Starting phenix.real_space_refine on Sat Oct 31 08:07:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.map" model { file = "/net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wf0_65920/10_2026/9wf0_65920.cif" } resolution = 3.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 217 5.16 5 C 25572 2.51 5 N 7291 2.21 5 O 7700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40780 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3163 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 2 Chain: "B" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3198 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3162 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 393} Chain breaks: 2 Chain: "D" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3218 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2789 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 347} Chain breaks: 3 Chain: "F" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3167 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3163 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 392} Chain breaks: 1 Chain: "H" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3196 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 396} Chain breaks: 2 Chain: "I" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3230 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 400} Chain breaks: 2 Chain: "J" Number of atoms: 3217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3217 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 399} Chain breaks: 2 Chain: "K" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3187 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3129 Classifications: {'peptide': 409} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2961 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Time building chain proxies: 8.80, per 1000 atoms: 0.22 Number of scatterers: 40780 At special positions: 0 Unit cell: (134.829, 134.196, 225.981, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 217 16.00 O 7700 8.00 N 7291 7.00 C 25572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 38 " - pdb=" SG CYS G 38 " distance=1.71 Simple disulfide: pdb=" SG CYS B 38 " - pdb=" SG CYS H 38 " distance=2.19 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS I 38 " distance=2.04 Simple disulfide: pdb=" SG CYS D 38 " - pdb=" SG CYS J 38 " distance=2.07 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS K 38 " distance=1.76 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS M 38 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9768 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 61 sheets defined 42.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU A 88 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 89' Processing helix chain 'A' and resid 141 through 148 Processing helix chain 'A' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.551A pdb=" N THR A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 266 Processing helix chain 'A' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 314 through 323 Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 357 through 382 removed outlier: 4.236A pdb=" N LEU A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU B 88 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 89 " --> pdb=" O GLU B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 85 through 89' Processing helix chain 'B' and resid 126 through 130 Processing helix chain 'B' and resid 141 through 148 Processing helix chain 'B' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 266 Processing helix chain 'B' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 357 through 382 removed outlier: 4.154A pdb=" N LEU B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 400 Processing helix chain 'B' and resid 400 through 409 Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.578A pdb=" N ASN B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU C 88 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA C 89 " --> pdb=" O GLU C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 89' Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR C 203 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 266 Processing helix chain 'C' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) Proline residue: C 284 - end of helix Processing helix chain 'C' and resid 313 through 323 Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'C' and resid 357 through 383 removed outlier: 3.874A pdb=" N LEU C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 400 Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU D 88 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA D 89 " --> pdb=" O GLU D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' Processing helix chain 'D' and resid 126 through 130 Processing helix chain 'D' and resid 141 through 148 Processing helix chain 'D' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR D 203 " --> pdb=" O HIS D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 266 Processing helix chain 'D' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE D 280 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 314 through 323 Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 357 through 384 removed outlier: 4.137A pdb=" N LEU D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 400 Processing helix chain 'D' and resid 400 through 409 Processing helix chain 'D' and resid 417 through 430 removed outlier: 3.578A pdb=" N ASN D 430 " --> pdb=" O ARG D 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU E 88 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA E 89 " --> pdb=" O GLU E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 89' Processing helix chain 'E' and resid 126 through 130 Processing helix chain 'E' and resid 141 through 148 Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR E 203 " --> pdb=" O HIS E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA E 228 " --> pdb=" O ARG E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 266 Processing helix chain 'E' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE E 280 " --> pdb=" O PRO E 276 " (cutoff:3.500A) Proline residue: E 284 - end of helix Processing helix chain 'E' and resid 314 through 323 Processing helix chain 'E' and resid 330 through 337 Processing helix chain 'E' and resid 357 through 377 Processing helix chain 'E' and resid 420 through 430 removed outlier: 3.578A pdb=" N ASN E 430 " --> pdb=" O ARG E 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU F 88 " --> pdb=" O GLY F 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA F 89 " --> pdb=" O GLU F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 141 through 148 Processing helix chain 'F' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 203 removed outlier: 3.551A pdb=" N THR F 203 " --> pdb=" O HIS F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA F 228 " --> pdb=" O ARG F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 266 Processing helix chain 'F' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE F 280 " --> pdb=" O PRO F 276 " (cutoff:3.500A) Proline residue: F 284 - end of helix Processing helix chain 'F' and resid 314 through 323 Processing helix chain 'F' and resid 330 through 337 Processing helix chain 'F' and resid 357 through 382 removed outlier: 4.023A pdb=" N LEU F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR F 380 " --> pdb=" O GLN F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 400 Processing helix chain 'F' and