Starting phenix.real_space_refine on Thu Mar 5 09:05:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.map" model { file = "/net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh3_10192/03_2026/6sh3_10192.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 112 5.16 5 C 13412 2.51 5 N 3584 2.21 5 O 3899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21021 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2976 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 358} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.50, per 1000 atoms: 0.21 Number of scatterers: 21021 At special positions: 0 Unit cell: (157.791, 155.673, 132.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 14 15.00 O 3899 8.00 N 3584 7.00 C 13412 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: 1.80 Conformation dependent library (CDL) restraints added in 995.9 milliseconds 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4858 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 45.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 removed outlier: 3.515A pdb=" N LYS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 199 removed outlier: 4.182A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.640A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.684A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.818A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.839A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 removed outlier: 3.515A pdb=" N LYS B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 199 removed outlier: 4.182A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.640A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.684A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.818A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.839A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 removed outlier: 3.515A pdb=" N LYS C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 199 removed outlier: 4.182A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.639A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.683A pdb=" N ARG C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.818A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.840A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 82 removed outlier: 3.835A pdb=" N GLY D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 removed outlier: 3.515A pdb=" N LYS D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 199 removed outlier: 4.183A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.640A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.683A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.817A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.840A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU D 395 " --> pdb=" O PRO D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.066A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 106 removed outlier: 3.515A pdb=" N LYS E 105 " --> pdb=" O THR E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 199 removed outlier: 4.182A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.639A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.684A pdb=" N ARG E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.819A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.839A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 411 " --> pdb=" O ASP E 407 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 81 removed outlier: 3.835A pdb=" N GLY F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.516A pdb=" N LYS F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 199 removed outlier: 4.181A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.639A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.684A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.818A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.839A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU F 395 " --> pdb=" O PRO F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS F 411 " --> pdb=" O ASP F 407 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.582A pdb=" N ALA F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 82 removed outlier: 3.834A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE G 73 " --> pdb=" O ARG G 69 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL G 78 " --> pdb=" O LYS G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 removed outlier: 3.515A pdb=" N LYS G 105 " --> pdb=" O THR G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 199 removed outlier: 4.182A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 199 " --> pdb=" O ALA G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.639A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 246 Processing helix chain 'G' and resid 248 through 255 removed outlier: 3.683A pdb=" N ARG G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 284 Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.819A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.839A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 390 through 402 removed outlier: 3.522A pdb=" N GLU G 395 " --> pdb=" O PRO G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 417 removed outlier: 4.065A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS G 411 " --> pdb=" O ASP G 407 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.581A pdb=" N ALA G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.668A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 152 " --> pdb=" O HIS A 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP A 142 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 110 " --> pdb=" O TRP A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.335A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 