Starting phenix.real_space_refine on Fri Sep 11 15:42:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cfs_30346/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cfs_30346/09_2026/7cfs_30346.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 chiralities: 2 Time building chain proxies: 2.27, per 1000 atoms: 0.23 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: 0.63 Conformation dependent library (CDL) restraints added in 250.6 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: 0.18 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: 1.38 Time building geometry restraints manager: 0.85 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: 5216 16.89 - 33.78: 632 33.78 - 50.68: 135 50.68 - 67.57: 39 67.57 - 84.46: 21 Dihedral angle restraints: 6043 sinusoidal: 2307 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 6040 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: 0.510 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.020 Find NCS groups from input model: 0.240 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 15.945 84.427 3580 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/Z covalent geometry : bond 0.00761 / 0.34 (10209) covalent geometry : angle 0.93645 / 0.48 (13882) SS BOND : bond 0.11288 / 7.34 ( 21) SS BOND : angle 9.99785 / 7.67 ( 42) hydrogen bonds : bond 0.30271 / 20.08 ( 294) hydrogen bonds : angle 10.91542 / 7.45 ( 810) link_NAG-ASN : bond 0.00236 / 0.13 ( 6) link_NAG-ASN : angle 3.27069 / 1.81 ( 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 : 0.382 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: 0.1068 time to fit residues: 27.1302 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 : 0.230 ------------------------------------------------------------------------------- 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... 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 = 0.3844 r_free = 0.3844 target = 0.159611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115063 restraints weight = 13256.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118601 restraints weight = 7455.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120801 restraints weight = 5490.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121836 restraints weight = 4682.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122694 restraints weight = 4322.238| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2013 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= 0.115 Angle : 0.569 7.393 13942 Z= 0.291 Chirality : 0.041 0.127 1557 Planarity : 0.004 0.035 1789 Dihedral : 7.172 59.029 1427 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.92 % Allowed : 15.02 % Favored : 83.06 % 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: -3.92 (0.20), residues: 1272 helix: -2.76 (0.20), residues: 372 sheet: -3.36 (0.25), residues: 276 loop : -1.98 (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 0.014 0.001 PHE B 50 TRP 0.005 0.001 TRP B 46 HIS 0.006 0.001 HIS B 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10209) covalent geometry : angle 0.56158 / 0.29 (13882) SS BOND : bond 0.00146 / 0.09 ( 21) SS BOND : angle 1.32614 / 0.84 ( 42) hydrogen bonds : bond 0.03285 / 2.18 ( 294) hydrogen bonds : angle 5.87948 / 4.07 ( 810) link_NAG-ASN : bond 0.00050 / 0.03 ( 6) link_NAG-ASN : angle 1.95149 / 1.08 ( 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 177 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.353 Fit side-chains REVERT: A 63 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7557 (tm-30) REVERT: A 313 ASP cc_start: 0.7494 (t70) cc_final: 0.7218 (t0) REVERT: A 330 MET cc_start: 0.9373 (mtt) cc_final: 0.8678 (mtt) REVERT: A 342 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7141 (t80) REVERT: A 351 ASP cc_start: 0.7838 (t0) cc_final: 0.7568 (t0) REVERT: A 421 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 291 LYS cc_start: 0.8268 (tppt) cc_final: 0.7842 (tttp) REVERT: B 313 ASP cc_start: 0.7538 (t70) cc_final: 0.7102 (t0) REVERT: B 330 MET cc_start: 0.9346 (mtt) cc_final: 0.8610 (mtt) REVERT: B 342 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8602 (t80) REVERT: C 211 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8022 (mtpp) REVERT: C 233 TRP cc_start: 0.8019 (p90) cc_final: 0.7698 (p90) REVERT: C 313 ASP cc_start: 0.7448 (t70) cc_final: 0.7121 (t0) REVERT: C 330 MET cc_start: 0.9298 (mtt) cc_final: 0.8755 (mtt) REVERT: C 342 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.7163 (t80) REVERT: C 351 ASP cc_start: 0.7898 (t0) cc_final: 0.7680 (t0) REVERT: C 421 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7602 (tt0) outliers start: 19 outliers final: 9 residues processed: 175 average time/residue: 0.0855 time to fit residues: 22.1206 Evaluate side-chains 143 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 423 LYS 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: 0.9980 chunk 112 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN 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 = 0.3836 r_free = 0.3836 target = 0.159023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.115585 restraints weight = 13252.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118317 restraints weight = 7742.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119658 restraints weight = 5936.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120453 restraints weight = 5011.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120625 restraints weight = 4888.221| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2388 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= 0.124 Angle : 0.548 7.409 13942 Z= 0.279 Chirality : 0.040 0.127 1557 Planarity : 0.003 0.032 1789 Dihedral : 6.794 59.353 1427 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.52 % Allowed : 17.14 % Favored : 80.34 % 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: -3.12 (0.22), residues: 1272 helix: -1.77 (0.24), residues: 375 sheet: -2.99 (0.26), residues: 282 loop : -1.65 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 160 TYR 0.016 0.001 TYR C 67 PHE 0.009 0.001 PHE C 301 TRP 0.006 0.001 TRP B 46 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (10209) covalent geometry : angle 0.53751 / 0.28 (13882) SS BOND : bond 0.00285 / 0.18 ( 21) SS BOND : angle 1.53314 / 0.99 ( 42) hydrogen bonds : bond 0.02884 / 1.89 ( 294) hydrogen bonds : angle 5.44601 / 3.80 ( 810) link_NAG-ASN : bond 0.00075 / 0.04 ( 6) link_NAG-ASN : angle 1.97099 / 1.10 ( 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 163 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7600 (t70) cc_final: 0.7305 (t0) REVERT: A 342 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.7220 (t80) REVERT: A 351 ASP cc_start: 0.8089 (t0) cc_final: 0.7844 (t0) REVERT: B 291 LYS cc_start: 0.8231 (tppt) cc_final: 0.7991 (ttmt) REVERT: B 327 MET cc_start: 0.8495 (mtp) cc_final: 0.8203 (mtp) REVERT: B 330 MET cc_start: 0.9382 (mtt) cc_final: 0.8587 (mtt) REVERT: B 342 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8640 (t80) REVERT: B 399 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 211 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8036 (mtpp) REVERT: C 313 ASP cc_start: 0.7508 (t70) cc_final: 0.7202 (t0) REVERT: C 342 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.7065 (t80) REVERT: C 351 ASP cc_start: 0.8228 (t0) cc_final: 0.7942 (t0) REVERT: C 421 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7651 (tt0) outliers start: 25 outliers final: 10 residues processed: 153 average time/residue: 0.0695 time to fit residues: 16.6054 Evaluate side-chains 144 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 45 LEU Chi-restraints excluded: chain B residue 61 CYS 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 423 LYS Chi-restraints excluded: chain C residue 342 TYR Chi-restraints excluded: chain C residue 423 LYS 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: 10.0000 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 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 = 0.3838 r_free = 0.3838 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115617 restraints weight = 13148.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118901 restraints weight = 7964.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121066 restraints weight = 5406.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121285 restraints weight = 4711.