resid 400 through 409 Processing helix chain 'F' and resid 417 through 430 removed outlier: 3.578A pdb=" N ASN F 430 " --> pdb=" O ARG F 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU G 88 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA G 89 " --> pdb=" O GLU G 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 85 through 89' Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA G 228 " --> pdb=" O ARG G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 266 Processing helix chain 'G' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE G 280 " --> pdb=" O PRO G 276 " (cutoff:3.500A) Proline residue: G 284 - end of helix Processing helix chain 'G' and resid 313 through 323 Processing helix chain 'G' and resid 330 through 337 Processing helix chain 'G' and resid 357 through 383 removed outlier: 3.947A pdb=" N LEU G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 409 removed outlier: 4.909A pdb=" N ASP G 402 " --> pdb=" O LEU G 398 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL G 403 " --> pdb=" O ASP G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN G 430 " --> pdb=" O ARG G 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU H 88 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA H 89 " --> pdb=" O GLU H 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 85 through 89' Processing helix chain 'H' and resid 126 through 130 Processing helix chain 'H' and resid 141 through 148 Processing helix chain 'H' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU H 169 " --> pdb=" O GLY H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR H 203 " --> pdb=" O HIS H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 266 Processing helix chain 'H' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE H 280 " --> pdb=" O PRO H 276 " (cutoff:3.500A) Proline residue: H 284 - end of helix Processing helix chain 'H' and resid 313 through 323 removed outlier: 3.535A pdb=" N ASP H 317 " --> pdb=" O ASP H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 337 Processing helix chain 'H' and resid 357 through 378 Processing helix chain 'H' and resid 378 through 383 Processing helix chain 'H' and resid 391 through 409 removed outlier: 4.836A pdb=" N ASP H 402 " --> pdb=" O LEU H 398 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL H 403 " --> pdb=" O ASP H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN H 430 " --> pdb=" O ARG H 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU I 88 " --> pdb=" O GLY I 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA I 89 " --> pdb=" O GLU I 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 85 through 89' Processing helix chain 'I' and resid 126 through 130 Processing helix chain 'I' and resid 141 through 148 Processing helix chain 'I' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU I 169 " --> pdb=" O GLY I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 203 removed outlier: 3.553A pdb=" N THR I 203 " --> pdb=" O HIS I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'I' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA I 228 " --> pdb=" O ARG I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 266 Processing helix chain 'I' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE I 280 " --> pdb=" O PRO I 276 " (cutoff:3.500A) Proline residue: I 284 - end of helix Processing helix chain 'I' and resid 313 through 323 removed outlier: 3.533A pdb=" N ASP I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 337 Processing helix chain 'I' and resid 357 through 382 removed outlier: 3.892A pdb=" N LEU I 379 " --> pdb=" O ALA I 375 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR I 380 " --> pdb=" O GLN I 376 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP I 382 " --> pdb=" O GLN I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 409 removed outlier: 5.122A pdb=" N ASP I 402 " --> pdb=" O LEU I 398 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VAL I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 417 through 430 removed outlier: 3.578A pdb=" N ASN I 430 " --> pdb=" O ARG I 426 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU J 88 " --> pdb=" O GLY J 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA J 89 " --> pdb=" O GLU J 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 85 through 89' Processing helix chain 'J' and resid 126 through 130 Processing helix chain 'J' and resid 141 through 148 Processing helix chain 'J' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU J 169 " --> pdb=" O GLY J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR J 203 " --> pdb=" O HIS J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'J' and resid 220 through 241 removed outlier: 3.539A pdb=" N ALA J 228 " --> pdb=" O ARG J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 266 Processing helix chain 'J' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE J 280 " --> pdb=" O PRO J 276 " (cutoff:3.500A) Proline residue: J 284 - end of helix Processing helix chain 'J' and resid 314 through 323 Processing helix chain 'J' and resid 330 through 337 Processing helix chain 'J' and resid 357 through 382 removed outlier: 3.883A pdb=" N LEU J 379 " --> pdb=" O ALA J 375 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR J 380 " --> pdb=" O GLN J 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP J 382 " --> pdb=" O GLN J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 400 Processing helix chain 'J' and resid 400 through 409 Processing helix chain 'J' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN J 430 " --> pdb=" O ARG J 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU K 88 " --> pdb=" O GLY K 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA K 89 " --> pdb=" O GLU K 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 85 through 89' Processing helix chain 'K' and resid 126 through 130 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU K 169 " --> pdb=" O GLY K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'K' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA K 228 " --> pdb=" O ARG K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 266 Processing helix chain 'K' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE K 280 " --> pdb=" O PRO K 276 " (cutoff:3.500A) Proline residue: K 284 - end of helix Processing helix chain 'K' and resid 315 through 323 Processing helix chain 'K' and resid 330 through 337 Processing helix chain 'K' and resid 357 through 382 removed outlier: 4.006A pdb=" N LEU K 379 " --> pdb=" O ALA K 375 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR K 380 " --> pdb=" O GLN K 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU K 381 " --> pdb=" O ILE K 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP K 382 " --> pdb=" O GLN K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 400 Processing helix chain 'K' and resid 400 through 409 Processing helix chain 'K' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN K 430 " --> pdb=" O ARG K 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU L 88 " --> pdb=" O GLY L 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA L 89 " --> pdb=" O GLU L 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 85 through 89' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'L' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU L 169 " --> pdb=" O GLY L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR L 203 " --> pdb=" O HIS L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 220 through 241 removed outlier: 3.539A pdb=" N