Starting phenix.real_space_refine on Tue Aug 26 17:12:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.map" model { file = "/net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xll_38452/08_2025/8xll_38452.cif" } resolution = 3.1 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= 0.001 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 238 5.16 5 C 25052 2.51 5 N 6842 2.21 5 O 7346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39478 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 202} Chain: "C" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1671 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 205} Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1639 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1631 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "G" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 206} Chain: "H" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1631 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "I" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1662 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain: "J" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1618 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 198} Chain: "K" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1639 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1624 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 199} Chain: "M" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1671 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 205} Chain: "O" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1618 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 198} Chain: "P" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1679 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 206} Chain: "R" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 202} Chain: "S" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1648 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 202} Chain: "T" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1631 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 200} Chain: "U" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1639 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 201} Chain: "V" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Chain: "W" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1624 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 199} Chain: "X" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1624 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 199} Chain: "Y" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1647 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 10.11, per 1000 atoms: 0.26 Number of scatterers: 39478 At special positions: 0 Unit cell: (174.573, 172.431, 167.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 238 16.00 O 7346 8.00 N 6842 7.00 C 25052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9490 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 77 sheets defined 43.0% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 267 through 275 removed outlier: 3.531A pdb=" N PHE A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.041A pdb=" N ASN A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 358 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.816A pdb=" N MET A 365 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP A 366 " --> pdb=" O GLU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 429 through 446 Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.953A pdb=" N LEU A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 5.744A pdb=" N ASP B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'B' and resid 362 through 366 removed outlier: 4.045A pdb=" N ASP B 366 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 446 Processing helix chain 'B' and resid 447 through 453 removed outlier: 4.218A pdb=" N LEU B 451 " --> pdb=" O PRO B 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 257 through 276 removed outlier: 5.821A pdb=" N ASP C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 4.181A pdb=" N ALA C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 4.073A pdb=" N ASN C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 Processing helix chain 'C' and resid 341 through 357 removed outlier: 3.591A pdb=" N GLU C 345 " --> pdb=" O TYR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 429 through 446 removed outlier: 3.538A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 453 removed outlier: 4.224A pdb=" N LEU C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 276 removed outlier: 3.554A pdb=" N LYS D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.896A pdb=" N PHE D 285 " --> pdb=" O PHE D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 4.082A pdb=" N ASN D 300 " --> pdb=" O GLN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.613A pdb=" N THR D 338 " --> pdb=" O ASN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.507A pdb=" N ASP D 364 " --> pdb=" O ALA D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 378 No H-bonds generated for 'chain 'D' and resid 376 through 378' Processing helix chain 'D' and resid 429 through 446 removed outlier: 3.531A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 453 removed outlier: 3.946A pdb=" N LEU D 451 " --> pdb=" O PRO D 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 276 removed outlier: 6.342A pdb=" N ASP E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.681A pdb=" N PHE E 285 " --> pdb=" O PHE E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 336 through 339 Processing helix chain 'E' and resid 340 through 357 Processing helix chain 'E' and resid 429 through 446 Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 268 through 276 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 305 through 308 Processing helix chain 'F' and resid 336 through 339 Processing helix chain 'F' and resid 340 through 357 removed outlier: 3.575A pdb=" N LYS F 357 " --> pdb=" O GLU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 446 removed outlier: 3.581A pdb=" N ALA F 433 " --> pdb=" O ASP F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'G' and resid 240 through 244 removed outlier: 4.188A pdb=" N ASN G 244 " --> pdb=" O LYS G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 244' Processing helix chain 'G' and resid 258 through 276 removed outlier: 5.485A pdb=" N ASP G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 296 through 301 removed outlier: 4.005A pdb=" N ASN G 300 " --> pdb=" O GLN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 357 Processing helix chain 'G' and resid 375 through 379 removed outlier: 3.650A pdb=" N PHE G 378 " --> pdb=" O GLY G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 446 Processing helix chain 'G' and resid 447 through 453 removed outlier: 4.138A pdb=" N LEU G 451 " --> pdb=" O PRO G 447 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 267 Processing helix chain 'H' and resid 267 through 275 Processing helix chain 'H' and resid 281 through 296 removed outlier: 3.508A pdb=" N PHE H 285 " --> pdb=" O PHE H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 357 Processing helix chain 'H' and resid 361 through 365 removed outlier: 3.605A pdb=" N MET H 365 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 446 Processing helix chain 'H' and resid 447 through 452 removed outlier: 4.161A pdb=" N LEU H 451 " --> pdb=" O PRO H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 257 through 276 removed outlier: 5.927A pdb=" N ASP I 269 " --> pdb=" O ALA I 265 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N ALA I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 336 through 339 Processing helix chain 'I' and resid 340 through 357 Processing helix chain 'I' and resid 362 through 366 removed outlier: 3.904A pdb=" N MET I 365 " --> pdb=" O ILE I 362 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP I 366 " --> pdb=" O GLU I 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 362 through 366' Processing helix chain 'I' and resid 376 through 379 Processing helix chain 'I' and resid 429 through 446 Processing helix chain 'I' and resid 447 through 453 removed outlier: 3.878A pdb=" N LEU I 451 " --> pdb=" O PRO I 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 267 removed outlier: 3.898A pdb=" N GLN J 261 " --> pdb=" O MET J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 276 Processing helix chain 'J' and resid 281 through 296 removed outlier: 3.647A pdb=" N PHE J 285 " --> pdb=" O PHE J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 339 removed outlier: 3.582A pdb=" N THR J 338 " --> pdb=" O ASN J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 357 removed outlier: 3.684A pdb=" N LYS J 357 " --> pdb=" O GLU J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 361 through 365 Processing helix chain 'J' and resid 429 through 446 Processing helix chain 'J' and resid 447 through 453 removed outlier: 3.819A pdb=" N LEU J 451 " --> pdb=" O PRO J 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 267 Processing helix chain 'K' and resid 268 through 276 removed outlier: 3.592A pdb=" N LEU K 272 " --> pdb=" O LYS K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 296 removed outlier: 4.548A pdb=" N ALA K 284 " --> pdb=" O GLY K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 4.086A pdb=" N ASN K 300 " --> pdb=" O GLN K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 357 Processing helix chain 'K' and resid 361 through 366 removed outlier: 3.808A pdb=" N MET K 365 " --> pdb=" O ALA K 361 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP K 366 " --> pdb=" O ILE K 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 361 through 366' Processing helix chain 'K' and resid 429 through 446 Processing helix chain 'K' and resid 447 through 453 removed outlier: 4.003A pdb=" N LEU K 451 " --> pdb=" O PRO K 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 276 removed outlier: 5.357A pdb=" N ASP L 269 " --> pdb=" O ALA L 265 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA L 270 " --> pdb=" O ARG L 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 296 Processing helix chain 'L' and resid 296 through 301 removed outlier: 4.011A pdb=" N ASN L 300 " --> pdb=" O GLN L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 339 removed outlier: 3.573A pdb=" N THR L 338 " --> pdb=" O ASN L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 357 Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 376 through 379 Processing helix chain 'L' and resid 429 through 446 Processing helix chain 'L' and resid 447 through 453 removed outlier: 4.051A pdb=" N LEU L 451 " --> pdb=" O PRO L 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 276 removed outlier: 5.443A pdb=" N ASP M 269 " --> pdb=" O ALA M 265 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA M 270 " --> pdb=" O ARG M 266 " (cutoff:3.500A) Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 296 through 301 removed outlier: 4.267A pdb=" N ASN M 300 " --> pdb=" O GLN M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 339 Processing helix chain 'M' and resid 340 through 357 Processing helix chain 'M' and resid 429 through 446 Processing helix chain 'M' and resid 447 through 453 removed outlier: 3.942A pdb=" N LEU M 451 " --> pdb=" O PRO M 447 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 Processing helix chain 'N' and resid 258 through 267 Processing helix chain 'N' and resid 268 through 276 Processing helix chain 'N' and resid 281 through 296 removed outlier: 3.533A pdb=" N PHE N 285 " --> pdb=" O PHE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 4.036A pdb=" N ASN N 300 " --> pdb=" O GLN N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 335 through 339 removed outlier: 3.635A pdb=" N THR N 338 " --> pdb=" O ASN N 335 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET N 339 " --> pdb=" O VAL N 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 335 through 339' Processing helix chain 'N' and resid 340 through 358 Processing helix chain 'N' and resid 429 through 446 Processing helix chain 'N' and resid 447 through 453 removed outlier: 4.006A pdb=" N LEU N 451 " --> pdb=" O PRO N 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 257 through 276 removed outlier: 5.532A pdb=" N ASP O 269 " --> pdb=" O ALA O 265 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA O 270 " --> pdb=" O ARG O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 296 Processing helix chain 'O' and resid 340 through 357 Processing helix chain 'O' and resid 376 through 379 Processing helix chain 'O' and resid 429 through 446 Processing helix chain 'O' and resid 447 through 453 removed outlier: 3.938A pdb=" N LEU O 451 " --> pdb=" O PRO O 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 246 Processing helix chain 'P' and resid 257 through 276 removed outlier: 5.743A pdb=" N ASP P 269 " --> pdb=" O ALA P 265 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA P 270 " --> pdb=" O ARG P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 281 through 296 removed outlier: 3.861A pdb=" N PHE P 285 " --> pdb=" O PHE P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 339 Processing helix chain 'P' and resid 340 through 357 Processing helix chain 'P' and resid 429 through 446 Processing helix chain 'P' and resid 447 through 453 removed outlier: 3.643A pdb=" N LEU P 451 " --> pdb=" O PRO P 447 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 275 removed outlier: 5.974A pdb=" N ASP R 269 " --> pdb=" O ALA R 265 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ALA R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 296 Processing helix chain 'R' and resid 335 through 339 removed outlier: 3.903A pdb=" N THR R 338 " --> pdb=" O ASN R 335 " (cutoff:3.500A) Processing helix chain 'R' and resid 340 through 357 Processing helix chain 'R' and resid 429 through 446 Processing helix chain 'R' and resid 447 through 453 removed outlier: 4.030A pdb=" N LEU R 451 " --> pdb=" O PRO R 447 " (cutoff:3.500A) Processing helix chain 'S' and resid 257 through 276 removed outlier: 6.086A pdb=" N ASP S 269 " --> pdb=" O ALA S 265 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ALA S 270 " --> pdb=" O ARG S 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 281 through 296 removed outlier: 3.537A pdb=" N PHE S 285 " --> pdb=" O PHE S 281 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 301 Processing helix chain 'S' and resid 335 through 339 removed outlier: 3.906A pdb=" N THR S 338 " --> pdb=" O ASN S 335 " (cutoff:3.500A) Processing helix chain 'S' and resid 340 through 357 removed outlier: 3.817A pdb=" N GLU S 345 " --> pdb=" O TYR S 341 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS S 357 " --> pdb=" O GLU S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 366 removed outlier: 3.903A pdb=" N ASP S 366 " --> pdb=" O GLU S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 374 through 379 removed outlier: 4.116A pdb=" N VAL S 377 " --> pdb=" O ASN S 374 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE S 378 " --> pdb=" O GLY S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 429 through 446 Processing helix chain 'S' and resid 447 through 453 removed outlier: 4.204A pdb=" N LEU S 451 " --> pdb=" O PRO S 447 " (cutoff:3.500A) Processing helix chain 'T' and resid 257 through 267 Processing helix chain 'T' and resid 268 through 276 Processing helix chain 'T' and resid 281 through 296 removed outlier: 3.525A pdb=" N PHE T 285 " --> pdb=" O PHE T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 340 through 358 Processing helix chain 'T' and resid 429 through 446 Processing helix chain 'T' and resid 447 through 453 removed outlier: 4.129A pdb=" N LEU T 451 " --> pdb=" O PRO T 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 276 removed outlier: 3.636A pdb=" N GLN U 261 " --> pdb=" O