (mtpp) REVERT: C 313 ASP cc_start: 0.7387 (t70) cc_final: 0.7178 (t0) REVERT: C 330 MET cc_start: 0.9333 (mtt) cc_final: 0.8757 (mtt) REVERT: C 342 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.6859 (t80) REVERT: C 345 CYS cc_start: 0.5259 (m) cc_final: 0.4831 (m) outliers start: 39 outliers final: 30 residues processed: 164 average time/residue: 0.0694 time to fit residues: 17.9102 Evaluate side-chains 168 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.0980 chunk 92 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127214 restraints weight = 12983.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130039 restraints weight = 9303.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.131134 restraints weight = 6268.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131430 restraints weight = 4985.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131501 restraints weight = 4736.525| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10236 Z= 0.118 Angle : 0.537 7.324 13942 Z= 0.266 Chirality : 0.042 0.250 1557 Planarity : 0.003 0.041 1789 Dihedral : 5.631 59.967 1727 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.43 % Allowed : 22.58 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.25), residues: 1272 helix: -0.33 (0.27), residues: 399 sheet: -2.59 (0.29), residues: 288 loop : -0.94 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.011 0.001 TYR B 417 PHE 0.008 0.001 PHE C 442 TRP 0.005 0.001 TRP C 233 HIS 0.003 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00285 (10209) covalent geometry : angle 0.52838 (13882) SS BOND : bond 0.00190 ( 21) SS BOND : angle 1.24380 ( 42) hydrogen bonds : bond 0.02351 ( 294) hydrogen bonds : angle 5.02758 ( 810) link_NAG-ASN : bond 0.00048 ( 6) link_NAG-ASN : angle 2.02376 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8233 (tppt) cc_final: 0.7952 (ttpt) REVERT: A 330 MET cc_start: 0.9275 (mtt) cc_final: 0.8387 (mtt) REVERT: A 342 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.7196 (t80) REVERT: B 46 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7255 (m100) REVERT: B 327 MET cc_start: 0.8508 (mtp) cc_final: 0.8154 (mtp) REVERT: B 330 MET cc_start: 0.9311 (mtt) cc_final: 0.8479 (mtt) REVERT: B 342 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 399 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7762 (tm-30) REVERT: C 211 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8113 (mtpp) REVERT: C 313 ASP cc_start: 0.7369 (t70) cc_final: 0.7101 (t0) REVERT: C 330 MET cc_start: 0.9299 (mtt) cc_final: 0.8533 (mtt) REVERT: C 342 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.6853 (t80) outliers start: 34 outliers final: 28 residues processed: 158 average time/residue: 0.0685 time to fit residues: 17.0712 Evaluate side-chains 162 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126655 restraints weight = 13003.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.127203 restraints weight = 7389.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.128898 restraints weight = 6091.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129348 restraints weight = 5066.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129225 restraints weight = 5004.399| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10236 Z= 0.121 Angle : 0.550 9.407 13942 Z= 0.269 Chirality : 0.042 0.243 1557 Planarity : 0.003 0.038 1789 Dihedral : 5.585 59.975 1727 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.73 % Allowed : 22.98 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.25), residues: 1272 helix: -0.25 (0.27), residues: 399 sheet: -2.53 (0.29), residues: 288 loop : -0.87 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.011 0.001 TYR B 417 PHE 0.007 0.001 PHE B 442 TRP 0.006 0.001 TRP C 233 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00290 (10209) covalent geometry : angle 0.54178 (13882) SS BOND : bond 0.00210 ( 21) SS BOND : angle 1.30421 ( 42) hydrogen bonds : bond 0.02352 ( 294) hydrogen bonds : angle 4.96951 ( 810) link_NAG-ASN : bond 0.00045 ( 6) link_NAG-ASN : angle 1.99052 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8175 (tppt) cc_final: 0.7882 (ttpt) REVERT: A 330 MET cc_start: 0.9293 (mtt) cc_final: 0.8268 (mtt) REVERT: A 342 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.7203 (t80) REVERT: B 46 TRP cc_start: 0.8141 (OUTLIER) cc_final: 0.7244 (m100) REVERT: B 327 MET cc_start: 0.8511 (mtp) cc_final: 0.8097 (mtp) REVERT: B 330 MET cc_start: 0.9318 (mtt) cc_final: 0.8420 (mtt) REVERT: B 342 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8294 (t80) REVERT: B 399 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 211 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8091 (mtpp) REVERT: C 313 ASP cc_start: 0.7500 (t70) cc_final: 0.7211 (t0) REVERT: C 327 MET cc_start: 0.8012 (mtt) cc_final: 0.7730 (mtt) REVERT: C 330 MET cc_start: 0.9331 (mtt) cc_final: 0.8496 (mtt) REVERT: C 342 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.6824 (t80) outliers start: 37 outliers final: 30 residues processed: 161 average time/residue: 0.0659 time to fit residues: 16.6472 Evaluate side-chains 169 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 179 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 325 CYS Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 46 TRP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 441 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 109 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 ASN C 110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126683 restraints weight = 13031.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127225 restraints weight = 11006.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128775 restraints weight = 8260.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.129356 restraints weight = 6281.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129340 restraints weight = 6112.731| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10236 Z= 0.096 Angle : 0.529 7.573 13942 Z= 0.259 Chirality : 0.041 0.226 1557 Planarity : 0.003 0.034 1789 Dihedral : 5.470 59.587 1727 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.43 % Allowed : 23.29 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.25), residues: 1272 helix: -0.32 (0.26), residues: 429 sheet: -2.57 (0.30), residues: 273 loop : -0.74 (0.29), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 160 TYR 0.010 0.001 TYR A 417 PHE 0.007 0.001 PHE C 98 TRP 0.006 0.001 TRP C 233 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00231 (10209) covalent geometry : angle 0.52207 (13882) SS BOND : bond 0.00172 ( 21) SS BOND : angle 1.20036 ( 42) hydrogen bonds : bond 0.02147 ( 294) hydrogen bonds : angle 4.91488 ( 810) link_NAG-ASN : bond 0.00088 ( 6) link_NAG-ASN : angle 1.86902 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1510.18 seconds wall clock time: 26 minutes 43.51 seconds (1603.51 seconds total)