206 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN A 292 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER A 208 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER A 314 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE A 361 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 316 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A 363 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 318 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE A 380 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.668A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 152 " --> pdb=" O HIS B 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP B 142 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 110 " --> pdb=" O TRP B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.335A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 206 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ASN B 292 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER B 208 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER B 314 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N PHE B 361 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 316 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR B 363 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 318 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE B 380 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 4.669A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 152 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 142 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 110 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.336A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 206 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN C 292 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N SER C 208 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER C 314 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE C 361 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU C 316 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR C 363 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU C 318 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE C 380 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.668A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 152 " --> pdb=" O HIS D 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP D 142 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 110 " --> pdb=" O TRP D 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.335A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR D 206 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN D 292 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER D 208 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER D 314 " --> pdb=" O ILE D 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE D 361 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU D 316 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR D 363 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU D 318 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE D 380 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.668A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE E 152 " --> pdb=" O HIS E 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP E 142 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 110 " --> pdb=" O TRP E 142 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 115 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.335A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR E 206 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN E 292 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER E 208 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER E 314 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N PHE E 361 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU E 316 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR E 363 " --> pdb=" O LEU E 316 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU E 318 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE E 380 " --> pdb=" O ARG E 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.669A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 152 " --> pdb=" O HIS F 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP F 142 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 110 " --> pdb=" O TRP F 142 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.334A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR F 206 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN F 292 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N SER F 208 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N SER F 314 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE F 361 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU F 316 " --> pdb=" O PHE F 361 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR F 363 " --> pdb=" O LEU F 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU F 318 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE F 380 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 87 through 90 removed outlier: 4.668A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE G 152 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TRP G 142 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 110 " --> pdb=" O TRP G 142 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.335A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR G 206 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASN G 292 " --> pdb=" O TYR G 206 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N SER G 208 " --> pdb=" O ASN G 292 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N SER G 