ALA L 228 " --> pdb=" O ARG L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 266 Processing helix chain 'L' and resid 276 through 288 removed outlier: 4.137A pdb=" N PHE L 280 " --> pdb=" O PRO L 276 " (cutoff:3.500A) Proline residue: L 284 - end of helix Processing helix chain 'L' and resid 314 through 323 Processing helix chain 'L' and resid 330 through 337 Processing helix chain 'L' and resid 357 through 383 removed outlier: 4.255A pdb=" N LEU L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR L 380 " --> pdb=" O GLN L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 400 Processing helix chain 'L' and resid 400 through 409 Processing helix chain 'L' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN L 430 " --> pdb=" O ARG L 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 89 removed outlier: 3.889A pdb=" N LEU M 88 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA M 89 " --> pdb=" O GLU M 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 85 through 89' Processing helix chain 'M' and resid 141 through 148 Processing helix chain 'M' and resid 165 through 177 removed outlier: 3.750A pdb=" N LEU M 169 " --> pdb=" O GLY M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 203 removed outlier: 3.552A pdb=" N THR M 203 " --> pdb=" O HIS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'M' and resid 220 through 241 removed outlier: 3.540A pdb=" N ALA M 228 " --> pdb=" O ARG M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 266 Processing helix chain 'M' and resid 276 through 288 removed outlier: 4.136A pdb=" N PHE M 280 " --> pdb=" O PRO M 276 " (cutoff:3.500A) Proline residue: M 284 - end of helix Processing helix chain 'M' and resid 313 through 323 Processing helix chain 'M' and resid 330 through 337 Processing helix chain 'M' and resid 357 through 378 Processing helix chain 'M' and resid 394 through 400 removed outlier: 3.551A pdb=" N ASN M 400 " --> pdb=" O HIS M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 409 Processing helix chain 'M' and resid 417 through 430 removed outlier: 3.577A pdb=" N ASN M 430 " --> pdb=" O ARG M 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE A 51 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE A 57 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS A 45 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 33 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS A 45 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS A 31 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 47 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 29 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 30 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 76 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.799A pdb=" N CYS A 118 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 91 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 212 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 246 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY A 291 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE A 92 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS A 91 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 212 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 246 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET A 156 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL A 304 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE A 158 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR A 328 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS A 150 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE B 51 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 57 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 45 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 33 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS B 45 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS B 31 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN B 47 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU B 29 " --> pdb=" O GLN B 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 30 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 76 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.501A pdb=" N CYS B 118 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE B 92 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 91 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 212 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 246 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 291 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE B 92 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 91 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 212 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 246 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET B 156 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL B 304 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 158 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR B 328 " --> pdb=" O ASP B 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS B 150 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE C 51 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 57 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS C 45 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C 33 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS C 45 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS C 31 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 47 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU C 29 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 30 " --> pdb=" O THR C 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 76 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 Processing sheet with id=AB4, first strand: chain 'C' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE C 92 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS C 91 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 212 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 246 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 291 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE C 92 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS C 91 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 212 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 246 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET C 156 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL C 304 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 158 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR C 328 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS C 150 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE D 51 " --> pdb=" O GLN D 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 57 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS D 45 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE D 33 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS D 45 " --> pdb=" O CYS D 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS D 31 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 47 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU D 29 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 30 " --> pdb=" O THR D 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR D 76 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 81 through 82 removed outlier: 3.670A pdb=" N PHE D 82 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS D 118 " --> pdb=" O PHE D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.533A pdb=" N ILE