MET U 257 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASP U 269 " --> pdb=" O ALA U 265 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ALA U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 296 Processing helix chain 'U' and resid 336 through 339 Processing helix chain 'U' and resid 340 through 357 removed outlier: 3.518A pdb=" N LYS U 357 " --> pdb=" O GLU U 353 " (cutoff:3.500A) Processing helix chain 'U' and resid 376 through 379 Processing helix chain 'U' and resid 429 through 446 Processing helix chain 'U' and resid 447 through 452 removed outlier: 3.946A pdb=" N LEU U 451 " --> pdb=" O PRO U 447 " (cutoff:3.500A) Processing helix chain 'V' and resid 257 through 276 removed outlier: 5.638A pdb=" N ASP V 269 " --> pdb=" O ALA V 265 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALA V 270 " --> pdb=" O ARG V 266 " (cutoff:3.500A) Processing helix chain 'V' and resid 280 through 296 removed outlier: 4.477A pdb=" N ALA V 284 " --> pdb=" O GLY V 280 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 339 Processing helix chain 'V' and resid 341 through 357 removed outlier: 3.736A pdb=" N GLU V 345 " --> pdb=" O TYR V 341 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS V 357 " --> pdb=" O GLU V 353 " (cutoff:3.500A) Processing helix chain 'V' and resid 361 through 366 removed outlier: 3.577A pdb=" N ASP V 366 " --> pdb=" O ILE V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 375 through 379 removed outlier: 3.703A pdb=" N PHE V 378 " --> pdb=" O GLY V 375 " (cutoff:3.500A) Processing helix chain 'V' and resid 429 through 446 Processing helix chain 'V' and resid 447 through 453 removed outlier: 3.891A pdb=" N LEU V 451 " --> pdb=" O PRO V 447 " (cutoff:3.500A) Processing helix chain 'W' and resid 258 through 267 Processing helix chain 'W' and resid 268 through 276 Processing helix chain 'W' and resid 281 through 296 Processing helix chain 'W' and resid 296 through 301 removed outlier: 4.146A pdb=" N ASN W 300 " --> pdb=" O GLN W 296 " (cutoff:3.500A) Processing helix chain 'W' and resid 336 through 339 removed outlier: 3.718A pdb=" N MET W 339 " --> pdb=" O VAL W 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 336 through 339' Processing helix chain 'W' and resid 340 through 358 removed outlier: 3.791A pdb=" N LYS W 357 " --> pdb=" O GLU W 353 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 365 Processing helix chain 'W' and resid 429 through 446 removed outlier: 3.943A pdb=" N LEU W 437 " --> pdb=" O ALA W 433 " (cutoff:3.500A) Processing helix chain 'W' and resid 447 through 453 removed outlier: 3.507A pdb=" N LEU W 451 " --> pdb=" O PRO W 447 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 276 removed outlier: 5.433A pdb=" N ASP X 269 " --> pdb=" O ALA X 265 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA X 270 " --> pdb=" O ARG X 266 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 296 Processing helix chain 'X' and resid 297 through 301 Processing helix chain 'X' and resid 336 through 339 Processing helix chain 'X' and resid 341 through 357 removed outlier: 4.166A pdb=" N GLU X 345 " --> pdb=" O TYR X 341 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG X 346 " --> pdb=" O ALA X 342 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR X 347 " --> pdb=" O ASP X 343 " (cutoff:3.500A) Processing helix chain 'X' and resid 361 through 365 Processing helix chain 'X' and resid 375 through 379 removed outlier: 3.771A pdb=" N PHE X 378 " --> pdb=" O GLY X 375 " (cutoff:3.500A) Processing helix chain 'X' and resid 429 through 446 Processing helix chain 'X' and resid 447 through 453 removed outlier: 4.128A pdb=" N LEU X 451 " --> pdb=" O PRO X 447 " (cutoff:3.500A) Processing helix chain 'Y' and resid 257 through 275 removed outlier: 3.990A pdb=" N GLN Y 261 " --> pdb=" O MET Y 257 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG Y 266 " --> pdb=" O GLU Y 262 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP Y 269 " --> pdb=" O ALA Y 265 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 281 through 294 removed outlier: 3.524A pdb=" N LYS Y 287 " --> pdb=" O SER Y 283 " (cutoff:3.500A) Processing helix chain 'Y' and resid 337 through 341 removed outlier: 4.009A pdb=" N ASN Y 340 " --> pdb=" O GLU Y 337 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR Y 341 " --> pdb=" O THR Y 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 337 through 341' Processing helix chain 'Y' and resid 342 through 359 removed outlier: 3.567A pdb=" N GLU Y 359 " --> pdb=" O ALA Y 355 " (cutoff:3.500A) Processing helix chain 'Y' and resid 363 through 368 removed outlier: 4.033A pdb=" N GLY Y 368 " --> pdb=" O MET Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 431 through 442 Processing helix chain 'Y' and resid 448 through 453 Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421 removed outlier: 3.706A pdb=" N PHE M 382 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 334 removed outlier: 6.399A pdb=" N THR A 371 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 383 removed outlier: 3.765A pdb=" N PHE A 382 " --> pdb=" O PHE W 252 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS W 410 " --> pdb=" O ALA W 406 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA W 406 " --> pdb=" O LYS W 410 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU W 412 " --> pdb=" O PRO W 404 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG W 414 " --> pdb=" O ASP W 402 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP W 402 " --> pdb=" O ARG W 414 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N MET W 416 " --> pdb=" O ILE W 400 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE W 400 " --> pdb=" O MET W 416 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR W 418 " --> pdb=" O HIS W 398 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS W 398 " --> pdb=" O TYR W 418 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR W 371 " --> pdb=" O LEU W 395 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N MET W 397 " --> pdb=" O THR W 371 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER W 373 " --> pdb=" O MET W 397 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N GLY W 399 " --> pdb=" O SER W 373 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE W 370 " --> pdb=" O ASP W 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 333 through 334 removed outlier: 4.426A pdb=" N ASN B 374 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 371 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET B 397 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER B 373 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 333 through 334 removed outlier: 4.426A pdb=" N ASN B 374 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 371 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N MET B 397 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER B 373 " --> pdb=" O MET B 397 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE N 382 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 302 through 304 Processing sheet with id=AA9, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AB1, first strand: chain 'B' and resid 382 through 383 removed outlier: 3.865A pdb=" N PHE B 382 " --> pdb=" O PHE K 252 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 249 " --> pdb=" O TYR K 423 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG K 414 " --> pdb=" O ARG K 403 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG K 403 " --> pdb=" O ARG K 414 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR K 418 " --> pdb=" O GLY K 399 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY K 399 " --> pdb=" O TYR K 418 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA K 420 " --> pdb=" O MET K 397 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N MET K 397 " --> pdb=" O ALA K 420 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N THR K 422 " --> pdb=" O LEU K 395 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU K 395 " --> pdb=" O THR K 422 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR K 371 " --> pdb=" O ALA K 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 329 removed outlier: 4.527A pdb=" N ASN C 374 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA C 323 " --> pdb=" O ASN C 374 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR C 371 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET C 397 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER C 373 " --> pdb=" O MET C 397 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLY C 399 " --> pdb=" O SER C 373 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 395 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR C 422 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N MET C 397 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA C 420 " --> pdb=" O MET C 397 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N GLY C 399 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR C 418 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE O 382 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AB4, first strand: chain 'C' and resid 382 through 383 removed outlier: 3.671A pdb=" N PHE C 382 " --> pdb=" O PHE T 252 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N THR T 371 " --> pdb=" O LEU T 395 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N MET T 397 " --> pdb=" O THR T 371 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER T 373 " --> pdb=" O MET T 397 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N SER T 319 " --> pdb=" O ILE T 372 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN T 374 " --> pdb=" O SER T 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 382 through 383 removed outlier: 3.671A pdb=" N PHE C 382 " --> pdb=" O PHE T 252 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS T 410 " --> pdb=" O VAL T 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 318 through 320 removed outlier: 6.472A pdb=" N THR D 371 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET D 397 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER D 373 " --> pdb=" O MET D 397 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY D 399 " --> pdb=" O SER D 373 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA D 393 " --> pdb=" O ASP D 424 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ASP D 424 " --> pdb=" O ALA D 393 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU D 395 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N THR D 422 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N MET D 397 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA D 420 " --> pdb=" O MET D 397 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLY D 399 " --> pdb=" O TYR D 418 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR D 418 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 249 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE G 382 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 302 through 303 Processing sheet with id=AB8, first strand: chain 'D' and resid 322 through 323 Processing sheet with id=AB9, first strand: chain 'D' and resid 382 through 383 removed outlier: 3.865A pdb=" N PHE D 382 " --> pdb=" O PHE P 252 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA P 420 " --> pdb=" O GLY P 396 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR P 371 " --> pdb=" O ALA P 393 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER P 319 " --> pdb=" O ILE P 372 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN P 374 " --> pdb=" O SER P 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 382 through 383 removed outlier: 3.865A pdb=" N PHE D 382 " --> pdb=" O PHE P 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS P 410 " --> pdb=" O VAL P 407 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 332 through 334 removed outlier: 5.910A pdb=" N ASP E 317 " --> pdb=" O PHE E 370 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE E 372 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER E 319 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASN E 374 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR E 371 " --> pdb=" O LEU E 395 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET E 397 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER E 373 " --> pdb=" O MET E 397 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 332 through 334 removed outlier: 5.910A pdb=" N ASP E 317 " --> pdb=" O PHE E 370 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE E 372 " --> pdb=" O ASP E 317 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER E 319 " --> pdb=" O ILE E 372 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASN E 374 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR E 371 " --> pdb=" O LEU E 395 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET E 397 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER E 373 " --> pdb=" O MET E 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE L 382 " --> pdb=" O PHE E 252 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 301 through 304 Processing sheet with id=AC5, first strand: chain 'E' and resid 382 through 383 removed outlier: 3.723A pdb=" N PHE E 382 " --> pdb=" O PHE U 252 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA U 406 " --> pdb=" O LYS U 410 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU U 412 " --> pdb=" O PRO U 404 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ARG U 414 " --> pdb=" O ASP U 402 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP U 402 " --> pdb=" O ARG U 414 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET U 416 " --> pdb=" O ILE U 400 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE U 400 " --> pdb=" O MET U 416 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N TYR U 418 " --> pdb=" O HIS U 398 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS U 398 " --> pdb=" O TYR U 418 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR U 371 " --> pdb=" O LEU U 395 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N MET U 397 " --> pdb=" O THR U 371 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N SER U 373 " --> pdb=" O MET U 397 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLY U 399 " --> pdb=" O SER U 373 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 250 through 256 removed outlier: 7.125A pdb=" N THR F 371 " --> pdb=" O LEU F 395 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP F 317 " --> pdb=" O PHE F 370 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE F 372 " --> pdb=" O ASP F 317 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER F 319 " --> pdb=" O ILE F 372 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 250 through 256 Processing sheet with id=AC8, first strand: chain 'F' and resid 302 through 303 Processing sheet with id=AC9, first strand: chain 'F' and resid 382 through 383 removed outlier: 3.574A pdb=" N PHE F 382 " --> pdb=" O PHE H 252 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR H 371 " --> pdb=" O LEU H 395 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N MET H 397 " --> pdb=" O THR H 371 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER H 373 " --> pdb=" O MET H 397 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER H 319 " --> pdb=" O ILE H 372 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASN H 374 " --> pdb=" O SER H 319 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 382 through 383 removed outlier: 3.574A pdb=" N PHE F 382 " --> pdb=" O PHE H 252 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 393 through 407 removed outlier: 3.593A pdb=" N HIS G 398 " --> pdb=" O TYR G 418 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR G 418 " --> pdb=" O HIS G 398 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE G 400 " --> pdb=" O MET G 416 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET G 416 