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121305 restraints weight = 4599.085| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10236 Z= 0.119 Angle : 0.531 7.577 13942 Z= 0.269 Chirality : 0.040 0.130 1557 Planarity : 0.003 0.029 1789 Dihedral : 6.476 59.712 1427 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.23 % Allowed : 18.55 % Favored : 78.23 % 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: -2.54 (0.24), residues: 1272 helix: -1.04 (0.27), residues: 375 sheet: -2.81 (0.28), residues: 282 loop : -1.39 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.011 0.001 TYR B 417 PHE 0.011 0.001 PHE C 442 TRP 0.006 0.001 TRP A 46 HIS 0.002 0.000 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10209) covalent geometry : angle 0.52196 / 0.27 (13882) SS BOND : bond 0.00275 / 0.18 ( 21) SS BOND : angle 1.47284 / 0.89 ( 42) hydrogen bonds : bond 0.02498 / 1.64 ( 294) hydrogen bonds : angle 5.18556 / 3.63 ( 810) link_NAG-ASN : bond 0.00071 / 0.04 ( 6) link_NAG-ASN : angle 1.89976 / 1.06 ( 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 178 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6222 (OUTLIER) cc_final: 0.5744 (m) REVERT: A 330 MET cc_start: 0.9349 (mtt) cc_final: 0.8434 (mtt) REVERT: A 342 TYR cc_start: 0.8950 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 351 ASP cc_start: 0.8076 (t0) cc_final: 0.7820 (t0) REVERT: B 179 CYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5984 (m) REVERT: B 291 LYS cc_start: 0.8251 (tppt) cc_final: 0.8022 (ttmt) REVERT: B 327 MET cc_start: 0.8491 (mtp) cc_final: 0.8198 (mtp) REVERT: B 330 MET cc_start: 0.9382 (mtt) cc_final: 0.8568 (mtt) REVERT: B 342 TYR cc_start: 0.9078 (OUTLIER) cc_final: 0.8617 (t80) REVERT: B 345 CYS cc_start: 0.5227 (m) cc_final: 0.4926 (m) REVERT: B 351 ASP cc_start: 0.7973 (t0) cc_final: 0.7717 (t0) REVERT: B 399 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7692 (tm-30) REVERT: C 211 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8050 (mtpp) REVERT: C 313 ASP cc_start: 0.7427 (t70) cc_final: 0.7148 (t0) REVERT: C 330 MET cc_start: 0.9447 (mtt) cc_final: 0.8746 (mtt) REVERT: C 342 TYR cc_start: 0.9010 (OUTLIER) cc_final: 0.6974 (t80) REVERT: C 351 ASP cc_start: 0.8185 (t0) cc_final: 0.7905 (t0) REVERT: C 421 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7639 (tt0) outliers start: 32 outliers final: 19 residues processed: 165 average time/residue: 0.0795 time to fit residues: 20.2758 Evaluate side-chains 156 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 342 TYR Chi-restraints excluded: chain A residue 361 CYS 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 451 LEU Chi-restraints excluded: chain B residue 453 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 423 LYS Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 GLN B 72 HIS B 438 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.155998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111935 restraints weight = 13307.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115449 restraints weight = 7522.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117532 restraints weight = 5555.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118708 restraints weight = 4742.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119133 restraints weight = 4374.475| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10236 Z= 0.199 Angle : 0.597 8.824 13942 Z= 0.302 Chirality : 0.042 0.129 1557 Planarity : 0.003 0.044 1789 Dihedral : 6.489 59.792 1427 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.23 % Allowed : 18.95 % Favored : 76.81 % 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: -2.39 (0.24), residues: 1272 helix: -0.66 (0.28), residues: 372 sheet: -2.68 (0.28), residues: 300 loop : -1.45 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.012 0.001 TYR C 417 PHE 0.014 0.001 PHE C 442 TRP 0.005 0.001 TRP B 46 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (10209) covalent geometry : angle 0.58464 / 0.30 (13882) SS BOND : bond 0.00323 / 0.21 ( 21) SS BOND : angle 1.80227 / 1.08 ( 42) hydrogen bonds : bond 0.02918 / 1.90 ( 294) hydrogen bonds : angle 5.26982 / 3.71 ( 810) link_NAG-ASN : bond 0.00049 / 0.03 ( 6) link_NAG-ASN : angle 2.30464 / 1.27 ( 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 179 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 330 MET cc_start: 0.9419 (mtt) cc_final: 0.8496 (mtt) REVERT: A 342 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.7159 (t80) REVERT: B 179 CYS cc_start: 0.6455 (OUTLIER) cc_final: 0.6192 (m) REVERT: B 291 LYS cc_start: 0.8279 (tppt) cc_final: 0.8065 (ttmt) REVERT: B 327 MET cc_start: 0.8550 (mtp) cc_final: 0.8238 (mtp) REVERT: B 330 MET cc_start: 0.9364 (mtt) cc_final: 0.8595 (mtt) REVERT: B 342 TYR cc_start: 0.9038 (OUTLIER) cc_final: 0.8534 (t80) REVERT: B 399 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 211 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8072 (mtpp) REVERT: C 313 ASP cc_start: 