D 92 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 91 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 212 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 246 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY D 291 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 99 through 102 removed outlier: 6.533A pdb=" N ILE D 92 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS D 91 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 212 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 246 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET D 156 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL D 304 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 158 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR D 328 " --> pdb=" O ASP D 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS D 150 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE E 51 " --> pdb=" O GLN E 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 57 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS E 45 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE E 33 " --> pdb=" O ILE E 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS E 45 " --> pdb=" O CYS E 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS E 31 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN E 47 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU E 29 " --> pdb=" O GLN E 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE E 30 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR E 76 " --> pdb=" O ILE E 30 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 81 through 83 removed outlier: 3.747A pdb=" N PHE E 82 " --> pdb=" O CYS E 118 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS E 118 " --> pdb=" O PHE E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 91 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 212 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 246 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 291 " --> pdb=" O ILE E 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 91 " --> pdb=" O THR E 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 212 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 246 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N MET E 156 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL E 304 " --> pdb=" O MET E 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE E 158 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR E 328 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN F 55 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE F 51 " --> pdb=" O GLN F 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE F 57 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS F 45 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE F 33 " --> pdb=" O ILE F 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS F 45 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS F 31 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN F 47 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU F 29 " --> pdb=" O GLN F 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE F 30 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR F 76 " --> pdb=" O ILE F 30 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 81 through 83 removed outlier: 3.620A pdb=" N PHE F 82 " --> pdb=" O CYS F 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS F 118 " --> pdb=" O PHE F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE F 92 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 91 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 212 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 246 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE F 92 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS F 91 " --> pdb=" O THR F 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 212 " --> pdb=" O LYS F 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 246 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET F 156 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL F 304 " --> pdb=" O MET F 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE F 158 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR F 328 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS F 150 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN G 55 " --> pdb=" O PHE G 51 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE G 51 " --> pdb=" O GLN G 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE G 57 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS G 45 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE G 33 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LYS G 45 " --> pdb=" O CYS G 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS G 31 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN G 47 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU G 29 " --> pdb=" O GLN G 47 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE G 30 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR G 76 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE G 92 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS G 91 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU G 212 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 246 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE G 92 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS G 91 " --> pdb=" O THR G 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU G 212 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 246 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET G 156 " --> pdb=" O TYR G 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL G 304 " --> pdb=" O MET G 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE G 158 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR G 328 " --> pdb=" O ASP G 343 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS G 150 " --> pdb=" O LEU G 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.957A pdb=" N GLN H 55 " --> pdb=" O PHE H 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE H 51 " --> pdb=" O GLN H 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE H 57 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS H 45 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE H 33 " --> pdb=" O ILE H 43 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS H 45 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS H 31 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN H 47 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU H 29 " --> pdb=" O GLN H 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE H 30 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR H 76 " --> pdb=" O ILE H 30 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE H 92 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 91 " --> pdb=" O THR H 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU H 212 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 246 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY H 291 " --> pdb=" O ILE H 298 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE H 92 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS H 91 " --> pdb=" O THR H 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU H 212 " --> pdb=" O LYS H 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 246 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET H 156 " --> pdb=" O TYR H 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL H 304 " --> pdb=" O MET H 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE H 158 " --> pdb=" O