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP G 402 " --> pdb=" O ARG G 414 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ARG G 414 " --> pdb=" O ASP G 402 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU G 412 " --> pdb=" O PRO G 404 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA G 406 " --> pdb=" O LYS G 410 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS G 410 " --> pdb=" O ALA G 406 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE P 382 " --> pdb=" O PHE G 252 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 302 through 304 removed outlier: 4.024A pdb=" N VAL G 302 " --> pdb=" O VAL G 311 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 311 " --> pdb=" O VAL G 302 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 332 through 334 Processing sheet with id=AD5, first strand: chain 'G' and resid 322 through 323 Processing sheet with id=AD6, first strand: chain 'H' and resid 302 through 303 Processing sheet with id=AD7, first strand: chain 'H' and resid 322 through 323 Processing sheet with id=AD8, first strand: chain 'H' and resid 382 through 383 removed outlier: 3.705A pdb=" N PHE H 382 " --> pdb=" O PHE R 252 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 249 " --> pdb=" O TYR R 423 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR R 371 " --> pdb=" O LEU R 395 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE R 372 " --> pdb=" O SER R 319 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 382 through 383 removed outlier: 3.705A pdb=" N PHE H 382 " --> pdb=" O PHE R 252 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU R 249 " --> pdb=" O TYR R 423 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS R 410 " --> pdb=" O VAL R 407 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 332 through 334 removed outlier: 6.815A pdb=" N THR I 371 " --> pdb=" O LEU I 395 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N MET I 397 " --> pdb=" O THR I 371 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N SER I 373 " --> pdb=" O MET I 397 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N GLY I 399 " --> pdb=" O SER I 373 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ALA I 393 " --> pdb=" O ASP I 424 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP I 424 " --> pdb=" O ALA I 393 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU I 395 " --> pdb=" O THR I 422 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR I 422 " --> pdb=" O LEU I 395 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N MET I 397 " --> pdb=" O ALA I 420 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA I 420 " --> pdb=" O MET I 397 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY I 399 " --> pdb=" O TYR I 418 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR I 418 " --> pdb=" O GLY I 399 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE V 382 " --> pdb=" O PHE I 252 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 302 through 304 Processing sheet with id=AE3, first strand: chain 'I' and resid 322 through 324 Processing sheet with id=AE4, first strand: chain 'I' and resid 382 through 383 removed outlier: 3.653A pdb=" N PHE I 382 " --> pdb=" O PHE S 252 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THR S 371 " --> pdb=" O LEU S 395 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 382 through 383 removed outlier: 3.653A pdb=" N PHE I 382 " --> pdb=" O PHE S 252 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE S 401 " --> pdb=" O MET S 416 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 318 through 320 removed outlier: 6.624A pdb=" N THR J 371 " --> pdb=" O LEU J 395 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET J 397 " --> pdb=" O THR J 371 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER J 373 " --> pdb=" O MET J 397 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 318 through 320 removed outlier: 6.624A pdb=" N THR J 371 " --> pdb=" O LEU J 395 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET J 397 " --> pdb=" O THR J 371 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER J 373 " --> pdb=" O MET J 397 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE X 382 " --> pdb=" O PHE J 252 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 302 through 304 Processing sheet with id=AE9, first strand: chain 'J' and resid 322 through 324 Processing sheet with id=AF1, first strand: chain 'J' and resid 382 through 383 removed outlier: 3.593A pdb=" N LEU Y 249 " --> pdb=" O HIS Y 425 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR Y 251 " --> pdb=" O TYR Y 423 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL Y 419 " --> pdb=" O VAL Y 255 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 302 through 304 Processing sheet with id=AF3, first strand: chain 'K' and resid 382 through 383 removed outlier: 3.687A pdb=" N PHE K 382 " --> pdb=" O PHE N 252 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LYS N 410 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA N 406 " --> pdb=" O LYS N 410 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU N 412 " --> pdb=" O PRO N 404 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG N 414 " --> pdb=" O ASP N 402 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASP N 402 " --> pdb=" O ARG N 414 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET N 416 " --> pdb=" O ILE N 400 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE N 400 " --> pdb=" O MET N 416 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N TYR N 418 " --> pdb=" O HIS N 398 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS N 398 " --> pdb=" O TYR N 418 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR N 371 " --> pdb=" O ALA N 393 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE N 318 " --> pdb=" O ILE N 333 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 332 through 333 removed outlier: 6.387A pdb=" N SER L 319 " --> pdb=" O ILE L 372 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N ASN L 374 " --> pdb=" O SER L 319 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR L 371 " --> pdb=" O LEU L 395 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET L 397 " --> pdb=" O THR L 371 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER L 373 " --> pdb=" O MET L 397 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY L 399 " --> pdb=" O SER L 373 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA L 393 " --> pdb=" O ASP L 424 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASP L 424 " --> pdb=" O ALA L 393 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU L 395 " --> pdb=" O THR L 422 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR L 422 " --> pdb=" O LEU L 395 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N MET L 397 " --> pdb=" O ALA L 420 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA L 420 " --> pdb=" O MET L 397 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY L 399 " --> pdb=" O TYR L 418 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR L 418 " --> pdb=" O GLY L 399 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE U 382 " --> pdb=" O PHE L 252 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 302 through 304 Processing sheet with id=AF6, first strand: chain 'L' and resid 322 through 324 Processing sheet with id=AF7, first strand: chain 'M' and resid 332 through 334 removed outlier: 6.693A pdb=" N THR M 371 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET M 397 " --> pdb=" O THR M 371 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER M 373 " --> pdb=" O MET M 397 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 332 through 334 removed outlier: 6.693A pdb=" N THR M 371 " --> pdb=" O LEU M 395 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET M 397 " --> pdb=" O THR M 371 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER M 373 " --> pdb=" O MET M 397 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE W 382 " --> pdb=" O PHE M 252 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 322 through 323 removed outlier: 3.669A pdb=" N VAL M 322 " --> pdb=" O VAL M 329 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL M 329 " --> pdb=" O VAL M 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'N' and resid 302 through 304 removed outlier: 3.549A pdb=" N VAL N 302 " --> pdb=" O VAL N 311 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 322 through 324 Processing sheet with id=AG3, first strand: chain 'O' and resid 318 through 320 removed outlier: 7.000A pdb=" N THR O 371 " --> pdb=" O LEU O 395 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET O 397 " --> pdb=" O THR O 371 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER O 373 " --> pdb=" O MET O 397 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLY O 399 " --> pdb=" O SER O 373 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA O 393 " --> pdb=" O ASP O 424 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP O 424 " --> pdb=" O ALA O 393 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU O 395 " --> pdb=" O THR O 422 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR O 422 " --> pdb=" O LEU O 395 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET O 397 " --> pdb=" O ALA O 420 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA O 420 " --> pdb=" O MET O 397 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLY O 399 " --> pdb=" O TYR O 418 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR O 418 " --> pdb=" O GLY O 399 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE T 382 " --> pdb=" O PHE O 252 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 301 through 304 removed outlier: 3.791A pdb=" N VAL O 302 " --> pdb=" O VAL O 311 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL O 311 " --> pdb=" O VAL O 302 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 322 through 323 Processing sheet with id=AG6, first strand: chain 'P' and resid 301 through 304 Processing sheet with id=AG7, first strand: chain 'R' and resid 302 through 304 Processing sheet with id=AG8, first strand: chain 'S' and resid 302 through 304 Processing sheet with id=AG9, first strand: chain 'S' and resid 382 through 383 removed outlier: 3.685A pdb=" N PHE S 382 " --> pdb=" O PHE V 252 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 382 through 383 removed outlier: 3.685A pdb=" N PHE S 382 " --> pdb=" O PHE V 252 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 303 through 304 removed outlier: 3.579A pdb=" N GLU T 309 " --> pdb=" O ASP T 304 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 302 through 304 Processing sheet with id=AH4, first strand: chain 'U' and resid 322 through 324 removed outlier: 3.818A pdb=" N VAL U 329 " --> pdb=" O VAL U 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'V' and resid 302 through 304 Processing sheet with id=AH6, first strand: chain 'V' and resid 318 through 319 Processing sheet with id=AH7, first strand: chain 'V' and resid 322 through 324 Processing sheet with id=AH8, first strand: chain 'W' and resid 302 through 304 removed outlier: 3.746A pdb=" N GLU W 309 " --> pdb=" O ASP W 304 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 249 through 256 removed outlier: 4.507A pdb=" N TYR X 418 " --> pdb=" O GLY X 399 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLY X 399 " --> pdb=" O TYR X 418 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA X 420 " --> pdb=" O MET X 397 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N MET X 397 " --> pdb=" O ALA X 420 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR X 422 " --> pdb=" O LEU X 395 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU X 395 " --> pdb=" O THR X 422 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'X' and resid 302 through 304 removed outlier: 3.615A pdb=" N GLU X 309 " --> pdb=" O ASP X 304 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'X' and resid 332 through 334 Processing sheet with id=AI3, first strand: chain 'Y' and resid 302 through 304 removed outlier: 4.327A pdb=" N ASP Y 304 " --> pdb=" O VAL Y 311 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL Y 311 " --> pdb=" O ASP Y 304 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 320 through 322 removed outlier: 7.921A pdb=" N SER Y 373 " --> pdb=" O MET Y 397 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Y' and resid 408 through 409 2024 hydrogen bonds defined for protein. 5610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.64 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6798 1.32 - 1.45: 9608 1.45 - 1.57: 23263 1.57 - 1.70: 3 1.70 - 1.83: 454 Bond restraints: 40126 Sorted by residual: bond pdb=" N LEU V 452 " pdb=" CA LEU V 452 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.33e-02 5.65e+03 9.00e+00 bond pdb=" C PRO W 389 " pdb=" O PRO W 389 " ideal model delta sigma weight residual 1.240 1.208 0.033 1.12e-02 7.97e+03 8.61e+00 bond pdb=" C PRO Y 389 " pdb=" O PRO Y 389 " ideal model delta sigma weight residual 1.240 1.208 0.032 1.12e-02 7.97e+03 8.16e+00 bond pdb=" N ILE Y 387 " pdb=" CA ILE Y 387 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.40e+00 bond pdb=" C ASN W 388 " pdb=" N PRO W 389 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.18e-02 7.18e+03 7.13e+00 ... (remaining 40121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 53448 2.24 - 4.49: 744 4.49 - 6.73: 88 6.73 - 8.98: 16 8.98 - 11.22: 6 Bond angle restraints: 54302 Sorted by residual: angle pdb=" N ILE Y 386 " pdb=" CA ILE Y 386 " pdb=" C ILE Y 386 " ideal model delta sigma weight residual 108.48 97.26 11.22 1.44e+00 4.82e-01 6.07e+01 angle pdb=" O GLN M 296 " pdb=" C GLN M 296 " pdb=" N PRO M 297 " ideal model delta sigma weight residual 121.27 117.15 4.12 8.00e-01 1.56e+00 2.65e+01 angle pdb=" C PRO Y 385 " pdb=" N ILE Y 386 " pdb=" CA ILE Y 386 " ideal model delta sigma weight residual 123.06 116.05 7.01 1.38e+00 5.25e-01 2.58e+01 angle pdb=" O ASN T 388 " pdb=" C ASN T 388 " pdb=" N PRO T 389 " ideal model delta sigma weight residual 121.32 115.85 5.47 1.15e+00 7.56e-01 2.26e+01 angle pdb=" CA PRO T 389 " pdb=" C PRO T 389 " pdb=" O PRO T 389 " ideal model delta sigma weight residual 120.73 117.02 3.71 7.90e-01 1.60e+00 2.21e+01 ... (remaining 54297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 20708 17.95 - 35.90: 2949 35.90 - 53.85: 727 53.85 - 71.80: 120 71.80 - 89.75: 29 Dihedral angle restraints: 24533 sinusoidal: 9866 harmonic: 14667 Sorted by residual: dihedral pdb=" CA PRO W 389 " pdb=" C PRO W 389 " pdb=" N PRO W 390 " pdb=" CA PRO W 390 " ideal model delta harmonic sigma weight residual 0.00 30.28 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA PRO R 389 " pdb=" C PRO R 389 " pdb=" N PRO R 390 " pdb=" CA PRO R 390 " ideal model delta harmonic sigma weight residual 0.00 -28.52 28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ALA B 247 " pdb=" C ALA B 247 " pdb=" N MET B 248 " pdb=" CA MET B 248 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 24530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 5128 0.056 - 0.111: 1064 0.111 - 0.167: 128 0.167 - 0.223: 3 0.223 - 0.279: 3 Chirality restraints: 6326 Sorted by residual: chirality pdb=" CB ILE Y 333 " pdb=" CA ILE Y 333 " pdb=" CG1 ILE Y 333 " pdb=" CG2 ILE Y 333 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CB ILE Y 387 " pdb=" CA ILE Y 387 " pdb=" CG1 ILE Y 387 " pdb=" CG2 ILE Y 387 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE Y 386 " pdb=" N ILE Y 386 " pdb=" C ILE Y 386 " pdb=" CB ILE Y 386 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 6323 not shown) Planarity restraints: 7082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN T 388 " 0.023 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ASN T 388 " -0.075 2.00e-02 2.50e+03 pdb=" O ASN T 388 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO T 389 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO Y 385 