314 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE G 361 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU G 316 " --> pdb=" O PHE G 361 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N THR G 363 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU G 318 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ILE G 380 " --> pdb=" O ARG G 260 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2514 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: 2.84 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6589 1.34 - 1.46: 3931 1.46 - 1.57: 10725 1.57 - 1.69: 21 1.69 - 1.81: 210 Bond restraints: 21476 Sorted by residual: bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP D 501 " pdb=" C5 ADP D 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 21471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 28138 2.17 - 4.34: 714 4.34 - 6.52: 79 6.52 - 8.69: 71 8.69 - 10.86: 27 Bond angle restraints: 29029 Sorted by residual: angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.36 -7.05 8.90e-01 1.26e+00 6.28e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.34 -7.03 8.90e-01 1.26e+00 6.25e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.21e+01 angle pdb=" N PRO E 403 " pdb=" CA PRO E 403 " pdb=" CB PRO E 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.21e+01 angle pdb=" N PRO F 403 " pdb=" CA PRO F 403 " pdb=" CB PRO F 403 " ideal model delta sigma weight residual 103.31 110.32 -7.01 8.90e-01 1.26e+00 6.20e+01 ... (remaining 29024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 11631 16.92 - 33.85: 996 33.85 - 50.77: 148 50.77 - 67.70: 47 67.70 - 84.62: 16 Dihedral angle restraints: 12838 sinusoidal: 5264 harmonic: 7574 Sorted by residual: dihedral pdb=" CA GLN G 218 " pdb=" C GLN G 218 " pdb=" N PRO G 219 " pdb=" CA PRO G 219 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA GLN E 218 " pdb=" C GLN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN F 218 " pdb=" C GLN F 218 " pdb=" N PRO F 219 " pdb=" CA PRO F 219 " ideal model delta harmonic sigma weight residual -180.00 -152.47 -27.53 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2178 0.046 - 0.093: 769 0.093 - 0.139: 171 0.139 - 0.185: 67 0.185 - 0.232: 28 Chirality restraints: 3213 Sorted by residual: chirality pdb=" CA ASP E 285 " pdb=" N ASP E 285 " pdb=" C ASP E 285 " pdb=" CB ASP E 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP B 285 " pdb=" N ASP B 285 " pdb=" C ASP B 285 " pdb=" CB ASP B 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA ASP G 285 " pdb=" N ASP G 285 " pdb=" C ASP G 285 " pdb=" CB ASP G 285 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3210 not shown) Planarity restraints: 3640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 74 " 0.023 2.00e-02 2.50e+03 4.44e-02 1.98e+01 pdb=" C LYS B 74 " -0.077 2.00e-02 2.50e+03 pdb=" O LYS B 74 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA B 75 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 74 " -0.023 2.00e-02 2.50e+03 4.42e-02 1.96e+01 pdb=" C LYS E 74 " 0.077 2.00e-02 2.50e+03 pdb=" O LYS E 74 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA E 75 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 74 " -0.023 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C LYS G 74 " 0.076 2.00e-02 2.50e+03 pdb=" O LYS G 74 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA G 75 " -0.026 2.00e-02 2.50e+03 ... (remaining 3637 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5874 2.81 - 3.33: 19133 3.33 - 3.85: 32415 3.85 - 4.38: 37848 4.38 - 4.90: 65298 Nonbonded interactions: 160568 Sorted by model distance: nonbonded pdb=" O PHE E 412 " pdb=" OG SER E 415 " model vdw 2.287 3.040 nonbonded pdb=" O PHE B 412 " pdb=" OG SER B 415 " model vdw 2.287 3.040 nonbonded pdb=" O PHE A 412 " pdb=" OG SER A 415 " model vdw 2.287 3.040 nonbonded pdb=" O PHE C 412 " pdb=" OG SER C 415 " model vdw 2.287 3.040 nonbonded pdb=" O PHE D 412 " pdb=" OG SER D 415 " model vdw 2.288 3.040 ... (remaining 160563 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.800 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.006 0.110 21476 Z= 0.323 Angle : 0.912 10.861 29029 Z= 0.494 Chirality : 0.053 0.232 3213 Planarity : 0.007 0.067 3640 Dihedral : 13.400 84.622 7980 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.15), residues: 2576 helix: -1.02 (0.14), residues: 1036 sheet: -2.90 (0.17), residues: 651 loop : -2.76 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 223 TYR 0.031 0.002 TYR D 259 PHE 0.009 0.001 PHE D 276 TRP 0.006 0.001 TRP C 102 HIS 0.002 0.001 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00603 (21476) covalent geometry : angle 0.91176 (29029) hydrogen bonds : bond 0.15994 ( 880) hydrogen bonds : angle 6.36165 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 397 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8813 (mm) cc_final: 0.8422 (mm) REVERT: A 119 ASN cc_start: 0.7560 (p0) cc_final: 0.7329 (p0) REVERT: A 243 TYR cc_start: 0.7090 (m-10) cc_final: 0.6880 (m-80) REVERT: A 399 MET cc_start: 0.7293 (tpt) cc_final: 0.7049 (tpp) REVERT: B 246 MET cc_start: 0.9126 (mmt) cc_final: 0.8489 (mmm) REVERT: B 440 HIS cc_start: 0.7598 (m-70) cc_final: 0.7300 (m-70) REVERT: C 395 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: D 119 ASN cc_start: 0.7487 (p0) cc_final: 0.7212 (p0) REVERT: E 73 ILE cc_start: 0.8951 (mm) cc_final: 0.8687 (mm) REVERT: F 119 ASN cc_start: 0.7575 (p0) cc_final: 0.7259 (p0) REVERT: F 246 MET cc_start: 0.9051 (mmt) cc_final: 0.8729 (mmt) REVERT: F 417 LYS cc_start: 0.7445 (mmmt) cc_final: 0.7201 (mmtt) REVERT: G 243 TYR cc_start: 0.7243 (m-10) cc_final: 0.7032 (m-80) REVERT: G 397 MET cc_start: 0.7299 (mmm) cc_final: 0.7012 (mmm) outliers start: 14 