VAL H 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR H 328 " --> pdb=" O ASP H 343 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS H 150 " --> pdb=" O LEU H 137 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 17 through 20 removed outlier: 6.956A pdb=" N GLN I 55 " --> pdb=" O PHE I 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE I 51 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE I 57 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS I 45 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE I 33 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS I 45 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS I 31 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN I 47 " --> pdb=" O GLU I 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU I 29 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE I 30 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR I 76 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE I 92 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS I 91 " --> pdb=" O THR I 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU I 212 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 246 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY I 291 " --> pdb=" O ILE I 298 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE I 92 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS I 91 " --> pdb=" O THR I 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU I 212 " --> pdb=" O LYS I 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU I 246 " --> pdb=" O ILE I 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET I 156 " --> pdb=" O TYR I 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL I 304 " --> pdb=" O MET I 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE I 158 " --> pdb=" O VAL I 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR I 328 " --> pdb=" O ASP I 343 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS I 150 " --> pdb=" O LEU I 137 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.956A pdb=" N GLN J 55 " --> pdb=" O PHE J 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE J 51 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE J 57 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS J 45 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE J 33 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS J 45 " --> pdb=" O CYS J 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS J 31 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN J 47 " --> pdb=" O GLU J 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU J 29 " --> pdb=" O GLN J 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE J 30 " --> pdb=" O THR J 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR J 76 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 81 through 84 removed outlier: 3.665A pdb=" N CYS J 118 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR J 116 " --> pdb=" O MET J 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE J 92 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS J 91 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU J 212 " --> pdb=" O LYS J 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 246 " --> pdb=" O ILE J 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY J 291 " --> pdb=" O ILE J 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 99 through 102 removed outlier: 6.535A pdb=" N ILE J 92 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS J 91 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU J 212 " --> pdb=" O LYS J 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU J 246 " --> pdb=" O ILE J 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET J 156 " --> pdb=" O TYR J 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL J 304 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE J 158 " --> pdb=" O VAL J 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR J 328 " --> pdb=" O ASP J 343 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS J 150 " --> pdb=" O LEU J 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 17 through 20 removed outlier: 6.956A pdb=" N GLN K 55 " --> pdb=" O PHE K 51 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N PHE K 51 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE K 57 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS K 45 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE K 33 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS K 45 " --> pdb=" O CYS K 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS K 31 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN K 47 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU K 29 " --> pdb=" O GLN K 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE K 30 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR K 76 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 81 through 84 removed outlier: 3.875A pdb=" N CYS K 118 " --> pdb=" O PHE K 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE K 92 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS K 91 " --> pdb=" O THR K 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU K 212 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 246 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY K 291 " --> pdb=" O ILE K 298 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE K 92 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS K 91 " --> pdb=" O THR K 210 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU K 212 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 246 " --> pdb=" O ILE K 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET K 156 " --> pdb=" O TYR K 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL K 304 " --> pdb=" O MET K 156 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE K 158 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR K 328 " --> pdb=" O ASP K 343 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS K 150 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 17 through 20 removed outlier: 6.956A pdb=" N GLN L 55 " --> pdb=" O PHE L 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE L 51 " --> pdb=" O GLN L 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE L 57 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS L 45 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE L 33 " --> pdb=" O ILE L 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS L 45 " --> pdb=" O CYS L 31 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS L 31 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN L 47 " --> pdb=" O GLU L 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU L 29 " --> pdb=" O GLN L 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE L 30 " --> pdb=" O THR L 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR L 76 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 81 through 83 removed outlier: 3.837A pdb=" N PHE L 82 " --> pdb=" O CYS L 118 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS L 118 " --> pdb=" O PHE L 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS L 91 " --> pdb=" O THR L 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU L 212 " --> pdb=" O LYS L 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 246 " --> pdb=" O ILE L 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY L 291 " --> pdb=" O ILE L 298 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS L 91 " --> pdb=" O THR L 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU L 212 " --> pdb=" O LYS L 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 