0.7465 (t70) cc_final: 0.7184 (t0) REVERT: C 330 MET cc_start: 0.9412 (mtt) cc_final: 0.8763 (mtt) REVERT: C 342 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.6813 (t80) REVERT: C 351 ASP cc_start: 0.8043 (t0) cc_final: 0.7831 (t0) outliers start: 42 outliers final: 27 residues processed: 164 average time/residue: 0.0708 time to fit residues: 18.3767 Evaluate side-chains 158 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 313 ASP 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 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 179 CYS 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 377 SER 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 378 MET Chi-restraints excluded: chain C residue 423 LYS 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: 3.9990 chunk 115 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 31 optimal weight: 0.0870 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 HIS C 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.162648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118105 restraints weight = 13341.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121066 restraints weight = 8132.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122347 restraints weight = 6167.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123341 restraints weight = 5112.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123499 restraints weight = 4982.359| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3098 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= 0.089 Angle : 0.523 9.146 13942 Z= 0.259 Chirality : 0.040 0.130 1557 Planarity : 0.003 0.041 1789 Dihedral : 6.100 59.928 1427 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.43 % Allowed : 19.76 % Favored : 76.81 % 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: -2.20 (0.24), residues: 1272 helix: -0.80 (0.27), residues: 411 sheet: -2.82 (0.28), residues: 279 loop : -1.03 (0.28), residues: 582 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 0.008 0.001 PHE B 442 TRP 0.006 0.001 TRP A 46 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (10209) covalent geometry : angle 0.51592 / 0.26 (13882) SS BOND : bond 0.00174 / 0.11 ( 21) SS BOND : angle 1.20727 / 0.74 ( 42) hydrogen bonds : bond 0.02186 / 1.48 ( 294) hydrogen bonds : angle 5.03105 / 3.56 ( 810) link_NAG-ASN : bond 0.00118 / 0.07 ( 6) link_NAG-ASN : angle 1.76351 / 0.99 ( 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 179 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 179 CYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5691 (m) REVERT: A 330 MET cc_start: 0.9446 (mtt) cc_final: 0.8455 (mtt) REVERT: A 342 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.7261 (t80) REVERT: B 46 TRP cc_start: 0.8095 (OUTLIER) cc_final: 0.7353 (m100) REVERT: B 291 LYS cc_start: 0.8297 (tppt) cc_final: 0.8043 (ttmt) REVERT: B 327 MET cc_start: 0.8443 (mtp) cc_final: 0.8051 (mtp) REVERT: B 330 MET cc_start: 0.9406 (mtt) cc_final: 0.8489 (mtt) REVERT: B 342 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8595 (t80) REVERT: B 399 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7725 (tm-30) REVERT: C 58 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8158 (mm) REVERT: C 211 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8070 (mtpp) REVERT: C 313 ASP cc_start: 0.7434 (t70) cc_final: 0.7195 (t0) REVERT: C 330 MET cc_start: 0.9435 (mtt) cc_final: 0.8743 (mtt) REVERT: C 342 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.6717 (t80) REVERT: C 351 ASP cc_start: 0.8236 (t0) cc_final: 0.7992 (t0) REVERT: C 421 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7604 (tt0) REVERT: C 423 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (mtpp) outliers start: 34 outliers final: 19 residues processed: 171 average time/residue: 0.0700 time to fit residues: 18.9921 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 : 0.386 ------------------------------------------------------------------------------- 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 313 ASP 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 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 C residue 58 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 4 optimal weight: 0.0670 chunk 110 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128698 restraints weight = 13074.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.129773 restraints weight = 9274.