outliers final: 0 residues processed: 411 average time/residue: 0.1558 time to fit residues: 96.4230 Evaluate side-chains 249 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.0980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 309 ASN B 248 ASN B 287 ASN B 309 ASN C 125 ASN C 248 ASN C 304 ASN C 309 ASN D 248 ASN D 309 ASN E 248 ASN E 309 ASN F 248 ASN F 309 ASN G 82 GLN G 248 ASN G 309 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126524 restraints weight = 25431.597| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.66 r_work: 0.3290 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21476 Z= 0.119 Angle : 0.634 6.686 29029 Z= 0.310 Chirality : 0.043 0.169 3213 Planarity : 0.006 0.067 3640 Dihedral : 6.270 55.133 2929 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.34 % Allowed : 12.43 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.17), residues: 2576 helix: 0.37 (0.17), residues: 1043 sheet: -2.51 (0.18), residues: 637 loop : -2.18 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 379 TYR 0.017 0.001 TYR D 259 PHE 0.026 0.001 PHE B 412 TRP 0.008 0.001 TRP G 102 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00255 (21476) covalent geometry : angle 0.63393 (29029) hydrogen bonds : bond 0.03310 ( 880) hydrogen bonds : angle 4.36121 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 313 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8494 (mm) cc_final: 0.8124 (mm) REVERT: A 243 TYR cc_start: 0.7516 (m-10) cc_final: 0.7262 (m-80) REVERT: A 383 LYS cc_start: 0.8261 (ptmm) cc_final: 0.8061 (ptmt) REVERT: B 202 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7909 (mttm) REVERT: B 246 MET cc_start: 0.8975 (mmt) cc_final: 0.8659 (mmm) REVERT: B 375 MET cc_start: 0.8252 (mmt) cc_final: 0.7916 (mmt) REVERT: B 440 HIS cc_start: 0.7972 (m-70) cc_final: 0.7678 (m-70) REVERT: D 73 ILE cc_start: 0.8622 (mm) cc_final: 0.8398 (mm) REVERT: D 230 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7886 (pt) REVERT: D 383 LYS cc_start: 0.8370 (ptmm) cc_final: 0.8135 (ptmt) REVERT: E 73 ILE cc_start: 0.8570 (mm) cc_final: 0.8283 (mm) REVERT: F 246 MET cc_start: 0.8960 (mmt) cc_final: 0.8513 (mmt) REVERT: F 304 ASN cc_start: 0.8001 (m-40) cc_final: 0.7632 (t0) REVERT: G 383 LYS cc_start: 0.8250 (ptmm) cc_final: 0.8008 (ptmt) REVERT: G 395 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7388 (tm-30) outliers start: 53 outliers final: 23 residues processed: 359 average time/residue: 0.1287 time to fit residues: 74.3702 Evaluate side-chains 288 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 212 optimal weight: 10.0000 chunk 148 optimal weight: 0.0000 chunk 133 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 96 optimal weight: 0.0370 chunk 116 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 226 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 overall best weight: 0.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 125 ASN C 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125620 restraints weight = 25345.259| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.69 r_work: 0.3315 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21476 Z= 0.101 Angle : 0.592 6.944 29029 Z= 0.286 Chirality : 0.042 0.203 3213 Planarity : 0.005 0.050 3640 Dihedral : 5.692 48.085 2926 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.92 % Allowed : 14.20 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.17), residues: 2576 helix: 0.96 (0.17), residues: 1043 sheet: -2.04 (0.19), residues: 595 loop : -1.76 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 379 TYR 0.015 0.001 TYR E 259 PHE 0.016 0.001 PHE B 412 TRP 0.006 0.000 TRP G 102 HIS 0.001 0.000 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00212 (21476) covalent geometry : angle 0.59230 (29029) hydrogen bonds : bond 0.02607 ( 880) hydrogen bonds : angle 3.91996 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8419 (mm) cc_final: 0.8048 (mm) REVERT: A 152 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7601 (mt) REVERT: A 160 MET cc_start: 0.8463 (mtm) cc_final: 0.8260 (mtt) REVERT: A 243 TYR cc_start: 0.7420 (m-10) cc_final: 0.7155 (m-80) REVERT: A 379 ARG cc_start: 0.6495 (mtt-85) cc_final: 0.6261 (mtm-85) REVERT: B 152 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7376 (mt) REVERT: B 202 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7826 (mttm) REVERT: B 246 MET cc_start: 0.8895 (mmt) cc_final: 0.8576 (mmm) REVERT: D 73 ILE cc_start: 0.8568 (mm) cc_final: 0.8339 (mm) REVERT: D 152 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7481 (mt) REVERT: E 73 ILE cc_start: 0.8548 (mm) cc_final: 0.8251 (mm) REVERT: E 152 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7509 (mt) REVERT: E 396 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7762 (mmmt) REVERT: F 152 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7394 (mt) REVERT: F 246 MET cc_start: 0.8917 (mmt) cc_final: 0.8466 (mmt) REVERT: F 304 ASN cc_start: 0.8059 (m-40) cc_final: 0.7598 (t0) REVERT: G 152 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7577 (mt) REVERT: G 386 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7441 (m) REVERT: G 395 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7272 (tm-30) outliers start: 66 outliers final: 35 residues processed: 337 average time/residue: 0.1183 time to fit residues: 66.0536 Evaluate side-chains 300 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 161 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 225 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 47 optimal weight: 0.0270 chunk 43 optimal weight: 6.9990 chunk 141 optimal weight: 0.0980 chunk 176 optimal weight: 0.0870 chunk 149 optimal weight: 1.9990 overall best weight: 1.