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C PRO Y 385 " -0.071 2.00e-02 2.50e+03 pdb=" O PRO Y 385 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE Y 386 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 386 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ILE Y 386 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE Y 386 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE Y 387 " -0.024 2.00e-02 2.50e+03 ... (remaining 7079 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 638 2.67 - 3.22: 36246 3.22 - 3.78: 60502 3.78 - 4.34: 81864 4.34 - 4.90: 138265 Nonbonded interactions: 317515 Sorted by model distance: nonbonded pdb=" OG1 THR U 371 " pdb=" OE1 GLN U 391 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR W 324 " pdb=" O GLY W 327 " model vdw 2.124 3.040 nonbonded pdb=" OG1 THR T 371 " pdb=" OE1 GLN T 391 " model vdw 2.146 3.040 nonbonded pdb=" OG1 THR C 371 " pdb=" OE1 GLN C 391 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR J 371 " pdb=" OE1 GLN J 391 " model vdw 2.162 3.040 ... (remaining 317510 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 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'B' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'C' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'D' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'E' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'F' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'G' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'H' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'I' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'J' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'K' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'L' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'M' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'N' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'O' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'P' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'R' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'S' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'T' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'U' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'V' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'W' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'X' and (resid 247 through 453 or (resid 454 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2)))) selection = (chain 'Y' and resid 247 through 454) } 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 individual isotropic 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: 6.290 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: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.520 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 40126 Z= 0.179 Angle : 0.674 11.223 54302 Z= 0.372 Chirality : 0.046 0.279 6326 Planarity : 0.005 0.063 7082 Dihedral : 17.392 89.750 15043 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.27 % Favored : 95.51 % Rotamer: Outliers : 0.54 % Allowed : 28.78 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.19 % Cis-general : 0.02 % Twisted Proline : 0.46 % 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 aren not related in a simple way. whole: -0.12 (0.12), residues: 5033 helix: 1.02 (0.12), residues: 1801 sheet: -0.83 (0.15), residues: 1176 loop : -0.46 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 334 TYR 0.032 0.001 TYR Y 423 PHE 0.032 0.002 PHE Y 401 HIS 0.016 0.001 HIS Y 398 Details of bonding type rmsd covalent geometry : bond 0.00396 (40126) covalent geometry : angle 0.67385 (54302) hydrogen bonds : bond 0.18857 ( 1936) hydrogen bonds : angle 7.34332 ( 5610) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 754 time to evaluate : 1.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ILE cc_start: 0.7585 (tt) cc_final: 0.7356 (tt) REVERT: B 320 VAL cc_start: 0.8370 (t) cc_final: 0.8163 (t) REVERT: D 258 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7936 (p) REVERT: G 320 VAL cc_start: 0.9235 (p) cc_final: 0.8978 (m) REVERT: H 338 THR cc_start: 0.8211 (p) cc_final: 0.8000 (p) REVERT: J 360 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6794 (tp) REVERT: K 402 ASP cc_start: 0.7906 (m-30) cc_final: 0.7619 (m-30) REVERT: R 345 GLU cc_start: 0.7466 (mp0) cc_final: 0.6791 (mp0) REVERT: R 417 MET cc_start: 0.8430 (ptp) cc_final: 0.8216 (ptp) REVERT: V 365 MET cc_start: 0.4778 (mmm) cc_final: 0.3040 (mtt) REVERT: W 438 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.8133 (mtp85) REVERT: X 248 MET cc_start: 0.5062 (mpp) cc_final: 0.4852 (mpp) REVERT: X 261 GLN cc_start: 0.8360 (mm110) cc_final: 0.8143 (mm110) REVERT: Y 262 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7385 (tm-30) REVERT: Y 282 MET cc_start: 0.8203 (mmm) cc_final: 0.7900 (mmp) REVERT: Y 401 PHE cc_start: 0.5321 (m-80) cc_final: 0.4999 (m-80) REVERT: Y 441 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8235 (ttpt) outliers start: 23 outliers final: 13 residues processed: 761 average time/residue: 0.2147 time to fit residues: 269.2148 Evaluate side-chains 711 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 695 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain J residue 360 LEU Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain T residue 257 MET Chi-restraints excluded: chain V residue 294 GLN Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain Y residue 344 ILE Chi-restraints excluded: chain Y residue 387 ILE Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 428 ILE Chi-restraints excluded: chain Y residue 441 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0970 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 494 optimal weight: 0.3980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 294 GLN H 388 ASN I 391 GLN J 391 GLN M 243 GLN N 243 GLN O 275 HIS U 294 GLN V 300 ASN ** X 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 276 ASN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126868 restraints weight = 53511.809| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.18 r_work: 0.3339 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 40126 Z= 0.143 Angle : 0.571 8.248 54302 Z= 0.302 Chirality : 0.045 0.241 6326 Planarity : 0.005 0.056 7082 Dihedral : 5.483 72.061 5548 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.52 % Favored : 96.34 % Rotamer: Outliers : 4.23 % Allowed : 24.92 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.13 (0.12), residues: 5033 helix: 1.26 (0.12), residues: 1865 sheet: -0.74 (0.15), residues: 1155 loop : -0.38 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 426 TYR 0.015 0.001 TYR Y 418 PHE 0.027 0.002 PHE Y 436 HIS 0.007 0.001 HIS F 398 Details of bonding type rmsd covalent geometry : bond 0.00339 (40126) covalent geometry : angle 0.57112 (54302) hydrogen bonds : bond 0.03740 ( 1936) hydrogen bonds : angle 5.26047 ( 5610) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 839 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.8983 (t0) REVERT: A 438 ARG cc_start: 0.8483 (mtm110) cc_final: 0.8249 (mtp85) REVERT: B 345 GLU cc_start: 0.7656 (tp30) cc_final: 0.7275 (mm-30) REVERT: C 410 LYS cc_start: 0.8426 (ptpp) cc_final: 0.7643 (pttm) REVERT: D 276 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7618 (t0) REVERT: D 345 GLU cc_start: 0.7501 (tp30) cc_final: 0.7200 (mm-30) REVERT: E 397 MET cc_start: 0.8494 (mmm) cc_final: 0.7896 (mtt) REVERT: F 296 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7440 (mt0) REVERT: F 305 ASP cc_start: 0.2539 (OUTLIER) cc_final: 0.1906 (p0) REVERT: F 353 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6643 (mm-30) REVERT: F 366 ASP cc_start: 0.5728 (OUTLIER) cc_final: 0.5519 (m-30) REVERT: H 282 MET cc_start: 0.8974 (mmm) cc_final: 0.8616 (tpt) REVERT: H 424 ASP cc_start: 0.8234 (p0) cc_final: 0.7980 (p0) REVERT: J 269 ASP cc_start: 0.7554 (p0) cc_final: 0.7180 (m-30) REVERT: J 453 ASP cc_start: 0.8954 (t0) cc_final: 0.8723 (t0) REVERT: K 378 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.4909 (p90) REVERT: K 402 ASP cc_start: 0.8139 (m-30) cc_final: 0.7899 (m-30) REVERT: L 248 MET cc_start: 0.5401 (tpp) cc_final: 0.5186 (mmm) REVERT: L 295 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: L 359 GLU cc_start: 0.7711 (mp0) cc_final: 0.7436 (mp0) REVERT: M 253 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8636 (t0) REVERT: M 417 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.5870 (tpt) REVERT: N 371 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8621 (m) REVERT: O 453 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: P 253 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8845 (t0) REVERT: P 431 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.8006 (ttp80) REVERT: S 357 LYS cc_start: 0.6693 (mtmt) cc_final: 0.6470 (mmtm) REVERT: S 410 LYS cc_start: 0.7935 (mmtm) cc_final: 0.7658 (mmtt) REVERT: U 388 ASN cc_start: 0.7660 (t0) cc_final: 0.7455 (t0) REVERT: V 365 MET cc_start: 0.5281 (mmm) cc_final: 0.3101 (mtt) REVERT: V 424 ASP cc_start: 0.8291 (t0) cc_final: 0.8060 (t0) REVERT: V 453 ASP cc_start: 0.8473 (t0) cc_final: 0.8205 (t0) REVERT: W 429 ASP cc_start: 0.7787 (p0) cc_final: 0.7563 (p0) REVERT: X 261 GLN cc_start: 0.8167 (mm110) cc_final: 0.7920 (mm110) REVERT: Y 275 HIS cc_start: 0.6221 (m170) cc_final: 0.5917 (m170) REVERT: Y 282 MET cc_start: 0.8549 (mmm) cc_final: 0.7804 (mmm) REVERT: Y 401 PHE cc_start: 0.5548 (m-80) cc_final: 0.5157 (m-80) REVERT: Y 422 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8373 (p) outliers start: 180 outliers final: 98 residues processed: 948 average time/residue: 0.2067 time to fit residues: 325.2255 Evaluate side-chains 840 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 729 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 296 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 348 ILE Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 371 THR Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 272 LEU Chi-restraints excluded: chain P residue 283 SER Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 377 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 269 ASP Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 397 MET Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 322 VAL Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 348 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 264 ARG Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 365 MET Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 377 VAL Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain X residue 300 ASN Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain Y residue 263 MET Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 344 ILE Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 387 ILE Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 417 MET Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 423 TYR Chi-restraints excluded: chain Y residue 435 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 343 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 338 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 GLN C 388 ASN F 398 HIS H 391 GLN N 275 HIS P 391 GLN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 267 HIS T 300 ASN ** T 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 GLN Y 276 ASN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117132 restraints weight = 53312.099| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.16 r_work: 0.3208 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 40126 Z= 0.260 Angle : 0.682 8.275 54302 Z= 0.360 Chirality : 0.050 0.262 6326 Planarity : 0.006 0.057 7082 Dihedral : 5.647 71.046 5526 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.31 % Favored : 95.55 % Rotamer: Outliers : 6.58 % Allowed : 22.60 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: -0.16 (0.12), residues: 5033 helix: 0.85 (0.12), residues: 1874 sheet: -0.86 (0.15), residues: 1093 loop : -0.42 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Y 448 TYR 0.030 0.002 TYR Y 418 PHE 0.039 0.003 PHE Y 271 HIS 0.011 0.002 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00641 (40126) covalent geometry : angle 0.68174 (54302) hydrogen bonds : bond 0.04449 ( 1936) hydrogen bonds : angle 5.08733 ( 5610) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 775 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.9066 (t0) REVERT: A 348 ILE cc_start: 0.8473 (mm) cc_final: 0.8184 (mt) REVERT: A 417 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7737 (ttp) REVERT: A 439 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8249 (tptp) REVERT: B 248 MET cc_start: 0.7485 (tpp) cc_final: 0.7223 (tpp) REVERT: B 339 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7743 (mtt) REVERT: C 294 GLN cc_start: 0.8570 (mt0) cc_final: 0.8176 (mm-40) REVERT: C 314 ASP cc_start: 0.8040 (t0) cc_final: 0.7779 (t0) REVERT: D 276 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.7906 (t0) REVERT: D 353 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6777 (mm-30) REVERT: D 412 GLU cc_start: 0.8491 (pm20) cc_final: 0.7832 (pt0) REVERT: E 258 SER cc_start: 0.9322 (t) cc_final: 0.9052 (p) REVERT: F 296 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7452 (mt0) REVERT: F 305 ASP cc_start: 0.2524 (OUTLIER) cc_final: 0.1932 (p0) REVERT: F 353 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7188 (mm-30) REVERT: F 453 ASP cc_start: 0.8617 (t0) cc_final: 0.8394 (t0) REVERT: G 258 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8823 (m) REVERT: G 314 ASP cc_start: 0.6822 (p0) cc_final: 0.6377 (p0) REVERT: G 343 ASP cc_start: 0.8375 (t0) cc_final: 0.8078 (t0) REVERT: H 303 ILE cc_start: 0.7767 (mp) cc_final: 0.7556 (mm) REVERT: H 346 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7430 (ttp-110) REVERT: H 350 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: I 273 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8215 (ttmm) REVERT: I 362 ILE cc_start: 0.6325 (OUTLIER) cc_final: 0.5968 (mp) REVERT: I 454 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7909 (mp) REVERT: J 271 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: J 277 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7962 (pp) REVERT: J 318 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8333 (mp) REVERT: K 326 ARG cc_start: 0.4455 (OUTLIER) cc_final: 0.3792 (ptt90) REVERT: K 378 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.4921 (p90) REVERT: L 295 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: L 354 LYS cc_start: 0.6211 (mmtp) cc_final: 0.5785 (mmmt) REVERT: L 359 GLU cc_start: 0.7827 (mp0) cc_final: 0.7437 (mp0) REVERT: M 253 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8404 (t0) REVERT: M 417 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6597 (tpt) REVERT: N 371 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8599 (m) REVERT: N 391 GLN cc_start: 0.7997 (mt0) cc_final: 0.7221 (mt0) REVERT: O 316 ILE cc_start: 0.8526 (mt) cc_final: 0.8266 (mt) REVERT: O 391 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7319 (mt0) REVERT: P 253 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8872 (t0) REVERT: S 410 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7844 (mmtt) REVERT: T 346 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.7884 (ttm110) REVERT: T 405 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8577 (m) REVERT: U 317 ASP cc_start: 0.8109 (m-30) cc_final: 0.7744 (m-30) REVERT: U 328 LEU cc_start: 0.4911 (mt) cc_final: 0.4328 (pt) REVERT: U 388 ASN cc_start: 0.7921 (t0) cc_final: 0.7683 (t0) REVERT: V 432 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7916 (mt-10) REVERT: X 248 MET cc_start: 0.5909 (mpp) cc_final: 0.5619 (mpp) REVERT: X 268 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8156 (ttpp) REVERT: Y 259 ASN cc_start: 0.8223 (m-40) cc_final: 0.7982 (t0) REVERT: Y 262 