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.131112 restraints weight = 7174.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131549 restraints weight = 5356.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131536 restraints weight = 5182.230| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10236 Z= 0.118 Angle : 0.531 8.413 13942 Z= 0.265 Chirality : 0.041 0.212 1557 Planarity : 0.003 0.038 1789 Dihedral : 6.034 59.267 1427 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.63 % Allowed : 21.57 % 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: -2.05 (0.25), residues: 1272 helix: -0.68 (0.26), residues: 417 sheet: -2.54 (0.30), residues: 264 loop : -1.13 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.012 0.001 TYR B 417 PHE 0.009 0.001 PHE B 442 TRP 0.005 0.001 TRP B 46 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10209) covalent geometry : angle 0.52135 / 0.26 (13882) SS BOND : bond 0.00248 / 0.14 ( 21) SS BOND : angle 1.46287 / 0.91 ( 42) hydrogen bonds : bond 0.02332 / 1.54 ( 294) hydrogen bonds : angle 4.99868 / 3.53 ( 810) link_NAG-ASN : bond 0.00073 / 0.04 ( 6) link_NAG-ASN : angle 1.93468 / 1.08 ( 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 177 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9381 (mtt) cc_final: 0.8486 (mtt) REVERT: A 342 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.7265 (t80) REVERT: B 46 TRP cc_start: 0.8142 (OUTLIER) cc_final: 0.7434 (m100) REVERT: B 58 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7311 (pp) REVERT: B 291 LYS cc_start: 0.8351 (tppt) cc_final: 0.8147 (ttmt) REVERT: B 327 MET cc_start: 0.8472 (mtp) cc_final: 0.8155 (mtp) REVERT: B 330 MET cc_start: 0.9310 (mtt) cc_final: 0.8480 (mtt) REVERT: B 342 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8606 (t80) REVERT: B 399 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 63 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 211 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8089 (mtpp) REVERT: C 330 MET cc_start: 0.9345 (mtt) cc_final: 0.8754 (mtt) REVERT: C 342 TYR cc_start: 0.8874 (OUTLIER) cc_final: 0.6724 (t80) REVERT: C 421 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7749 (tt0) outliers start: 36 outliers final: 26 residues processed: 167 average time/residue: 0.0713 time to fit residues: 19.1141 Evaluate side-chains 166 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 138 LEU 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 313 ASP 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 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 58 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 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 51 LEU Chi-restraints excluded: chain C residue 75 THR 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 377 SER Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.128531 restraints weight = 13082.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.131290 restraints weight = 9401.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132781 restraints weight = 6280.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132808 restraints weight = 5005.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.132861 restraints weight = 4906.945| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10236 Z= 0.109 Angle : 0.535 8.868 13942 Z= 0.263 Chirality : 0.041 0.264 1557 Planarity : 0.003 0.060 1789 Dihedral : 5.970 59.582 1427 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.73 % Allowed : 22.38 % Favored : 73.89 % 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: -1.99 (0.25), residues: 1272 helix: -0.61 (0.26), residues: 417 sheet: -2.65 (0.29), residues: 279 loop : -0.95 (0.29), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.011 0.001 TYR C 417 PHE 0.008 0.001 PHE C 442 TRP 0.005 0.001 TRP C 233 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (10209) covalent geometry : angle 0.52621 / 0.26 (13882) SS BOND : bond 0.00180 / 0.11 ( 21) SS BOND : angle 1.45348 / 0.88 ( 42) hydrogen bonds : bond 0.02281 / 1.52 ( 294) hydrogen bonds : angle 4.96921 / 3.51 ( 810) link_NAG-ASN : bond 0.00071 / 0.04 ( 6) link_NAG-ASN : angle 1.88304 / 1.05 ( 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 180 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9312 (mtt) cc_final: 0.8390 (mtt) REVERT: A 342 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.7225 (t80) REVERT: B 46 TRP cc_start: 0.8197 (OUTLIER) cc_final: 0.7398 (m100) REVERT: B 