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 141 HIS B 123 HIS C 141 HIS C 304 ASN E 141 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121372 restraints weight = 25596.945| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.71 r_work: 0.3289 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21476 Z= 0.128 Angle : 0.603 7.135 29029 Z= 0.289 Chirality : 0.043 0.164 3213 Planarity : 0.005 0.066 3640 Dihedral : 5.557 45.240 2926 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.83 % Allowed : 15.48 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2576 helix: 1.23 (0.17), residues: 1043 sheet: -2.02 (0.18), residues: 637 loop : -1.49 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 379 TYR 0.018 0.001 TYR F 266 PHE 0.012 0.001 PHE D 412 TRP 0.004 0.001 TRP F 102 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00293 (21476) covalent geometry : angle 0.60261 (29029) hydrogen bonds : bond 0.02558 ( 880) hydrogen bonds : angle 3.85052 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8439 (mm) cc_final: 0.8059 (mm) REVERT: A 243 TYR cc_start: 0.7371 (m-10) cc_final: 0.7147 (m-80) REVERT: A 379 ARG cc_start: 0.6620 (mtt-85) cc_final: 0.6406 (mtm-85) REVERT: B 51 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6110 (t80) REVERT: B 202 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7904 (mttm) REVERT: B 246 MET cc_start: 0.8829 (mmt) cc_final: 0.8505 (mmm) REVERT: C 152 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7706 (mp) REVERT: D 73 ILE cc_start: 0.8532 (mm) cc_final: 0.8294 (mm) REVERT: D 152 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7615 (mt) REVERT: E 73 ILE cc_start: 0.8627 (mm) cc_final: 0.8336 (mm) REVERT: E 152 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7668 (mt) REVERT: E 202 LYS cc_start: 0.8251 (mtmm) cc_final: 0.8039 (mttm) REVERT: E 396 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7735 (mmmt) REVERT: F 152 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7598 (mt) REVERT: F 246 MET cc_start: 0.8956 (mmt) cc_final: 0.8466 (mmt) REVERT: F 304 ASN cc_start: 0.8073 (m-40) cc_final: 0.7566 (t0) REVERT: G 152 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7585 (mt) REVERT: G 160 MET cc_start: 0.8115 (mtt) cc_final: 0.7550 (mtt) REVERT: G 386 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7432 (m) outliers start: 64 outliers final: 45 residues processed: 319 average time/residue: 0.1218 time to fit residues: 64.4754 Evaluate side-chains 308 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 106 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 62 optimal weight: 0.0020 chunk 201 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 118 optimal weight: 0.1980 chunk 39 optimal weight: 7.9990 overall best weight: 2.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 304 ASN D 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119368 restraints weight = 25624.665| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.78 r_work: 0.3212 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21476 Z= 0.189 Angle : 0.649 7.322 29029 Z= 0.314 Chirality : 0.045 0.172 3213 Planarity : 0.006 0.062 3640 Dihedral : 5.684 46.244 2926 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.01 % Allowed : 16.32 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.17), residues: 2576 helix: 1.33 (0.17), residues: 1029 sheet: -2.18 (0.18), residues: 665 loop : -1.34 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 379 TYR 0.023 0.002 TYR E 259 PHE 0.012 0.002 PHE D 276 TRP 0.005 0.001 TRP A 142 HIS 0.004 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00444 (21476) covalent geometry : angle 0.64919 (29029) hydrogen bonds : bond 0.02863 ( 880) hydrogen bonds : angle 3.99778 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 267 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8547 (mm) cc_final: 0.8138 (mm) REVERT: A 243 TYR cc_start: 0.7466 (m-10) cc_final: 0.7105 (m-80) REVERT: B 51 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6209 (t80) REVERT: B 202 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8047 (mttm) REVERT: E 73 ILE cc_start: 0.8677 (mm) cc_final: 0.8375 (mm) REVERT: E 141 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8296 (m-70) REVERT: E 202 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8162 (mttm) REVERT: E 396 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7736 (mmmt) REVERT: F 246 MET cc_start: 0.8999 (mmt) cc_final: 0.8540 (mmt) REVERT: F 304 ASN cc_start: 0.8077 (m-40) cc_final: 0.7502 (t0) REVERT: G 229 ILE cc_start: 0.8304 (mm) cc_final: 0.8046 (mm) REVERT: G 386 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7351 (m) outliers start: 68 outliers final: 57 residues processed: 315 average time/residue: 0.1229 time to fit residues: 64.3110 Evaluate side-chains 314 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 254 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 100 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 218 optimal weight: 0.9980 chunk 156 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN C 440 HIS D 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.153192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119599 restraints weight = 25638.989| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.73 r_work: 0.3225 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21476 Z= 0.145 Angle : 0.613 7.986 29029 Z= 0.294 Chirality : 0.043 0.166 3213 Planarity : 0.005 0.063 3640 Dihedral : 5.563 45.059 2926 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.41 % Allowed : 16.76 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.18), residues: 2576 helix: 1.42 (0.17), residues: 1043 sheet: -2.05 (0.19), residues: 665 loop : -1.35 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.018 0.001 TYR E 259 PHE 0.011 0.001 PHE G 52 TRP 0.003 0.001 TRP F 98 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00337 (21476) covalent geometry : angle 0.61279 (29029) hydrogen bonds : bond 0.02506 ( 880) hydrogen bonds : angle 3.86320 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 267 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ILE cc_start: 0.8554 (mm) cc_final: 0.8141 (mm) REVERT: A 209 PHE cc_start: 0.6960 (t80) cc_final: 0.6735 (t80) REVERT: A 243 TYR cc_start: 0.7365 (m-10) cc_final: 0.7152 (m-80) REVERT: B 202 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7978 (mttm) REVERT: D 255 ARG cc_start: 0.8236 (mpt180) cc_final: 0.7606 (mpt180) REVERT: E 51 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.5853 (t80) REVERT: E 73 ILE cc_start: 0.8665 (mm) cc_final: 0.8367 (mm) REVERT: E 141 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.8348 (m-70) REVERT: E 202 LYS cc_start: 0.8318 (mtmm) cc_final: 0.8083 (mttm) REVERT: E 396 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7710 (mmmt) REVERT: E 428 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7087 (mp) REVERT: F 51 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6451 (t80) REVERT: F 246 MET cc_start: 0.8973 (mmt) cc_final: 0.8516 (mmt) REVERT: F 304 ASN cc_start: 0.8060 (m-40) cc_final: 0.7506 (t0) REVERT: G 51 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.6027 (t80) REVERT: G 160 MET cc_start: 0.8290 (mtt) cc_final: 0.7739 (mtt) REVERT: G 229 ILE cc_start: 0.8326 (mm) cc_final: 0.8093 (mm) REVERT: G 386 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7356 (m) outliers start: 77 outliers final: 56 residues processed: 324 average time/residue: 0.1198 time to fit residues: 64.7445 Evaluate side-chains 316 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 155 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN C 440 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.152056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118821 restraints weight = 25792.780| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.82 r_work: 0.3226 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21476 Z= 0.184 Angle : 0.648 9.384 29029 Z= 0.311 Chirality : 0.045 0.171 3213 Planarity : 0.005 0.065 3640 Dihedral : 5.624 45.027 2926 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.94 % Allowed : 17.34 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.18), residues: 2576 helix: 1.50 (0.18), residues: 1022 sheet: -2.05 (0.19), residues: 665 loop : -1.32 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 379 TYR 0.020 0.002 TYR C 259 PHE 0.012 0.001 PHE D 276 TRP 0.005 0.001 TRP A 142 HIS 0.004 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00435 (21476) covalent geometry : angle 0.64803 (29029) hydrogen bonds : bond 0.02708 ( 880) hydrogen bonds : angle 3.97061 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 262 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6251 (t80) REVERT: A 73 ILE cc_start: 0.8579 (mm) cc_final: 0.8156 (mm) REVERT: A 209 PHE cc_start: 0.7061 (t80) cc_final: 0.6831 (t80) REVERT: A 243 TYR cc_start: 0.7526 (m-10) cc_final: 0.7267 (m-80) REVERT: B 51 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6733 (t80) REVERT: B 202 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8142 (mttm) REVERT: C 51 TYR cc_start: 0.6654 (OUTLIER) cc_final: 0.6234 (t80) REVERT: D 51 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.6215 (t80) REVERT: E 51 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5978 (t80) REVERT: E 73 ILE cc_start: 0.8702 (mm) cc_final: 0.8405 (mm) REVERT: E 141 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.8313 (m-70) REVERT: E 202 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8176 (mttm) REVERT: E 428 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7114 (mp) REVERT: F 51 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6526 (t80) REVERT: F 152 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7898 (mp) REVERT: F 246 MET cc_start: 0.8989 (mmt) cc_final: 0.8478 (mmt) REVERT: F 304 ASN cc_start: 0.8058 (m-40) cc_final: 0.7497 (t0) REVERT: G 51 TYR cc_start: 0.6777 (OUTLIER) cc_final: 0.6332 (t80) REVERT: G 52 PHE cc_start: 0.7936 (m-10) cc_final: 0.7552 (m-10) REVERT: G 160 MET cc_start: 0.8354 (mtt) cc_final: 0.7799 (mtt) REVERT: G 229 ILE cc_start: 0.8363 (mm) cc_final: 0.8120 (mm) REVERT: G 386 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7365 (m) REVERT: G 428 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7077 (tt) outliers start: 89 outliers final: 59 residues processed: 327 average time/residue: 0.1226 time to fit residues: 67.0144 Evaluate side-chains 323 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 161 ILE Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 420 ASP Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 93 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 164 optimal weight: 0.0270 chunk 232 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN C 440 HIS ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120748 restraints weight = 25492.602| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.62 r_work: 0.3293 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21476 Z= 0.107 Angle : 0.598 9.299 29029 Z= 0.284 Chirality : 0.042 0.160 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.381 42.949 2926 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.45 % Allowed : 18.13 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.18), residues: 2576 helix: 1.71 (0.18), residues: 1029 sheet: -1.77 (0.19), residues: 651 loop : -1.17 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 379 TYR 0.013 0.001 