246 " --> pdb=" O ILE L 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET L 156 " --> pdb=" O TYR L 302 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL L 304 " --> pdb=" O MET L 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE L 158 " --> pdb=" O VAL L 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR L 328 " --> pdb=" O ASP L 343 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS L 150 " --> pdb=" O LEU L 137 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 17 through 20 removed outlier: 6.958A pdb=" N GLN M 55 " --> pdb=" O PHE M 51 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE M 51 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE M 57 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS M 45 " --> pdb=" O ILE M 61 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE M 33 " --> pdb=" O ILE M 43 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYS M 45 " --> pdb=" O CYS M 31 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N CYS M 31 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN M 47 " --> pdb=" O GLU M 29 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU M 29 " --> pdb=" O GLN M 47 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE M 30 " --> pdb=" O THR M 76 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR M 76 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE M 92 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS M 91 " --> pdb=" O THR M 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU M 212 " --> pdb=" O LYS M 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU M 246 " --> pdb=" O ILE M 181 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY M 291 " --> pdb=" O ILE M 298 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'M' and resid 99 through 102 removed outlier: 6.534A pdb=" N ILE M 92 " --> pdb=" O VAL M 100 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS M 91 " --> pdb=" O THR M 210 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU M 212 " --> pdb=" O LYS M 91 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU M 246 " --> pdb=" O ILE M 181 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N MET M 156 " --> pdb=" O TYR M 302 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL M 304 " --> pdb=" O MET M 156 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE M 158 " --> pdb=" O VAL M 304 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR M 328 " --> pdb=" O ASP M 343 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 136 through 137 removed outlier: 4.547A pdb=" N CYS M 150 " --> pdb=" O LEU M 137 " (cutoff:3.500A) 2141 hydrogen bonds defined for protein. 6237 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: 9.62 Time building geometry restraints manager: 4.15 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: 14025 1.34 - 1.46: 6370 1.46 - 1.58: 20718 1.58 - 1.70: 0 1.70 - 1.81: 334 Bond restraints: 41447 Sorted by residual: bond pdb=" C ALA I 8 " pdb=" N HIS I 9 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.85e+00 bond pdb=" C GLY K 66 " pdb=" N LEU K 67 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.46e-02 4.69e+03 8.24e+00 bond pdb=" C GLY I 66 " pdb=" N LEU I 67 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.46e-02 4.69e+03 8.16e+00 bond pdb=" C GLY A 66 " pdb=" N LEU A 67 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.46e-02 4.69e+03 8.02e+00 bond pdb=" C GLY J 66 " pdb=" N LEU J 67 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.46e-02 4.69e+03 7.98e+00 ... (remaining 41442 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 55092 2.04 - 4.09: 953 4.09 - 6.13: 101 6.13 - 8.18: 28 8.18 - 10.22: 1 Bond angle restraints: 56175 Sorted by residual: angle pdb=" C ALA I 8 " pdb=" N HIS I 9 " pdb=" CA HIS I 9 " ideal model delta sigma weight residual 120.68 112.53 8.15 1.52e+00 4.33e-01 2.88e+01 angle pdb=" C PHE D 4 " pdb=" CA PHE D 4 " pdb=" CB PHE D 4 " ideal model delta sigma weight residual 116.63 110.92 5.71 1.16e+00 7.43e-01 2.43e+01 angle pdb=" CA MET M 370 " pdb=" CB MET M 370 " pdb=" CG MET M 370 " ideal model delta sigma weight residual 114.10 120.75 -6.65 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA MET B 370 " pdb=" CB MET B 370 " pdb=" CG MET B 370 " ideal model delta sigma weight residual 114.10 120.75 -6.65 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CA MET D 370 " pdb=" CB MET D 370 " pdb=" CG MET D 370 " ideal model delta sigma weight residual 114.10 120.74 -6.64 2.00e+00 2.50e-01 1.10e+01 ... (remaining 56170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 21573 17.92 - 35.84: 2820 35.84 - 53.76: 578 53.76 - 71.67: 89 71.67 - 89.59: 108 Dihedral angle restraints: 25168 sinusoidal: 9980 harmonic: 15188 Sorted by residual: dihedral pdb=" CB CYS D 38 " pdb=" SG CYS D 38 " pdb=" SG CYS J 38 " pdb=" CB CYS J 38 " ideal model delta sinusoidal sigma weight residual -86.00 3.33 -89.33 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS A 38 " pdb=" SG CYS A 38 " pdb=" SG CYS G 38 " pdb=" CB CYS G 38 " ideal model delta sinusoidal sigma weight residual -86.00 3.18 -89.18 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS B 38 " pdb=" SG CYS B 38 " pdb=" SG CYS H 38 " pdb=" CB CYS H 38 " ideal model delta sinusoidal sigma weight residual -86.00 -0.58 -85.42 1 1.00e+01 1.00e-02 8.83e+01 ... (remaining 25165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4397 0.034 - 0.067: 1358 0.067 - 0.101: 506 0.101 - 0.134: 238 0.134 - 0.168: 17 Chirality restraints: 6516 Sorted by residual: chirality pdb=" CA MET C 370 " pdb=" N MET C 370 " pdb=" C MET C 370 " pdb=" CB MET C 370 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CA MET G 370 " pdb=" N MET G 370 " pdb=" C MET G 370 " pdb=" CB MET G 370 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 chirality pdb=" CA MET H 370 " pdb=" N MET H 370 " pdb=" C MET H 370 " pdb=" CB MET H 370 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 6513 not shown) Planarity restraints: 7419 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 308 " 0.025 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" C SER M 308 " -0.087 2.00e-02 2.50e+03 pdb=" O SER M 308 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU M 309 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 308 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C SER G 308 " -0.085 2.00e-02 2.50e+03 pdb=" O SER G 308 " 0.032 2.00e-02 2.50e+03 pdb=" N GLU G 309 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 308 " -0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C SER H 308 " 0.073 2.00e-02 2.50e+03 pdb=" O SER H 308 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU H 309 " -0.025 2.00e-02 2.50e+03 ... (remaining 7416 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 15031 2.88 - 3.39: 40370 3.39 - 3.89: 66062 3.89 - 4.40: 73926 4.40 - 4.90: 121514 Nonbonded interactions: 316903 Sorted by model distance: nonbonded pdb=" O SER G 308 " pdb=" N GLU G 310 " model vdw 2.380 3.120 nonbonded pdb=" O SER M 308 " pdb=" N GLU M 310 " model vdw 2.438 3.120 nonbonded pdb=" O PHE I 4 " pdb=" O CYS I 7 " model vdw 2.490 3.040 nonbonded pdb=" O LYS G 366 " pdb=" OD1 ASP G 369 " model vdw 2.498 3.040 nonbonded pdb=" O LYS A 366 " pdb=" OD1 ASP A 369 " model vdw 2.499 3.040 ... (remaining 316898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'B' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'C' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'D' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'E' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 