327 MET cc_start: 0.8462 (mtp) cc_final: 0.8147 (mtp) REVERT: B 330 MET cc_start: 0.9267 (mtt) cc_final: 0.8429 (mtt) REVERT: B 342 TYR cc_start: 0.9031 (OUTLIER) cc_final: 0.8583 (t80) REVERT: B 399 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7652 (tm-30) REVERT: C 63 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7424 (tm-30) REVERT: C 211 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8090 (mtpp) REVERT: C 330 MET cc_start: 0.9303 (mtt) cc_final: 0.8705 (mtt) REVERT: C 342 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.6783 (t80) REVERT: C 421 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7752 (tt0) outliers start: 37 outliers final: 28 residues processed: 168 average time/residue: 0.0728 time to fit residues: 19.1842 Evaluate side-chains 171 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 138 LEU 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 313 ASP Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 342 TYR 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 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 51 LEU Chi-restraints excluded: chain C residue 75 THR 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 423 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 0.4980 chunk 92 optimal weight: 20.0000 chunk 121 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.169300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127163 restraints weight = 12976.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129927 restraints weight = 9881.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131377 restraints weight = 6459.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.131444 restraints weight = 5181.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.131826 restraints weight = 4879.397| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10236 Z= 0.137 Angle : 0.547 8.560 13942 Z= 0.271 Chirality : 0.042 0.293 1557 Planarity : 0.004 0.068 1789 Dihedral : 6.031 59.670 1427 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.63 % Allowed : 23.08 % 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: -1.91 (0.25), residues: 1272 helix: -0.49 (0.26), residues: 417 sheet: -2.66 (0.29), residues: 279 loop : -0.93 (0.29), residues: 576 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 0.009 0.001 PHE B 442 TRP 0.005 0.001 TRP C 233 HIS 0.004 0.001 HIS C 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10209) covalent geometry : angle 0.53791 / 0.27 (13882) SS BOND : bond 0.00244 / 0.16 ( 21) SS BOND : angle 1.41005 / 0.87 ( 42) hydrogen bonds : bond 0.02490 / 1.63 ( 294) hydrogen bonds : angle 5.03634 / 3.56 ( 810) link_NAG-ASN : bond 0.00041 / 0.02 ( 6) link_NAG-ASN : angle 2.00455 / 1.11 ( 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 169 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9330 (mtt) cc_final: 0.8400 (mtt) REVERT: A 342 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.7247 (t80) REVERT: B 46 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7317 (m100) REVERT: B 327 MET cc_start: 0.8489 (mtp) cc_final: 0.8157 (mtp) REVERT: B 330 MET cc_start: 0.9281 (mtt) cc_final: 0.8452 (mtt) REVERT: B 342 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8570 (t80) REVERT: B 345 CYS cc_start: 0.4774 (m) cc_final: 0.4393 (m) REVERT: B 399 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 63 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 211 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8096 (mtpp) REVERT: C 342 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.6652 (t80) outliers start: 36 outliers final: 31 residues processed: 159 average time/residue: 0.0746 time to fit residues: 18.6498 Evaluate side-chains 166 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 138 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 313 ASP 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 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 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 C residue 46 TRP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 75 THR 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 378 MET Chi-restraints excluded: chain C residue 423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 109 optimal weight: 0.0570 chunk 123 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125786 restraints weight = 12893.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125838 restraints weight = 11099.