TYR E 120 PHE 0.008 0.001 PHE D 412 TRP 0.004 0.001 TRP E 251 HIS 0.002 0.000 HIS E 141 Details of bonding type rmsd covalent geometry : bond 0.00240 (21476) covalent geometry : angle 0.59753 (29029) hydrogen bonds : bond 0.02236 ( 880) hydrogen bonds : angle 3.70697 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 272 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6057 (t80) REVERT: A 73 ILE cc_start: 0.8554 (mm) cc_final: 0.8152 (mm) REVERT: A 209 PHE cc_start: 0.7105 (t80) cc_final: 0.6841 (t80) REVERT: A 243 TYR cc_start: 0.7450 (m-10) cc_final: 0.7119 (m-80) REVERT: B 51 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6624 (t80) REVERT: B 152 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7568 (mt) REVERT: B 202 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7886 (mttm) REVERT: B 246 MET cc_start: 0.8844 (mmt) cc_final: 0.8539 (mmm) REVERT: C 51 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.6132 (t80) REVERT: C 141 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.8048 (m-70) REVERT: C 152 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7967 (mp) REVERT: D 51 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6187 (t80) REVERT: D 152 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7600 (mt) REVERT: D 399 MET cc_start: 0.7808 (tpt) cc_final: 0.7457 (tpp) REVERT: E 51 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.5960 (t80) REVERT: E 73 ILE cc_start: 0.8691 (mm) cc_final: 0.8397 (mm) REVERT: E 141 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.8233 (m-70) REVERT: E 152 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7646 (mt) REVERT: E 202 LYS cc_start: 0.8249 (mtmm) cc_final: 0.8018 (mttm) REVERT: E 428 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.7005 (mp) REVERT: F 51 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.6442 (t80) REVERT: F 152 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7975 (mp) REVERT: F 246 MET cc_start: 0.8915 (mmt) cc_final: 0.8511 (mmt) REVERT: F 304 ASN cc_start: 0.8014 (m-40) cc_final: 0.7463 (t0) REVERT: G 51 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.6099 (t80) REVERT: G 152 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7736 (mt) REVERT: G 160 MET cc_start: 0.8161 (mtt) cc_final: 0.7615 (mtt) REVERT: G 386 VAL cc_start: 0.7606 (OUTLIER) cc_final: 0.7312 (m) outliers start: 78 outliers final: 47 residues processed: 329 average time/residue: 0.1210 time to fit residues: 66.3033 Evaluate side-chains 325 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 216 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 257 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 chunk 222 optimal weight: 10.0000 chunk 5 optimal weight: 0.0070 chunk 86 optimal weight: 0.7980 chunk 188 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121416 restraints weight = 25594.261| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.67 r_work: 0.3310 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21476 Z= 0.121 Angle : 0.611 10.797 29029 Z= 0.289 Chirality : 0.042 0.164 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.295 42.110 2926 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.05 % Allowed : 18.62 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2576 helix: 1.81 (0.18), residues: 1029 sheet: -1.73 (0.19), residues: 665 loop : -1.24 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 379 TYR 0.014 0.001 TYR B 259 PHE 0.011 0.001 PHE F 412 TRP 0.004 0.001 TRP E 251 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00280 (21476) covalent geometry : angle 0.61091 (29029) hydrogen bonds : bond 0.02282 ( 880) hydrogen bonds : angle 3.68898 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 262 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.6618 (OUTLIER) cc_final: 0.6065 (t80) REVERT: A 73 ILE cc_start: 0.8549 (mm) cc_final: 0.8152 (mm) REVERT: A 209 PHE cc_start: 0.7115 (t80) cc_final: 0.6906 (t80) REVERT: A 243 TYR cc_start: 0.7471 (m-10) cc_final: 0.7190 (m-80) REVERT: B 51 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6485 (t80) REVERT: B 152 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7509 (mt) REVERT: B 202 LYS cc_start: 0.8275 (mtmm) cc_final: 0.8031 (mttm) REVERT: C 51 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.6202 (t80) REVERT: C 152 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 375 MET cc_start: 0.8068 (mmm) cc_final: 0.7545 (mmt) REVERT: D 51 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.6249 (t80) REVERT: D 152 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7604 (mt) REVERT: D 396 LYS cc_start: 0.7719 (mmtt) cc_final: 0.7466 (mmmt) REVERT: D 399 MET cc_start: 0.7846 (tpt) cc_final: 0.7490 (tpp) REVERT: E 51 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.6087 (t80) REVERT: E 73 ILE cc_start: 0.8710 (mm) cc_final: 0.8485 (mm) REVERT: E 141 HIS cc_start: 0.8623 (OUTLIER) cc_final: 0.8333 (m-70) REVERT: E 152 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7694 (mt) REVERT: E 428 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7046 (mp) REVERT: F 51 TYR cc_start: 0.6876 (OUTLIER) cc_final: 0.6460 (t80) REVERT: F 152 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7987 (mp) REVERT: F 246 MET cc_start: 0.8946 (mmt) cc_final: 0.8502 (mmt) REVERT: F 304 ASN cc_start: 0.8019 (m-40) cc_final: 0.7470 (t0) REVERT: G 51 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6126 (t80) REVERT: G 152 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7748 (mp) REVERT: G 160 MET cc_start: 0.8194 (mtt) cc_final: 0.7659 (mtt) REVERT: G 386 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7290 (m) outliers start: 69 outliers final: 46 residues processed: 309 average time/residue: 0.1151 time to