430)) selection = (chain 'F' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 104 or resid 127 through 308 or res \ id 314 through 377 or resid 419 through 430)) selection = (chain 'G' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'H' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'I' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'J' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 308 or resid 314 through 377 or resid 419 through 430)) selection = (chain 'K' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 104 or resid 127 throu \ gh 377 or resid 419 through 430)) selection = (chain 'L' and (resid 9 through 73 or (resid 74 and (name N or name CA or name C \ or name O or name CB )) or resid 75 through 104 or resid 127 through 308 or res \ id 314 through 377 or resid 419 through 430)) selection = (chain 'M' and (resid 9 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 308 or resid 314 throu \ gh 377 or resid 419 through 430)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.590 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: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 37.420 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.321 41453 Z= 0.185 Angle : 0.660 27.021 56187 Z= 0.365 Chirality : 0.042 0.168 6516 Planarity : 0.004 0.051 7419 Dihedral : 17.126 89.593 15382 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 0.99 % Allowed : 22.98 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 5255 helix: 0.23 (0.12), residues: 2077 sheet: -0.78 (0.19), residues: 853 loop : -0.93 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 368 TYR 0.025 0.001 TYR I 214 PHE 0.021 0.001 PHE I 4 HIS 0.002 0.001 HIS J 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (41447) covalent geometry : angle 0.63403 / 0.35 (56175) SS BOND : bond 0.18262 / 10.46 ( 6) SS BOND : angle 12.61105 / 6.98 ( 12) hydrogen bonds : bond 0.16252 / 10.94 ( 1881) hydrogen bonds : angle 7.80338 / 5.50 ( 6237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 774 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7714 (tp30) cc_final: 0.7314 (pp20) REVERT: A 181 ILE cc_start: 0.6719 (mp) cc_final: 0.6431 (mp) REVERT: A 315 ILE cc_start: 0.7765 (tp) cc_final: 0.7369 (tp) REVERT: A 400 ASN cc_start: 0.8604 (m-40) cc_final: 0.8207 (p0) REVERT: A 402 ASP cc_start: 0.8588 (m-30) cc_final: 0.7885 (t0) REVERT: A 430 ASN cc_start: 0.9247 (m-40) cc_final: 0.8246 (p0) REVERT: C 91 LYS cc_start: 0.8689 (mttp) cc_final: 0.8164 (mmmm) REVERT: C 170 MET cc_start: 0.9000 (tpp) cc_final: 0.8681 (ttm) REVERT: C 174 MET cc_start: 0.8769 (tpt) cc_final: 0.8539 (mmm) REVERT: C 329 LEU cc_start: 0.8597 (mt) cc_final: 0.8087 (tp) REVERT: D 172 MET cc_start: 0.8188 (tpp) cc_final: 0.7191 (tpt) REVERT: D 278 SER cc_start: 0.8527 (t) cc_final: 0.7260 (t) REVERT: E 32 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8332 (mm) REVERT: E 76 THR cc_start: 0.7749 (p) cc_final: 0.7509 (t) REVERT: F 70 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6742 (tt0) REVERT: F 91 LYS cc_start: 0.7249 (mttp) cc_final: 0.6963 (mmmm) REVERT: F 156 MET cc_start: 0.6065 (tpp) cc_final: 0.5420 (tpt) REVERT: F 201 LEU cc_start: 0.8895 (tp) cc_final: 0.8604 (mt) REVERT: F 230 LEU cc_start: 0.8826 (tt) cc_final: 0.8600 (pp) REVERT: F 237 TYR cc_start: 0.8981 (t80) cc_final: 0.8652 (t80) REVERT: F 285 LEU cc_start: 0.8885 (tt) cc_final: 0.8531 (mm) REVERT: G 91 LYS cc_start: 0.8851 (mttp) cc_final: 0.8506 (mtmt) REVERT: H 12 ARG cc_start: 0.6365 (mmm160) cc_final: 0.5948 (mtm110) REVERT: H 14 HIS cc_start: 0.7990 (t-90) cc_final: 0.7334 (p90) REVERT: H 82 PHE cc_start: 0.7394 (t80) cc_final: 0.6781 (t80) REVERT: H 91 LYS cc_start: 0.6746 (mttp) cc_final: 0.6501 (mtmt) REVERT: H 200 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8773 (mt-10) REVERT: H 201 LEU cc_start: 0.8880 (tp) cc_final: 0.8615 (tt) REVERT: H 371 LEU cc_start: 0.9077 (mm) cc_final: 0.8795 (mm) REVERT: I 91 LYS cc_start: 0.8230 (mttp) cc_final: 0.7828 (mtmt) REVERT: I 92 ILE cc_start: 0.7927 (mt) cc_final: 0.7540 (tt) REVERT: I 156 MET cc_start: 0.8060 (tpp) cc_final: 0.7453 (tpt) REVERT: I 172 MET cc_start: 0.9101 (tpp) cc_final: 0.8551 (tpp) REVERT: I 181 ILE cc_start: 0.8476 (mp) cc_final: 0.8253 (mm) REVERT: I 196 GLU cc_start: 0.8198 (pt0) cc_final: 0.7473 (pt0) REVERT: J 4 PHE cc_start: 0.4805 (OUTLIER) cc_final: 0.2893 (m-80) REVERT: J 32 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8938 (mm) REVERT: J 93 TYR cc_start: 0.8407 (m-80) cc_final: 0.7991 (m-80) REVERT: J 156 MET cc_start: 0.8683 (tpp) cc_final: 0.8437 (tpp) REVERT: J 236 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8202 (mt-10) REVERT: K 83 GLU cc_start: 0.7634 (tp30) cc_final: 0.6900 (pp20) REVERT: K 172 MET cc_start: 0.8660 (tpp) cc_final: 0.8129 (mmt) REVERT: K 206 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6837 (ttp-170) REVERT: K 380 TYR cc_start: 0.9268 (m-80) cc_final: 0.8938 (m-80) REVERT: L 88 LEU cc_start: 0.9094 (mt) cc_final: 0.8873 (mp) REVERT: L 91 LYS cc_start: 0.8562 (mttp) cc_final: 0.8142 (mttt) REVERT: L 197 PHE cc_start: 0.9037 (t80) cc_final: 0.8829 (t80) REVERT: L 212 LEU cc_start: 0.8080 (tt) cc_final: 0.7846 (tt) REVERT: L 304 VAL cc_start: 0.8695 (t) cc_final: 0.8462 (p) outliers start: 43 outliers final: 8 residues processed: 803 average time/residue: 0.2591 time to fit residues: 332.9577 Evaluate side-chains 428 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 417 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 395 ASP Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain M residue 70 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [394, 430, 41, 265, 523, 497, 414, 310, 488, 366, 223] chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 50.0000 chunk 223 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 GLN A 199 HIS B 47 GLN B 65 GLN B 199 HIS B 400 ASN C 14 HIS C 47 GLN C 199 HIS C 409 GLN D 2 ASN D 199 HIS D 282 GLN D 400 ASN E 47 GLN E 199 HIS E 338 HIS F 47 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 HIS F 226 ASN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN G 199 HIS G 346 HIS H 47 GLN H 202 GLN I 47 GLN I 199 HIS I 359 GLN I 423 ASN I 430 ASN J 47 GLN J 199 HIS J 400 ASN K 47 GLN K 199 HIS ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN L 378 GLN M 47 GLN M 199 HIS ** M 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 423 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.077078 restraints weight = 101909.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.077471 restraints weight = 68292.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.078148 restraints weight = 51005.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.078600 restraints weight = 45576.