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127338 restraints weight = 8542.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127999 restraints weight = 6629.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.130507 restraints weight = 6211.694| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10236 Z= 0.119 Angle : 0.542 9.547 13942 Z= 0.266 Chirality : 0.042 0.291 1557 Planarity : 0.004 0.064 1789 Dihedral : 5.985 59.987 1427 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.53 % Allowed : 23.59 % Favored : 72.88 % 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: -1.79 (0.25), residues: 1272 helix: -0.41 (0.26), residues: 417 sheet: -2.59 (0.30), residues: 279 loop : -0.84 (0.29), residues: 576 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 0.011 0.001 PHE B 442 TRP 0.006 0.001 TRP C 233 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (10209) covalent geometry : angle 0.53410 / 0.26 (13882) SS BOND : bond 0.00199 / 0.13 ( 21) SS BOND : angle 1.26621 / 0.79 ( 42) hydrogen bonds : bond 0.02335 / 1.54 ( 294) hydrogen bonds : angle 4.98112 / 3.53 ( 810) link_NAG-ASN : bond 0.00063 / 0.04 ( 6) link_NAG-ASN : angle 1.95190 / 1.08 ( 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 172 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 MET cc_start: 0.9293 (mtt) cc_final: 0.8354 (mtt) REVERT: A 342 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.7185 (t80) REVERT: B 46 TRP cc_start: 0.8127 (OUTLIER) cc_final: 0.7180 (m100) REVERT: B 238 GLU cc_start: 0.7645 (pp20) cc_final: 0.7073 (tm-30) REVERT: B 327 MET cc_start: 0.8478 (mtp) cc_final: 0.8145 (mtp) REVERT: B 330 MET cc_start: 0.9222 (mtt) cc_final: 0.8368 (mtt) REVERT: B 342 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8491 (t80) REVERT: B 345 CYS cc_start: 0.4638 (m) cc_final: 0.4293 (m) REVERT: B 399 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7698 (tm-30) REVERT: C 63 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7521 (tm-30) REVERT: C 211 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8087 (mtpp) REVERT: C 330 MET cc_start: 0.9307 (mtt) cc_final: 0.8898 (mtt) REVERT: C 342 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 421 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7759 (tt0) outliers start: 35 outliers final: 30 residues processed: 162 average time/residue: 0.0685 time to fit residues: 17.9085 Evaluate side-chains 165 residues out of total 1119 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 138 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 313 ASP 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 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 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 51 LEU Chi-restraints excluded: chain C residue 75 THR 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 423 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.5980 chunk 109 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 77 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.132702 restraints weight = 13093.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135794 restraints weight = 9111.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136907 restraints weight = 6300.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137016 restraints weight = 4897.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.137096 restraints weight = 4595.802| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10236 Z= 0.084 Angle : 0.507 8.668 13942 Z= 0.248 Chirality : 0.041 0.260 1557 Planarity : 0.003 0.055 1789 Dihedral : 5.753 59.884 1427 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.33 % Allowed : 23.89 % Favored : 72.78 % 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: -1.57 (0.25), residues: 1272 helix: -0.18 (0.26), residues: 429 sheet: -2.50 (0.30), residues: 285 loop : -0.70 (0.30), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 160 TYR 0.010 0.001 TYR A 417 PHE 0.008 0.001 PHE C 98 TRP 0.004 0.000 TRP C 233 HIS 0.001 0.000 HIS B 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.08 (10209) covalent geometry : angle 0.50156 / 0.25 (13882) SS BOND : bond 0.00166 / 0.11 ( 21) SS BOND : angle 1.04492 / 0.65 ( 42) hydrogen bonds : bond 0.02009 / 1.35 ( 294) hydrogen bonds : angle 4.84859 / 3.43 ( 810) link_NAG-ASN : bond 0.00148 / 0.09 ( 6) link_NAG-ASN : angle 1.65991 / 0.94 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1515.12 seconds wall clock time: 26 minutes 51.82 seconds (1611.82 seconds total)