fit residues: 59.4556 Evaluate side-chains 319 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 51 TYR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 448 SER Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 223 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 110 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 115 optimal weight: 0.0970 chunk 204 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 141 HIS C 304 ASN D 304 ASN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.121766 restraints weight = 25519.132| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.65 r_work: 0.3288 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21476 Z= 0.116 Angle : 0.611 11.087 29029 Z= 0.288 Chirality : 0.042 0.159 3213 Planarity : 0.005 0.060 3640 Dihedral : 5.214 40.912 2926 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.79 % Allowed : 19.20 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2576 helix: 1.83 (0.18), residues: 1036 sheet: -1.59 (0.20), residues: 665 loop : -1.18 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 379 TYR 0.013 0.001 TYR G 259 PHE 0.014 0.001 PHE B 209 TRP 0.004 0.001 TRP E 251 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00268 (21476) covalent geometry : angle 0.61135 (29029) hydrogen bonds : bond 0.02204 ( 880) hydrogen bonds : angle 3.62816 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5152 Ramachandran restraints generated. 2576 Oldfield, 0 Emsley, 2576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 265 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 73 ILE cc_start: 0.8679 (mm) cc_final: 0.8261 (mm) REVERT: A 152 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7721 (mt) REVERT: A 243 TYR cc_start: 0.7424 (m-10) cc_final: 0.7192 (m-80) REVERT: B 152 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7605 (mt) REVERT: B 202 LYS cc_start: 0.8267 (mtmm) cc_final: 0.8013 (mttm) REVERT: C 51 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6121 (t80) REVERT: C 152 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7961 (mp) REVERT: D 51 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6226 (t80) REVERT: D 152 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7684 (mt) REVERT: D 396 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7460 (mmmt) REVERT: D 399 MET cc_start: 0.7826 (tpt) cc_final: 0.7471 (tpp) REVERT: E 51 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.6284 (t80) REVERT: E 73 ILE cc_start: 0.8693 (mm) cc_final: 0.8479 (mm) REVERT: E 141 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8260 (m-70) REVERT: E 152 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7676 (mt) REVERT: E 428 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7003 (mp) REVERT: F 51 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6541 (t80) REVERT: F 152 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7955 (mp) REVERT: F 246 MET cc_start: 0.8926 (mmt) cc_final: 0.8499 (mmt) REVERT: F 304 ASN cc_start: 0.8006 (m-40) cc_final: 0.7466 (t0) REVERT: G 51 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6163 (t80) REVERT: G 152 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7811 (mp) REVERT: G 160 MET cc_start: 0.8184 (mtt) cc_final: 0.7630 (mtt) REVERT: G 386 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7254 (m) outliers start: 63 outliers final: 44 residues processed: 310 average time/residue: 0.1181 time to fit residues: 61.5799 Evaluate side-chains 323 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 263 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 TYR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain C residue 51 TYR Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 310 MET Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 428 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 141 HIS Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 246 MET Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 310 MET Chi-restraints excluded: chain E residue 347 ASN Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 51 TYR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 423 VAL Chi-restraints excluded: chain G residue 51 TYR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 257 ILE Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain G residue 386 VAL Chi-restraints excluded: chain G residue 406 THR Chi-restraints excluded: chain G residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 161 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 164 optimal weight: 0.0370 chunk 100 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 148 optimal weight: 0.0270 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 ASN ** E 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.123485 restraints weight = 25535.673| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.66 r_work: 0.3313 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21476 Z= 0.099 Angle : 0.594 10.564 29029 Z= 0.279 Chirality : 0.041 0.156 3213 Planarity : 0.005 0.058 3640 Dihedral : 5.015 38.087 2926 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.34 % Allowed : 19.77 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.18), residues: 2576 helix: 1.93 (0.17), residues: 1050 sheet: -1.22 (0.21), residues: 609 loop : -1.19 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 379 TYR 0.013 0.001 TYR E 120 PHE 0.020 0.001 PHE A 209 TRP 0.005 0.001 TRP B 251 HIS 0.002 0.000 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00221 (21476) covalent geometry : angle 0.59402 (29029) hydrogen bonds : bond 0.02001 ( 880) hydrogen bonds : angle 3.48987 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6622.94 seconds wall clock time: 113 minutes 28.03 seconds (6808.03 seconds total)