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7622 (tm-30) REVERT: Y 274 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7722 (tttt) REVERT: Y 282 MET cc_start: 0.8849 (mmm) cc_final: 0.8265 (mmp) REVERT: Y 287 LYS cc_start: 0.8503 (tptt) cc_final: 0.7989 (tptt) REVERT: Y 291 PHE cc_start: 0.5802 (m-80) cc_final: 0.5503 (m-80) REVERT: Y 315 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.6155 (m-10) REVERT: Y 316 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8336 (pt) REVERT: Y 382 PHE cc_start: 0.8071 (p90) cc_final: 0.7744 (p90) REVERT: Y 401 PHE cc_start: 0.6201 (m-80) cc_final: 0.5435 (m-80) REVERT: Y 423 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6208 (t80) outliers start: 280 outliers final: 150 residues processed: 958 average time/residue: 0.2094 time to fit residues: 331.7026 Evaluate side-chains 859 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 680 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 273 LYS Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 296 GLN Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 253 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 349 ASN Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 294 GLN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 346 ARG Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain H residue 411 VAL Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 454 LEU Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 283 SER Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 317 ASP Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 449 VAL Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 258 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 417 MET Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 314 ASP Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 392 SER Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 421 LEU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 348 ILE Chi-restraints excluded: chain R residue 377 VAL Chi-restraints excluded: chain S residue 251 THR Chi-restraints excluded: chain S residue 269 ASP Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain T residue 302 VAL Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 405 VAL Chi-restraints excluded: chain T residue 411 VAL Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 348 ILE Chi-restraints excluded: chain V residue 400 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 264 ARG Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 302 VAL Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 339 MET Chi-restraints excluded: chain W residue 365 MET Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 377 VAL Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain Y residue 248 MET Chi-restraints excluded: chain Y residue 263 MET Chi-restraints excluded: chain Y residue 274 LYS Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 334 ARG Chi-restraints excluded: chain Y residue 344 ILE Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 423 TYR Chi-restraints excluded: chain Y residue 428 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 168 optimal weight: 9.9990 chunk 372 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 387 optimal weight: 3.9990 chunk 458 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 365 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 470 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 261 GLN J 294 GLN J 358 ASN J 425 HIS L 276 ASN N 243 GLN O 425 HIS S 243 GLN W 425 HIS Y 267 HIS Y 276 ASN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117718 restraints weight = 53090.948| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.13 r_work: 0.3211 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 40126 Z= 0.152 Angle : 0.552 8.423 54302 Z= 0.293 Chirality : 0.045 0.236 6326 Planarity : 0.005 0.061 7082 Dihedral : 5.326 73.014 5524 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.18 % Favored : 96.68 % Rotamer: Outliers : 5.21 % Allowed : 24.29 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.15 (0.12), residues: 5033 helix: 1.25 (0.12), residues: 1873 sheet: -0.74 (0.15), residues: 1078 loop : -0.37 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 448 TYR 0.019 0.001 TYR Y 418 PHE 0.037 0.002 PHE Y 436 HIS 0.009 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00369 (40126) covalent geometry : angle 0.55197 (54302) hydrogen bonds : bond 0.03332 ( 1936) hydrogen bonds : angle 4.76001 ( 5610) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 740 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9077 (t0) REVERT: A 269 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8165 (m-30) REVERT: A 348 ILE cc_start: 0.8562 (mm) cc_final: 0.8192 (mt) REVERT: A 417 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7958 (ttp) REVERT: A 439 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (tptp) REVERT: A 448 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7275 (mtp180) REVERT: B 339 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7805 (mtt) REVERT: B 345 GLU cc_start: 0.7626 (tp30) cc_final: 0.7415 (mm-30) REVERT: C 294 GLN cc_start: 0.8548 (mt0) cc_final: 0.8231 (mm-40) REVERT: C 314 ASP cc_start: 0.8269 (t0) cc_final: 0.7928 (t0) REVERT: C 350 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6698 (mt-10) REVERT: C 416 MET cc_start: 0.8940 (mmt) cc_final: 0.8622 (mmt) REVERT: C 431 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.7952 (ttm-80) REVERT: D 353 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6515 (mm-30) REVERT: D 412 GLU cc_start: 0.8260 (pm20) cc_final: 0.7942 (pt0) REVERT: E 258 SER cc_start: 0.9295 (t) cc_final: 0.9079 (p) REVERT: E 357 LYS cc_start: 0.8703 (mptt) cc_final: 0.8404 (mptt) REVERT: F 296 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: F 353 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7242 (mm-30) REVERT: G 258 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8777 (m) REVERT: G 273 LYS cc_start: 0.8639 (tptp) cc_final: 0.8424 (tptm) REVERT: G 295 GLU cc_start: 0.7735 (mp0) cc_final: 0.7076 (mp0) REVERT: G 343 ASP cc_start: 0.8365 (t0) cc_final: 0.8084 (t0) REVERT: G 417 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.6932 (tpt) REVERT: H 346 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7165 (ttp-110) REVERT: H 350 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: J 271 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: J 294 GLN cc_start: 0.8612 (mt0) cc_final: 0.8219 (mt0) REVERT: J 318 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8391 (mm) REVERT: J 446 ASP cc_start: 0.8166 (t0) cc_final: 0.7780 (t70) REVERT: K 276 ASN cc_start: 0.8484 (m-40) cc_final: 0.8186 (m110) REVERT: K 326 ARG cc_start: 0.4449 (OUTLIER) cc_final: 0.3720 (ptt90) REVERT: K 378 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.4807 (p90) REVERT: L 295 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: L 354 LYS cc_start: 0.6235 (mmtp) cc_final: 0.5951 (mmmt) REVERT: L 357 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6830 (ttmt) REVERT: M 253 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8409 (t0) REVERT: M 414 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8849 (mtt180) REVERT: N 345 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7675 (mm-30) REVERT: N 371 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8696 (m) REVERT: N 391 GLN cc_start: 0.8005 (mt0) cc_final: 0.7217 (mt0) REVERT: O 274 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8345 (ttpp) REVERT: O 391 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7305 (mt0) REVERT: O 417 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.6979 (tpt) REVERT: O 453 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: P 253 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8857 (t0) REVERT: P 262 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: P 268 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8094 (ptmt) REVERT: P 431 ARG cc_start: 0.8478 (ptm-80) cc_final: 0.8236 (ttp80) REVERT: R 431 ARG cc_start: 0.7400 (ttp-110) cc_final: 0.7107 (ttp-110) REVERT: T 353 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6976 (mm-30) REVERT: V 432 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7861 (mt-10) REVERT: W 276 ASN cc_start: 0.8670 (t0) cc_final: 0.8387 (m-40) REVERT: W 429 ASP cc_start: 0.7901 (p0) cc_final: 0.7695 (p0) REVERT: X 248 MET cc_start: 0.6027 (mpp) cc_final: 0.5706 (mpp) REVERT: X 268 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8009 (ttpp) REVERT: X 330 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8840 (m) REVERT: X 366 ASP cc_start: 0.4736 (OUTLIER) cc_final: 0.4368 (t0) REVERT: X 432 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: Y 256 ASP cc_start: 0.7635 (t0) cc_final: 0.7411 (t0) REVERT: Y 259 ASN cc_start: 0.8223 (m-40) cc_final: 0.7996 (t0) REVERT: Y 262 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7808 (tm-30) REVERT: Y 273 LYS cc_start: 0.8345 (ttmm) cc_final: 0.7987 (ttmt) REVERT: Y 274 LYS cc_start: 0.7923 (tttt) cc_final: 0.7612 (tttt) REVERT: Y 282 MET cc_start: 0.8771 (mmm) cc_final: 0.8100 (mmp) REVERT: Y 291 PHE cc_start: 0.5760 (m-80) cc_final: 0.5137 (m-80) REVERT: Y 296 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: Y 315 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6077 (m-10) REVERT: Y 316 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8222 (mm) REVERT: Y 356 ARG cc_start: 0.7038 (tmt170) cc_final: 0.6510 (tmt170) outliers start: 222 outliers final: 138 residues processed: 875 average time/residue: 0.2144 time to fit residues: 308.2628 Evaluate side-chains 840 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 670 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 439 LYS Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 296 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 346 ARG Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 358 ASN Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 249 LEU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 338 THR Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 262 GLU Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 454 LEU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 273 LYS Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 377 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain S residue 429 ASP Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 269 ASP Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 298 VAL Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 400 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 264 ARG Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 365 MET Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 303 ILE Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 366 ASP Chi-restraints excluded: chain X residue 432 GLU Chi-restraints excluded: chain Y residue 248 MET Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 334 ARG Chi-restraints excluded: chain Y residue 339 MET Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 435 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 195 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 450 optimal weight: 0.9990 chunk 477 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 365 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 181 optimal weight: 0.3980 chunk 182 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN H 388 ASN H 391 GLN I 296 GLN O 425 HIS ** T 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 358 ASN V 391 GLN Y 276 ASN ** Y 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117536 restraints weight = 52704.835| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.06 r_work: 0.3191 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40126 Z= 0.150 Angle : 0.539 9.136 54302 Z= 0.286 Chirality : 0.045 0.235 6326 Planarity : 0.005 0.061 7082 Dihedral : 5.224 75.379 5522 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 5.33 % Allowed : 23.87 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.29 (0.12), residues: 5033 helix: 1.43 (0.12), residues: 1873 sheet: -0.67 (0.15), residues: 1126 loop : -0.35 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 431 TYR 0.024 0.001 TYR Y 423 PHE 0.050 0.002 PHE Y 436 HIS 0.010 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00362 (40126) covalent geometry : angle 0.53925 (54302) hydrogen bonds : bond 0.03224 ( 1936) hydrogen bonds : angle 4.64343 ( 5610) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 701 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 ASN cc_start: 0.9310 (OUTLIER) cc_final: 0.9091 (t0) REVERT: A 269 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: A 348 ILE cc_start: 0.8573 (mm) cc_final: 0.8225 (mt) REVERT: A 417 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8028 (ttp) REVERT: A 448 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7358 (mtp180) REVERT: B 339 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7859 (mtt) REVERT: B 345 GLU cc_start: 0.7734 (tp30) cc_final: 0.7463 (mm-30) REVERT: C 294 GLN cc_start: 0.8620 (mt0) cc_final: 0.8387 (mm-40) REVERT: C 314 ASP cc_start: 0.8352 (t0) cc_final: 0.7982 (t0) REVERT: C 350 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6717 (mt-10) REVERT: C 407 VAL cc_start: 0.8793 (t) cc_final: 0.8588 (m) REVERT: C 416 MET cc_start: 0.8958 (mmt) cc_final: 0.8658 (mmt) REVERT: C 431 ARG cc_start: 0.8356 (tmm-80) cc_final: 0.8015 (ttm-80) REVERT: D 248 MET cc_start: 0.6065 (OUTLIER) cc_final: 0.4926 (ttp) REVERT: D 276 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8451 (t0) REVERT: D 353 GLU cc_start: 0.7065 (tm-30) cc_final: 0.6855 (mm-30) REVERT: D 357 LYS cc_start: 0.8153 (mptt) cc_final: 0.7817 (ttmt) REVERT: E 357 LYS cc_start: 0.8676 (mptt) cc_final: 0.8390 (mptt) REVERT: E 391 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.6259 (mm-40) REVERT: F 296 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: F 305 ASP cc_start: 0.2421 (OUTLIER) cc_final: 0.1782 (p0) REVERT: G 258 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8765 (m) REVERT: G 343 ASP cc_start: 0.8416 (t0) cc_final: 0.8120 (t0) REVERT: G 417 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7043 (tpt) REVERT: H 350 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: I 303 ILE cc_start: 0.8479 (mp) cc_final: 0.8194 (mt) REVERT: I 362 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.5822 (mp) REVERT: J 271 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.6975 (m-80) REVERT: J 277 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8097 (pp) REVERT: J 318 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8396 (mm) REVERT: J 446 ASP cc_start: 0.8202 (t0) cc_final: 0.7805 (t70) REVERT: K 259 ASN cc_start: 0.8532 (t0) cc_final: 0.8281 (t0) REVERT: K 276 ASN cc_start: 0.8558 (m-40) cc_final: 0.8287 (m-40) REVERT: K 326 ARG cc_start: 0.4651 (OUTLIER) cc_final: 0.3811 (ptt90) REVERT: K 378 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.4703 (p90) REVERT: L 295 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: M 253 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8496 (t0) REVERT: M 330 VAL cc_start: 0.8849 (m) cc_final: 0.8560 (t) REVERT: M 414 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8879 (mtt180) REVERT: N 345 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7775 (mm-30) REVERT: N 371 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8675 (m) REVERT: N 391 GLN cc_start: 0.8003 (mt0) cc_final: 0.7206 (mt0) REVERT: O 417 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7003 (tpt) REVERT: O 453 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: P 253 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8872 (t0) REVERT: P 262 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: R 278 LYS cc_start: 0.8213 (mmmm) cc_final: 0.7941 (mmtt) REVERT: T 353 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7168 (mm-30) REVERT: T 357 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6881 (mmtt) REVERT: U 365 MET cc_start: 0.6972 (ttt) cc_final: 0.6711 (ttp) REVERT: V 432 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7913 (mt-10) REVERT: W 276 ASN cc_start: 0.8769 (t0) cc_final: 0.8470 (m-40) REVERT: W 429 ASP cc_start: 0.8007 (p0) cc_final: 0.7791 (p0) REVERT: X 248 MET cc_start: 0.5993 (mpp) cc_final: 0.5662 (mpp) REVERT: X 330 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8869 (m) REVERT: X 366 ASP cc_start: 0.4876 (OUTLIER) cc_final: 0.4456 (t0) REVERT: X 432 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: Y 259 ASN cc_start: 0.8190 (m-40) cc_final: 0.7965 (t0) REVERT: Y 271 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: Y 273 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7969 (ttmt) REVERT: Y 274 LYS cc_start: 0.8041 (tttt) cc_final: 0.7787 (tttt) REVERT: Y 282 MET cc_start: 0.8743 (mmm) cc_final: 0.8274 (mmp) REVERT: Y 291 PHE cc_start: 0.5679 (m-80) cc_final: 0.5350 (m-80) REVERT: Y 296 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: Y 315 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.6098 (m-10) REVERT: Y 316 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8341 (mm) REVERT: Y 334 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (mtt180) REVERT: Y 382 PHE cc_start: 0.7990 (p90) cc_final: 0.7730 (p90) outliers start: 227 outliers final: 146 residues processed: 847 average time/residue: 0.2304 time to fit residues: 321.8431 Evaluate side-chains 832 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 651 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 296 GLN Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain H residue 407 VAL Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 314 ASP Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 262 GLU Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 454 LEU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 273 LYS Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 348 ILE Chi-restraints excluded: chain R residue 377 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 298 VAL Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 400 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 377 VAL Chi-restraints excluded: chain W residue 378 PHE Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 366 ASP Chi-restraints excluded: chain X residue 426 ARG Chi-restraints excluded: chain X residue 432 GLU Chi-restraints excluded: chain Y residue 248 MET Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 334 ARG Chi-restraints excluded: chain Y residue 339 MET Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 422 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 199 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 361 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 389 optimal weight: 0.3980 chunk 484 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 388 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN D 261 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 ASN O 276 ASN O 425 HIS S 267 HIS ** T 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 267 HIS Y 276 ASN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.142253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114346 restraints weight = 53175.794| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.09 r_work: 0.3129 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 40126 Z= 0.216 Angle : 0.596 9.992 54302 Z= 0.314 Chirality : 0.047 0.247 6326 Planarity : 0.005 0.063 7082 Dihedral : 5.398 77.486 5522 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 5.92 % Allowed : 23.84 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.15 (0.12), residues: 5033 helix: 1.28 (0.12), residues: 1873 sheet: -0.77 (0.14), residues: 1196 loop : -0.33 (0.15), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 264 TYR 0.025 0.001 TYR Y 418 PHE 0.060 0.002 PHE Y 436 HIS 0.014 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00534 (40126) covalent geometry : angle 0.59630 (54302) hydrogen bonds : bond 0.03582 ( 1936) hydrogen bonds : angle 4.72843 ( 5610) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 660 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: A 417 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8214 (ttp) REVERT: A 448 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7363 (mtp180) REVERT: B 339 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7895 (mtt) REVERT: B 345 GLU cc_start: 0.7693 (tp30) cc_final: 0.7481 (mm-30) REVERT: C 294 GLN cc_start: 0.8607 (mt0) cc_final: 0.8323 (mm-40) REVERT: C 314 ASP cc_start: 0.8431 (t0) cc_final: 0.7989 (t0) REVERT: C 350 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6879 (mt-10) REVERT: C 407 VAL cc_start: 0.8810 (t) cc_final: 0.8599 (m) REVERT: C 416 MET cc_start: 0.9004 (mmt) cc_final: 0.8730 (mmt) REVERT: C 431 ARG cc_start: 0.8385 (tmm-80) cc_final: 0.8044 (ttm-80) REVERT: D 248 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.5248 (ttp) REVERT: D 357 LYS cc_start: 0.8044 (mptt) cc_final: 0.7728 (ttmt) REVERT: E 337 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: E 357 LYS cc_start: 0.8757 (mptt) cc_final: 0.8536 (mptt) REVERT: E 391 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6548 (mm-40) REVERT: F 296 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: F 305 ASP cc_start: 0.2524 (OUTLIER) cc_final: 0.1856 (p0) REVERT: F 353 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7709 (mm-30) REVERT: G 258 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8750 (m) REVERT: G 343 ASP cc_start: 0.8419 (t0) cc_final: 0.8142 (t0) REVERT: G 417 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: H 346 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7363 (ttp-110) REVERT: H 350 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: H 425 HIS cc_start: 0.8086 (t-170) cc_final: 0.7527 (p90) REVERT: I 272 LEU cc_start: 0.9100 (tt) cc_final: 0.8896 (tp) REVERT: I 273 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (ttmm) REVERT: I 303 ILE cc_start: 0.8510 (mp) cc_final: 0.8274 (mt) REVERT: I 362 ILE cc_start: 0.6315 (OUTLIER) cc_final: 0.5872 (mp) REVERT: I 439 LYS cc_start: 0.8700 (tttt) cc_final: 0.8480 (tttt) REVERT: J 277 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8247 (pp) REVERT: J 318 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8349 (mp) REVERT: K 276 ASN cc_start: 0.8625 (m-40) cc_final: 0.8302 (m-40) REVERT: K 326 ARG cc_start: 0.4520 (OUTLIER) cc_final: 0.3767 (ptt90) REVERT: K 378 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.4813 (p90) REVERT: L 295 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: M 253 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8516 (t0) REVERT: M 414 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8945 (mtt180) REVERT: N 345 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7751 (mm-30) REVERT: N 371 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8594 (m) REVERT: N 391 GLN cc_start: 0.8038 (mt0) cc_final: 0.7241 (mt0) REVERT: O 417 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7251 (tpt) REVERT: O 453 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: P 253 ASN cc_start: 0.9139 (OUTLIER) cc_final: 0.8891 (t0) REVERT: P 262 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: P 268 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8290 (ptmt) REVERT: R 263 MET cc_start: 0.8958 (ttp) cc_final: 0.8690 (ttm) REVERT: R 278 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7972 (mmtt) REVERT: R 339 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7678 (mtm) REVERT: R 359 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7047 (tm-30) REVERT: S 451 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8199 (pp) REVERT: U 365 MET cc_start: 0.7288 (ttt) cc_final: 0.6940 (ttp) REVERT: V 410 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8219 (mmtp) REVERT: V 432 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7874 (mt-10) REVERT: W 248 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.6258 (ppp) REVERT: X 248 MET cc_start: 0.6048 (mpp) cc_final: 0.5706 (mpp) REVERT: X 268 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8011 (ttpp) REVERT: X 330 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8924 (m) REVERT: X 432 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: Y 262 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7700 (tm-30) REVERT: Y 271 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: Y 273 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8102 (ttmt) REVERT: Y 315 TYR cc_start: 0.6522 (OUTLIER) cc_final: 0.6006 (m-10) REVERT: Y 316 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8354 (mm) REVERT: Y 334 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7987 (mtt180) REVERT: Y 346 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.7195 (ttm-80) REVERT: Y 382 PHE cc_start: 0.8091 (p90) cc_final: 0.7812 (p90) outliers start: 252 outliers final: 169 residues processed: 831 average time/residue: 0.2110 time to fit residues: 288.8815 Evaluate side-chains 837 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 630 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 377 VAL Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 296 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 258 SER Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 349 ASN Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 259 ASN Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 346 ARG Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 273 LYS Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 362 ILE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 302 VAL Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 365 MET Chi-restraints excluded: chain J residue 417 MET Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 317 ASP Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 310 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 255 VAL Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 294 GLN Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain N residue 451 LEU Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 268 LYS Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 313 ARG Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 392 SER Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 262 GLU Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 283 SER Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain P residue 454 LEU Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 273 LYS Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 348 ILE Chi-restraints excluded: chain R residue 377 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain S residue 429 ASP Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain T residue 328 LEU Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 298 VAL Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 348 ILE Chi-restraints excluded: chain V residue 400 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 248 MET Chi-restraints excluded: chain W residue 264 ARG Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 377 VAL Chi-restraints excluded: chain W residue 378 PHE Chi-restraints excluded: chain W residue 384 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 432 GLU Chi-restraints excluded: chain Y residue 248 MET Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 334 ARG Chi-restraints excluded: chain Y residue 339 MET Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 428 ILE Chi-restraints excluded: chain Y residue 435 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 377 optimal weight: 0.8980 chunk 416 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 479 optimal weight: 0.7980 chunk 343 optimal weight: 2.9990 chunk 489 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 319 optimal weight: 4.9990 chunk 494 optimal weight: 0.0770 chunk 299 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN D 276 ASN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 267 HIS J 358 ASN O 425 HIS Y 261 GLN Y 276 ASN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117956 restraints weight = 52580.795| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.11 r_work: 0.3222 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40126 Z= 0.121 Angle : 0.521 9.159 54302 Z= 0.276 Chirality : 0.044 0.206 6326 Planarity : 0.004 0.064 7082 Dihedral : 5.202 81.818 5522 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.22 % Favored : 96.68 % Rotamer: Outliers : 4.49 % Allowed : 25.42 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.45 (0.12), residues: 5033 helix: 1.61 (0.12), residues: 1872 sheet: -0.64 (0.15), residues: 1204 loop : -0.25 (0.15), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 326 TYR 0.011 0.001 TYR J 315 PHE 0.058 0.002 PHE Y 436 HIS 0.010 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00288 (40126) covalent geometry : angle 0.52099 (54302) hydrogen bonds : bond 0.02941 ( 1936) hydrogen bonds : angle 4.49668 ( 5610) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 673 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8337 (m-30) REVERT: A 273 LYS cc_start: 0.8174 (ttpp) cc_final: 0.7856 (mmmm) REVERT: A 448 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7497 (mtp180) REVERT: B 248 MET cc_start: 0.7057 (tpt) cc_final: 0.6810 (tpp) REVERT: B 339 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7948 (mtt) REVERT: B 345 GLU cc_start: 0.7547 (tp30) cc_final: 0.7334 (mm-30) REVERT: C 314 ASP cc_start: 0.8361 (t0) cc_final: 0.7967 (t0) REVERT: C 350 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7020 (mt-10) REVERT: C 353 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6490 (mm-30) REVERT: C 407 VAL cc_start: 0.8807 (t) cc_final: 0.8583 (m) REVERT: C 416 MET cc_start: 0.8898 (mmt) cc_final: 0.8607 (mmt) REVERT: C 431 ARG cc_start: 0.8379 (tmm-80) cc_final: 0.8003 (ttm-80) REVERT: D 248 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5193 (ttp) REVERT: D 357 LYS cc_start: 0.7917 (mptt) cc_final: 0.7695 (ttmt) REVERT: D 391 GLN cc_start: 0.8013 (mp10) cc_final: 0.7729 (mt0) REVERT: E 337 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: E 357 LYS cc_start: 0.8618 (mptt) cc_final: 0.8415 (mptt) REVERT: E 391 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6251 (mm-40) REVERT: F 305 ASP cc_start: 0.2305 (OUTLIER) cc_final: 0.1642 (p0) REVERT: G 330 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8196 (t) REVERT: G 343 ASP cc_start: 0.8327 (t0) cc_final: 0.8081 (t0) REVERT: G 417 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.6891 (tpt) REVERT: G 429 ASP cc_start: 0.7751 (t70) cc_final: 0.7503 (t0) REVERT: H 425 HIS cc_start: 0.7945 (t-170) cc_final: 0.7532 (p90) REVERT: I 272 LEU cc_start: 0.9105 (tt) cc_final: 0.8892 (tp) REVERT: I 303 ILE cc_start: 0.8399 (mp) cc_final: 0.8199 (mt) REVERT: J 277 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8234 (pp) REVERT: J 318 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8456 (mm) REVERT: J 359 GLU cc_start: 0.7719 (pt0) cc_final: 0.7463 (pm20) REVERT: J 446 ASP cc_start: 0.8198 (t0) cc_final: 0.7798 (t70) REVERT: K 248 MET cc_start: 0.6855 (ptm) cc_final: 0.6596 (ppp) REVERT: K 276 ASN cc_start: 0.8544 (m-40) cc_final: 0.8280 (m-40) REVERT: K 326 ARG cc_start: 0.4617 (OUTLIER) cc_final: 0.3890 (ptt90) REVERT: K 378 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.4696 (p90) REVERT: L 295 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: L 314 ASP cc_start: 0.7088 (p0) cc_final: 0.6332 (m-30) REVERT: M 253 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8500 (t0) REVERT: M 414 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8854 (mtt180) REVERT: N 345 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7576 (mm-30) REVERT: N 371 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8665 (m) REVERT: N 391 GLN cc_start: 0.7951 (mt0) cc_final: 0.7177 (mt0) REVERT: O 296 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: O 326 ARG cc_start: 0.6483 (ttm-80) cc_final: 0.6216 (ttp-110) REVERT: O 417 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7108 (tpt) REVERT: O 453 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: P 253 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8870 (t0) REVERT: P 350 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: P 431 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8405 (ttt-90) REVERT: R 263 MET cc_start: 0.8885 (ttp) cc_final: 0.8613 (ttm) REVERT: R 278 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7970 (mmtt) REVERT: R 295 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: R 359 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7064 (tm-30) REVERT: S 431 ARG cc_start: 0.8440 (ttp80) cc_final: 0.7867 (ttm-80) REVERT: T 282 MET cc_start: 0.8599 (mmm) cc_final: 0.8298 (tpt) REVERT: T 294 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (mm-40) REVERT: U 350 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7255 (pt0) REVERT: U 365 MET cc_start: 0.7182 (ttt) cc_final: 0.6870 (ttp) REVERT: V 432 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7760 (mt-10) REVERT: W 429 ASP cc_start: 0.7906 (p0) cc_final: 0.7691 (p0) REVERT: X 248 MET cc_start: 0.6282 (mpp) cc_final: 0.5922 (mpp) REVERT: X 268 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7851 (ttpp) REVERT: X 330 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8903 (m) REVERT: X 438 ARG cc_start: 0.8786 (mtp85) cc_final: 0.8413 (mtp180) REVERT: Y 271 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.5990 (m-80) REVERT: Y 273 LYS cc_start: 0.8278 (ttmm) cc_final: 0.7972 (ttmt) REVERT: Y 296 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: Y 315 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.5927 (m-10) REVERT: Y 316 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8385 (mm) REVERT: Y 356 ARG cc_start: 0.6923 (ttt-90) cc_final: 0.6246 (ttt180) REVERT: Y 382 PHE cc_start: 0.7783 (p90) cc_final: 0.7522 (p90) REVERT: Y 414 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7378 (tpt170) REVERT: Y 441 LYS cc_start: 0.9015 (tppt) cc_final: 0.8734 (tptt) outliers start: 191 outliers final: 121 residues processed: 794 average time/residue: 0.2171 time to fit residues: 284.4672 Evaluate side-chains 773 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 621 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 381 LEU Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 417 MET Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 GLN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 253 ASN Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 273 LYS Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain T residue 294 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 314 ASP Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 348 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 248 MET Chi-restraints excluded: chain W residue 264 ARG Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 378 PHE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 339 MET Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 388 ASN Chi-restraints excluded: chain Y residue 395 LEU Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 435 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 220 optimal weight: 3.9990 chunk 194 optimal weight: 0.0570 chunk 350 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 444 optimal weight: 4.9990 chunk 300 optimal weight: 0.0770 chunk 80 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 448 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN E 425 HIS H 388 ASN I 296 GLN V 425 HIS W 296 GLN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118188 restraints weight = 52677.592| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.08 r_work: 0.3236 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40126 Z= 0.117 Angle : 0.521 9.207 54302 Z= 0.275 Chirality : 0.044 0.235 6326 Planarity : 0.004 0.066 7082 Dihedral : 5.113 84.594 5520 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 4.11 % Allowed : 25.70 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.57 (0.12), residues: 5033 helix: 1.74 (0.12), residues: 1870 sheet: -0.58 (0.15), residues: 1153 loop : -0.22 (0.15), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Y 334 TYR 0.011 0.001 TYR Y 423 PHE 0.052 0.002 PHE Y 436 HIS 0.012 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00280 (40126) covalent geometry : angle 0.52079 (54302) hydrogen bonds : bond 0.02876 ( 1936) hydrogen bonds : angle 4.41883 ( 5610) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 655 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7901 (mmmm) REVERT: A 417 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8103 (ttp) REVERT: A 448 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7608 (mtp180) REVERT: B 339 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7933 (mtt) REVERT: B 345 GLU cc_start: 0.7581 (tp30) cc_final: 0.7359 (mm-30) REVERT: B 438 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8322 (mmm-85) REVERT: C 314 ASP cc_start: 0.8393 (t0) cc_final: 0.7999 (t0) REVERT: C 350 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7004 (mt-10) REVERT: C 353 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: C 407 VAL cc_start: 0.8807 (t) cc_final: 0.8595 (m) REVERT: C 416 MET cc_start: 0.8869 (mmt) cc_final: 0.8581 (mmt) REVERT: C 431 ARG cc_start: 0.8378 (tmm-80) cc_final: 0.7990 (ttm-80) REVERT: D 282 MET cc_start: 0.8353 (tpp) cc_final: 0.8105 (tpt) REVERT: D 391 GLN cc_start: 0.7931 (mp10) cc_final: 0.7700 (mt0) REVERT: E 337 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: E 357 LYS cc_start: 0.8583 (mptt) cc_final: 0.8377 (mptt) REVERT: E 391 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6322 (mm-40) REVERT: F 305 ASP cc_start: 0.2312 (OUTLIER) cc_final: 0.1647 (p0) REVERT: G 330 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8223 (t) REVERT: G 343 ASP cc_start: 0.8363 (t0) cc_final: 0.8107 (t0) REVERT: G 417 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.6971 (tpt) REVERT: G 429 ASP cc_start: 0.7757 (t70) cc_final: 0.7524 (t0) REVERT: H 350 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: H 425 HIS cc_start: 0.7947 (t-170) cc_final: 0.7530 (p90) REVERT: J 277 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8184 (pp) REVERT: J 318 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8435 (mm) REVERT: J 446 ASP cc_start: 0.8200 (t0) cc_final: 0.7784 (t70) REVERT: K 248 MET cc_start: 0.6823 (ptm) cc_final: 0.6617 (ppp) REVERT: K 276 ASN cc_start: 0.8515 (m-40) cc_final: 0.8227 (m-40) REVERT: K 326 ARG cc_start: 0.4701 (OUTLIER) cc_final: 0.3979 (ptt90) REVERT: K 378 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.4681 (p90) REVERT: L 295 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: L 314 ASP cc_start: 0.7159 (p0) cc_final: 0.6423 (m-30) REVERT: M 253 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8550 (t0) REVERT: M 326 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7658 (ttp80) REVERT: M 330 VAL cc_start: 0.8892 (m) cc_final: 0.8645 (t) REVERT: M 414 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8836 (mtt180) REVERT: M 453 ASP cc_start: 0.8571 (t0) cc_final: 0.8213 (t0) REVERT: N 345 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7583 (mm-30) REVERT: N 371 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8694 (m) REVERT: N 391 GLN cc_start: 0.7953 (mt0) cc_final: 0.7202 (mt0) REVERT: O 296 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7834 (mt0) REVERT: O 417 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7160 (tpt) REVERT: O 453 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: P 350 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: P 431 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8408 (ttt-90) REVERT: R 263 MET cc_start: 0.8864 (ttp) cc_final: 0.8639 (ttm) REVERT: R 278 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7968 (mmtt) REVERT: R 295 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: R 359 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7102 (tm-30) REVERT: S 431 ARG cc_start: 0.8441 (ttp80) cc_final: 0.7891 (ttm-80) REVERT: T 294 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8525 (mm-40) REVERT: T 345 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7760 (mm-30) REVERT: T 353 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7399 (mm-30) REVERT: U 365 MET cc_start: 0.7204 (ttt) cc_final: 0.6906 (ttp) REVERT: V 282 MET cc_start: 0.8653 (mmm) cc_final: 0.8420 (tpt) REVERT: V 366 ASP cc_start: 0.6992 (p0) cc_final: 0.6726 (t70) REVERT: V 417 MET cc_start: 0.8863 (ttm) cc_final: 0.8422 (mtm) REVERT: W 429 ASP cc_start: 0.7939 (p0) cc_final: 0.7729 (p0) REVERT: X 248 MET cc_start: 0.6325 (mpp) cc_final: 0.5997 (mpp) REVERT: X 268 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7926 (ttpp) REVERT: X 330 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8895 (m) REVERT: X 438 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8417 (mtp180) REVERT: Y 271 PHE cc_start: 0.8080 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: Y 273 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7946 (ttmt) REVERT: Y 296 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: Y 315 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5961 (m-10) REVERT: Y 316 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8373 (mm) REVERT: Y 356 ARG cc_start: 0.6876 (ttt-90) cc_final: 0.6239 (ttt180) REVERT: Y 382 PHE cc_start: 0.7868 (p90) cc_final: 0.7605 (p90) REVERT: Y 426 ARG cc_start: 0.7757 (ttt90) cc_final: 0.7481 (ttt-90) REVERT: Y 441 LYS cc_start: 0.9016 (tppt) cc_final: 0.8710 (tptt) outliers start: 175 outliers final: 127 residues processed: 767 average time/residue: 0.2243 time to fit residues: 283.0776 Evaluate side-chains 773 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 615 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 295 GLU Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 296 GLN Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 417 MET Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain M residue 428 ILE Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 GLN Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain T residue 294 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 273 LYS Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 248 MET Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 296 GLN Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 395 LEU Chi-restraints excluded: chain Y residue 422 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 348 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 437 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 341 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** D 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 HIS H 388 ASN V 425 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.115795 restraints weight = 53023.643| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.06 r_work: 0.3202 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 40126 Z= 0.167 Angle : 0.556 10.070 54302 Z= 0.292 Chirality : 0.045 0.222 6326 Planarity : 0.005 0.068 7082 Dihedral : 5.216 84.074 5518 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.62 % Favored : 96.30 % Rotamer: Outliers : 4.42 % Allowed : 25.30 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.47 (0.12), residues: 5033 helix: 1.61 (0.12), residues: 1874 sheet: -0.59 (0.15), residues: 1220 loop : -0.23 (0.15), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 264 TYR 0.017 0.001 TYR Y 423 PHE 0.053 0.002 PHE Y 436 HIS 0.014 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00416 (40126) covalent geometry : angle 0.55560 (54302) hydrogen bonds : bond 0.03160 ( 1936) hydrogen bonds : angle 4.49228 ( 5610) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 633 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: A 273 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7984 (mmmm) REVERT: A 417 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: A 448 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: B 339 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7979 (mtt) REVERT: B 345 GLU cc_start: 0.7622 (tp30) cc_final: 0.7405 (mm-30) REVERT: B 438 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8350 (mmm-85) REVERT: C 314 ASP cc_start: 0.8427 (t0) cc_final: 0.8043 (t0) REVERT: C 350 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7061 (mt-10) REVERT: C 353 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6619 (mm-30) REVERT: C 407 VAL cc_start: 0.8863 (t) cc_final: 0.8662 (m) REVERT: C 416 MET cc_start: 0.8928 (mmt) cc_final: 0.8642 (mmt) REVERT: C 431 ARG cc_start: 0.8397 (tmm-80) cc_final: 0.8150 (ttm-80) REVERT: D 282 MET cc_start: 0.8380 (tpp) cc_final: 0.8163 (tpt) REVERT: D 391 GLN cc_start: 0.8009 (mp10) cc_final: 0.7750 (mt0) REVERT: E 337 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8265 (pt0) REVERT: E 357 LYS cc_start: 0.8627 (mptt) cc_final: 0.8405 (mptt) REVERT: E 391 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6519 (mm-40) REVERT: F 305 ASP cc_start: 0.2436 (OUTLIER) cc_final: 0.1758 (p0) REVERT: G 330 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8255 (t) REVERT: G 343 ASP cc_start: 0.8377 (t0) cc_final: 0.8134 (t0) REVERT: G 417 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.6921 (tpt) REVERT: G 429 ASP cc_start: 0.7784 (t70) cc_final: 0.7549 (t0) REVERT: H 350 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: H 425 HIS cc_start: 0.7929 (t-170) cc_final: 0.7502 (p90) REVERT: I 272 LEU cc_start: 0.9105 (tt) cc_final: 0.8891 (tp) REVERT: J 277 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8214 (pp) REVERT: J 318 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8298 (mp) REVERT: K 248 MET cc_start: 0.7058 (ptm) cc_final: 0.6599 (ppp) REVERT: K 276 ASN cc_start: 0.8527 (m-40) cc_final: 0.8210 (m-40) REVERT: K 326 ARG cc_start: 0.4896 (OUTLIER) cc_final: 0.3868 (ptt90) REVERT: K 357 LYS cc_start: 0.8326 (mptt) cc_final: 0.8121 (ttpp) REVERT: K 378 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.4716 (p90) REVERT: L 248 MET cc_start: 0.7355 (mmm) cc_final: 0.6000 (ttt) REVERT: L 295 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: L 314 ASP cc_start: 0.7283 (p0) cc_final: 0.6547 (m-30) REVERT: M 253 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8537 (t0) REVERT: M 326 ARG cc_start: 0.7944 (ttp80) cc_final: 0.6660 (ttt-90) REVERT: M 414 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8858 (mtt180) REVERT: M 453 ASP cc_start: 0.8605 (t0) cc_final: 0.8338 (t0) REVERT: N 345 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7616 (mm-30) REVERT: N 371 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8677 (m) REVERT: N 391 GLN cc_start: 0.7967 (mt0) cc_final: 0.7204 (mt0) REVERT: O 296 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7875 (mt0) REVERT: O 417 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7174 (tpt) REVERT: O 453 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: P 350 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: P 431 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8446 (ttt-90) REVERT: R 263 MET cc_start: 0.8886 (ttp) cc_final: 0.8678 (ttm) REVERT: R 278 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7963 (mmtt) REVERT: R 295 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: R 359 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7127 (tm-30) REVERT: S 282 MET cc_start: 0.8103 (mmm) cc_final: 0.7796 (tpp) REVERT: S 431 ARG cc_start: 0.8480 (ttp80) cc_final: 0.7966 (ttm-80) REVERT: S 451 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8151 (pp) REVERT: U 365 MET cc_start: 0.7314 (ttt) cc_final: 0.7065 (ttp) REVERT: V 366 ASP cc_start: 0.7034 (p0) cc_final: 0.6744 (t70) REVERT: V 417 MET cc_start: 0.8953 (ttm) cc_final: 0.8580 (mtm) REVERT: W 278 LYS cc_start: 0.8331 (ptpt) cc_final: 0.7993 (mmtt) REVERT: W 429 ASP cc_start: 0.7906 (p0) cc_final: 0.7703 (p0) REVERT: X 248 MET cc_start: 0.6345 (mpp) cc_final: 0.6027 (mpp) REVERT: X 268 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.7935 (ttpp) REVERT: X 330 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8942 (m) REVERT: X 438 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8409 (mtp180) REVERT: Y 262 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7588 (tm-30) REVERT: Y 271 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: Y 273 LYS cc_start: 0.8345 (ttmm) cc_final: 0.8022 (ttmt) REVERT: Y 296 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7945 (pt0) REVERT: Y 315 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: Y 316 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (mm) REVERT: Y 382 PHE cc_start: 0.7913 (p90) cc_final: 0.7628 (p90) REVERT: Y 414 ARG cc_start: 0.7961 (ttt180) cc_final: 0.7245 (tpt170) REVERT: Y 426 ARG cc_start: 0.7812 (ttt90) cc_final: 0.7608 (ttt-90) outliers start: 188 outliers final: 134 residues processed: 750 average time/residue: 0.2318 time to fit residues: 286.3604 Evaluate side-chains 790 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 624 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 294 GLN Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 295 GLU Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain H residue 388 ASN Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 365 MET Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 417 MET Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 GLN Chi-restraints excluded: chain O residue 311 VAL Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 309 GLU Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 360 LEU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 317 ASP Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 263 MET Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 330 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 397 MET Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 281 PHE Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 348 ILE Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 248 MET Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 422 THR Chi-restraints excluded: chain Y residue 435 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 255 optimal weight: 0.5980 chunk 435 optimal weight: 0.9990 chunk 429 optimal weight: 3.9990 chunk 391 optimal weight: 0.7980 chunk 462 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 395 optimal weight: 0.0270 chunk 411 optimal weight: 3.9990 chunk 398 optimal weight: 4.9990 chunk 485 optimal weight: 9.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN E 425 HIS H 388 ASN J 358 ASN T 294 GLN W 296 GLN ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117939 restraints weight = 52626.864| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.10 r_work: 0.3224 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 40126 Z= 0.119 Angle : 0.530 12.168 54302 Z= 0.279 Chirality : 0.044 0.231 6326 Planarity : 0.005 0.070 7082 Dihedral : 5.158 87.294 5518 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 4.16 % Allowed : 25.63 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.57 (0.12), residues: 5033 helix: 1.74 (0.12), residues: 1874 sheet: -0.58 (0.15), residues: 1224 loop : -0.19 (0.15), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 448 TYR 0.026 0.001 TYR Y 423 PHE 0.054 0.002 PHE Y 436 HIS 0.018 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00287 (40126) covalent geometry : angle 0.53011 (54302) hydrogen bonds : bond 0.02885 ( 1936) hydrogen bonds : angle 4.39804 ( 5610) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10066 Ramachandran restraints generated. 5033 Oldfield, 0 Emsley, 5033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 652 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8255 (ttpp) cc_final: 0.8030 (mmmm) REVERT: A 417 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: A 448 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: B 339 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7978 (mtt) REVERT: B 438 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8338 (mmm-85) REVERT: C 314 ASP cc_start: 0.8368 (t0) cc_final: 0.8011 (t0) REVERT: C 350 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6963 (mt-10) REVERT: C 353 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: C 407 VAL cc_start: 0.8863 (t) cc_final: 0.8661 (m) REVERT: C 416 MET cc_start: 0.8896 (mmt) cc_final: 0.8620 (mmm) REVERT: C 431 ARG cc_start: 0.8376 (tmm-80) cc_final: 0.8020 (ttm-80) REVERT: D 248 MET cc_start: 0.5922 (mmp) cc_final: 0.5330 (ttm) REVERT: D 282 MET cc_start: 0.8298 (tpp) cc_final: 0.8094 (tpt) REVERT: D 357 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7809 (ttmt) REVERT: E 337 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: E 391 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6488 (mm-40) REVERT: F 305 ASP cc_start: 0.2430 (OUTLIER) cc_final: 0.1762 (p0) REVERT: G 330 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (t) REVERT: G 343 ASP cc_start: 0.8361 (t0) cc_final: 0.8127 (t0) REVERT: G 417 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7012 (tpt) REVERT: G 429 ASP cc_start: 0.7768 (t70) cc_final: 0.7535 (t0) REVERT: H 350 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: H 425 HIS cc_start: 0.7874 (t-170) cc_final: 0.7515 (p90) REVERT: I 272 LEU cc_start: 0.9127 (tt) cc_final: 0.8924 (tp) REVERT: I 357 LYS cc_start: 0.7603 (mmtp) cc_final: 0.7325 (mttt) REVERT: J 277 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8202 (pp) REVERT: J 318 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8407 (mm) REVERT: K 248 MET cc_start: 0.6968 (ptm) cc_final: 0.6531 (ppp) REVERT: K 276 ASN cc_start: 0.8493 (m-40) cc_final: 0.8166 (m-40) REVERT: K 326 ARG cc_start: 0.4848 (OUTLIER) cc_final: 0.4017 (ptt90) REVERT: K 378 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.4890 (p90) REVERT: L 248 MET cc_start: 0.7319 (mmm) cc_final: 0.5991 (ttt) REVERT: L 295 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: L 314 ASP cc_start: 0.7316 (p0) cc_final: 0.6571 (m-30) REVERT: L 417 MET cc_start: 0.8035 (ttt) cc_final: 0.7401 (ttt) REVERT: M 253 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8534 (t0) REVERT: M 326 ARG cc_start: 0.7839 (ttp80) cc_final: 0.6782 (ttt-90) REVERT: M 414 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8858 (mmt90) REVERT: M 453 ASP cc_start: 0.8622 (t0) cc_final: 0.8385 (t0) REVERT: N 345 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7580 (mm-30) REVERT: N 371 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8693 (m) REVERT: N 391 GLN cc_start: 0.7919 (mt0) cc_final: 0.7187 (mt0) REVERT: O 296 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: O 417 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7159 (tpt) REVERT: O 453 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: P 350 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: P 431 ARG cc_start: 0.8651 (ttp80) cc_final: 0.8420 (ttt-90) REVERT: R 278 LYS cc_start: 0.8238 (mmmm) cc_final: 0.7972 (mmtt) REVERT: R 295 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: R 359 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7111 (tm-30) REVERT: S 431 ARG cc_start: 0.8478 (ttp80) cc_final: 0.7988 (ttm-80) REVERT: S 451 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8131 (pp) REVERT: U 330 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8469 (p) REVERT: U 350 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7287 (pt0) REVERT: U 365 MET cc_start: 0.7263 (ttt) cc_final: 0.7004 (ttp) REVERT: V 366 ASP cc_start: 0.7014 (p0) cc_final: 0.6729 (t70) REVERT: V 417 MET cc_start: 0.8876 (ttm) cc_final: 0.8495 (mtm) REVERT: W 278 LYS cc_start: 0.8272 (ptpt) cc_final: 0.8007 (mmtt) REVERT: W 429 ASP cc_start: 0.7923 (p0) cc_final: 0.7705 (p0) REVERT: X 248 MET cc_start: 0.6348 (mpp) cc_final: 0.6039 (mpp) REVERT: X 268 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7917 (ttpp) REVERT: X 330 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8930 (m) REVERT: X 438 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8277 (mtp180) REVERT: Y 262 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7603 (tm-30) REVERT: Y 271 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: Y 273 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7889 (ttmt) REVERT: Y 296 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7901 (pt0) REVERT: Y 315 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5937 (m-10) REVERT: Y 316 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8307 (mm) REVERT: Y 343 ASP cc_start: 0.5390 (m-30) cc_final: 0.4672 (m-30) REVERT: Y 356 ARG cc_start: 0.6852 (ttt-90) cc_final: 0.6211 (ttt180) REVERT: Y 382 PHE cc_start: 0.7822 (p90) cc_final: 0.7579 (p90) REVERT: Y 441 LYS cc_start: 0.9040 (tppt) cc_final: 0.8699 (tptt) outliers start: 177 outliers final: 127 residues processed: 765 average time/residue: 0.2523 time to fit residues: 317.2269 Evaluate side-chains 785 residues out of total 4257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 626 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 365 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 429 ASP Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 391 GLN Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 438 ARG Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 417 MET Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 296 GLN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain E residue 294 GLN Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 358 ASN Chi-restraints excluded: chain E residue 391 GLN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 302 VAL Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 378 PHE Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 296 GLN Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 417 MET Chi-restraints excluded: chain H residue 295 GLU Chi-restraints excluded: chain H residue 319 SER Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain H residue 366 ASP Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 371 THR Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 271 PHE Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 318 ILE Chi-restraints excluded: chain J residue 319 SER Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 358 ASN Chi-restraints excluded: chain J residue 392 SER Chi-restraints excluded: chain J residue 417 MET Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain K residue 326 ARG Chi-restraints excluded: chain K residue 377 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain K residue 439 LYS Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 295 GLU Chi-restraints excluded: chain L residue 298 VAL Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 397 MET Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 262 GLU Chi-restraints excluded: chain M residue 414 ARG Chi-restraints excluded: chain N residue 272 LEU Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 371 THR Chi-restraints excluded: chain N residue 377 VAL Chi-restraints excluded: chain O residue 262 GLU Chi-restraints excluded: chain O residue 281 PHE Chi-restraints excluded: chain O residue 296 GLN Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 330 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 417 MET Chi-restraints excluded: chain O residue 453 ASP Chi-restraints excluded: chain P residue 244 ASN Chi-restraints excluded: chain P residue 263 MET Chi-restraints excluded: chain P residue 350 GLU Chi-restraints excluded: chain P residue 369 THR Chi-restraints excluded: chain P residue 373 SER Chi-restraints excluded: chain R residue 246 CYS Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 294 GLN Chi-restraints excluded: chain R residue 295 GLU Chi-restraints excluded: chain R residue 311 VAL Chi-restraints excluded: chain R residue 339 MET Chi-restraints excluded: chain R residue 345 GLU Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 263 MET Chi-restraints excluded: chain S residue 294 GLN Chi-restraints excluded: chain S residue 310 VAL Chi-restraints excluded: chain S residue 324 THR Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain S residue 386 ILE Chi-restraints excluded: chain S residue 411 VAL Chi-restraints excluded: chain S residue 451 LEU Chi-restraints excluded: chain T residue 333 ILE Chi-restraints excluded: chain T residue 397 MET Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain U residue 319 SER Chi-restraints excluded: chain U residue 330 VAL Chi-restraints excluded: chain U residue 351 LEU Chi-restraints excluded: chain U residue 449 VAL Chi-restraints excluded: chain V residue 250 THR Chi-restraints excluded: chain V residue 281 PHE Chi-restraints excluded: chain V residue 313 ARG Chi-restraints excluded: chain V residue 316 ILE Chi-restraints excluded: chain V residue 324 THR Chi-restraints excluded: chain V residue 428 ILE Chi-restraints excluded: chain W residue 248 MET Chi-restraints excluded: chain W residue 281 PHE Chi-restraints excluded: chain W residue 303 ILE Chi-restraints excluded: chain W residue 317 ASP Chi-restraints excluded: chain W residue 324 THR Chi-restraints excluded: chain W residue 369 THR Chi-restraints excluded: chain W residue 387 ILE Chi-restraints excluded: chain W residue 394 ILE Chi-restraints excluded: chain W residue 412 GLU Chi-restraints excluded: chain W residue 416 MET Chi-restraints excluded: chain W residue 417 MET Chi-restraints excluded: chain X residue 268 LYS Chi-restraints excluded: chain X residue 330 VAL Chi-restraints excluded: chain X residue 421 LEU Chi-restraints excluded: chain Y residue 271 PHE Chi-restraints excluded: chain Y residue 276 ASN Chi-restraints excluded: chain Y residue 296 GLN Chi-restraints excluded: chain Y residue 311 VAL Chi-restraints excluded: chain Y residue 315 TYR Chi-restraints excluded: chain Y residue 316 ILE Chi-restraints excluded: chain Y residue 333 ILE Chi-restraints excluded: chain Y residue 384 THR Chi-restraints excluded: chain Y residue 422 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 235 optimal weight: 2.9990 chunk 416 optimal weight: 0.0770 chunk 440 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 494 optimal weight: 0.6980 chunk 275 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 261 optimal weight: 1.9990 chunk 498 optimal weight: 0.5980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN E 425 HIS H 388 ASN J 358 ASN ** P 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 294 GLN U 267 HIS ** Y 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119344 restraints weight = 52684.781| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.07 r_work: 0.3239 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 40126 Z= 0.108 Angle : 0.525 12.230 54302 Z= 0.276 Chirality : 0.043 0.227 6326 Planarity : 0.005 0.082 7082 Dihedral : 5.117 89.698 5518 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 3.85 % Allowed : 25.96 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.65 % Cis-general : 0.02 % 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 aren not related in a simple way. whole: 0.66 (0.12), residues: 5033 helix: 1.83 (0.12), residues: 1866 sheet: -0.52 (0.15), residues: 1251 loop : -0.17 (0.15), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Y 334 TYR 0.023 0.001 TYR Y 423 PHE 0.054 0.002 PHE Y 436 HIS 0.017 0.001 HIS Y 275 Details of bonding type rmsd covalent geometry : bond 0.00257 (40126) covalent geometry : angle 0.52486 (54302) hydrogen bonds : bond 0.02787 ( 1936) hydrogen bonds : angle 4.33627 ( 5610) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12230.33 seconds wall clock time: 209 minutes 4.08 seconds (12544.08 seconds total)