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078929 restraints weight = 39741.713| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 41453 Z= 0.186 Angle : 0.639 15.564 56187 Z= 0.329 Chirality : 0.045 0.225 6516 Planarity : 0.004 0.045 7419 Dihedral : 4.379 53.609 5839 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.32 % Allowed : 21.88 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.11), residues: 5255 helix: 0.34 (0.11), residues: 2118 sheet: -0.47 (0.19), residues: 785 loop : -0.93 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 254 TYR 0.020 0.001 TYR K 386 PHE 0.021 0.001 PHE I 248 HIS 0.009 0.001 HIS M 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (41447) covalent geometry : angle 0.63915 / 0.33 (56175) SS BOND : bond 0.00918 / 0.56 ( 6) SS BOND : angle 0.82555 / 0.37 ( 12) hydrogen bonds : bond 0.04665 / 3.21 ( 1881) hydrogen bonds : angle 5.45434 / 3.81 ( 6237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 414 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ASP cc_start: 0.8327 (m-30) cc_final: 0.7834 (t0) REVERT: A 430 ASN cc_start: 0.8133 (m-40) cc_final: 0.7336 (p0) REVERT: B 36 ASP cc_start: 0.8421 (p0) cc_final: 0.8216 (p0) REVERT: B 193 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8189 (tp30) REVERT: B 261 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8227 (t0) REVERT: B 412 MET cc_start: 0.8099 (mpp) cc_final: 0.7864 (mpp) REVERT: C 82 PHE cc_start: 0.8501 (t80) cc_final: 0.8175 (t80) REVERT: C 91 LYS cc_start: 0.8718 (mttp) cc_final: 0.8495 (mmmm) REVERT: C 329 LEU cc_start: 0.8847 (mt) cc_final: 0.8388 (tp) REVERT: C 371 LEU cc_start: 0.9214 (mm) cc_final: 0.8998 (mm) REVERT: C 380 TYR cc_start: 0.8393 (m-80) cc_final: 0.8162 (m-80) REVERT: D 172 MET cc_start: 0.8989 (tpp) cc_final: 0.8578 (tpt) REVERT: D 199 HIS cc_start: 0.8984 (OUTLIER) cc_final: 0.8730 (t70) REVERT: D 371 LEU cc_start: 0.8997 (mm) cc_final: 0.8617 (pp) REVERT: E 93 TYR cc_start: 0.8448 (m-10) cc_final: 0.7989 (m-10) REVERT: E 285 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8672 (mp) REVERT: F 91 LYS cc_start: 0.8644 (mttp) cc_final: 0.7996 (mtmt) REVERT: F 156 MET cc_start: 0.8223 (tpp) cc_final: 0.7813 (tpt) REVERT: G 57 ILE cc_start: 0.9330 (mp) cc_final: 0.9014 (mm) REVERT: G 91 LYS cc_start: 0.9010 (mttp) cc_final: 0.8667 (mtmt) REVERT: G 388 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7723 (mmm160) REVERT: H 82 PHE cc_start: 0.8228 (t80) cc_final: 0.7850 (t80) REVERT: H 309 GLU cc_start: 0.6131 (OUTLIER) cc_final: 0.4122 (tp30) REVERT: I 91 LYS cc_start: 0.8854 (mttp) cc_final: 0.8546 (mtpt) REVERT: I 92 ILE cc_start: 0.8899 (mt) cc_final: 0.8663 (tt) REVERT: I 156 MET cc_start: 0.8235 (tpp) cc_final: 0.7874 (tpp) REVERT: I 172 MET cc_start: 0.8703 (tpp) cc_final: 0.8426 (mpp) REVERT: I 181 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8581 (mm) REVERT: I 371 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8196 (mm) REVERT: I 393 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.6984 (m-30) REVERT: I 412 MET cc_start: 0.8270 (mmm) cc_final: 0.6712 (mmm) REVERT: J 4 PHE cc_start: 0.4678 (OUTLIER) cc_final: 0.2561 (m-80) REVERT: J 348 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8744 (pt) REVERT: J 380 TYR cc_start: 0.8611 (m-80) cc_final: 0.8248 (m-80) REVERT: K 138 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8458 (m) REVERT: K 206 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6721 (mtp180) REVERT: K 223 GLU cc_start: 0.8298 (tt0) cc_final: 0.8090 (tp30) REVERT: K 380 TYR cc_start: 0.9189 (m-80) cc_final: 0.8953 (m-80) REVERT: K 386 TYR cc_start: 0.5289 (t80) cc_final: 0.4921 (t80) REVERT: L 82 PHE cc_start: 0.7552 (t80) cc_final: 0.7292 (t80) REVERT: L 91 LYS cc_start: 0.8593 (mttp) cc_final: 0.8235 (mttt) REVERT: L 172 MET cc_start: 0.8895 (mtt) cc_final: 0.8662 (mtp) REVERT: L 252 MET cc_start: 0.8708 (tpp) cc_final: 0.8451 (tpp) REVERT: M 172 MET cc_start: 0.8216 (tpt) cc_final: 0.7802 (tpt) outliers start: 187 outliers final: 84 residues processed: 572 average time/residue: 0.2293 time to fit residues: 218.0150 Evaluate side-chains 443 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 348 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 14 HIS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 38 CYS Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 346 HIS Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 199 HIS Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 262 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 346 HIS Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 393 ASP Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 135 THR Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 38 CYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 376 GLN Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 302 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [92, 495, 17, 170, 262, 71, 313, 70, 91, 117, 323] chunk 92 optimal weight: 5.9990 chunk 495 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 313 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 91 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 HIS E 199 HIS F 78 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN G 346 HIS ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 359 GLN H 430 ASN ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN M 359 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.115295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.076486 restraints weight = 100744.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.078661 restraints weight = 65249.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078838 restraints weight = 40161.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079140 restraints weight = 40351.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.080616 restraints weight = 35512.538| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41453 Z= 0.116 Angle : 0.568 14.629 56187 Z= 0.286 Chirality : 0.043 0.286 6516 Planarity : 0.004 0.037 7419 Dihedral : 4.105 53.602 5828 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.12 % Allowed : 22.82 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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 (0.12), residues: 5255 helix: 0.60 (0.12), residues: 2083 sheet: -0.31 (0.20), residues: 762 loop : -0.77 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 336 TYR 0.019 0.001 TYR F 237 PHE 0.011 0.001 PHE I 4 HIS 0.010 0.001 HIS G 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (41447) covalent geometry : angle 0.56768 / 0.29 (56175) SS BOND : bond 0.00509 / 0.30 ( 6) SS BOND : angle 0.92726 / 0.48 ( 12) hydrogen bonds : bond 0.03984 / 2.76 ( 1881) hydrogen bonds : angle 5.03771 / 3.52 ( 6237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 381 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.8104 (m) cc_final: 0.7879 (p) REVERT: A 402 ASP cc_start: 0.8477 (m-30) cc_final: 0.7926 (t0) REVERT: A 430 ASN cc_start: 0.8362 (m-40) cc_final: 0.7507 (p0) REVERT: B 36 ASP cc_start: 0.8534 (p0) cc_final: 0.8303 (p0) REVERT: B 193 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8323 (tp30) REVERT: B 306 LEU cc_start: 0.8481 (pp) cc_final: 0.8165 (tt) REVERT: C 82 PHE cc_start: 0.8553 (t80) cc_final: 0.8169 (t80) REVERT: C 91 LYS cc_start: 0.8729 (mttp) cc_final: 0.8278 (mmmm) REVERT: C 282 GLN cc_start: 0.9022 (tp40) cc_final: 0.8562 (tm-30) REVERT: C 329 LEU cc_start: 0.8724 (mt) cc_final: 0.8257 (tp) REVERT: C 371 LEU cc_start: 0.9325 (mm) cc_final: 0.9105 (mm) REVERT: C 380 TYR cc_start: 0.8411 (m-80) cc_final: 0.8168 (m-80) REVERT: C 414 GLU cc_start: 0.8625 (tt0) cc_final: 0.8294 (tm-30) REVERT: D 172 MET cc_start: 0.9101 (tpp) cc_final: 0.8689 (tpt) REVERT: D 199 HIS cc_start: 0.9066 (OUTLIER) cc_final: 0.8651 (t70) REVERT: D 371 LEU cc_start: 0.9097 (mm) cc_final: 0.8627 (pp) REVERT: E 172 MET cc_start: 0.8254 (tpp) cc_final: 0.8001 (tpp) REVERT: E 285 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8737 (mp) REVERT: E 370 MET cc_start: 0.8713 (tmm) cc_final: 0.8513 (ptt) REVERT: F 91 LYS cc_start: 0.8366 (mttp) cc_final: 0.7718 (mtmt) REVERT: F 156 MET cc_start: 0.8144 (tpp) cc_final: 0.7561 (tpt) REVERT: F 371 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8515 (mm) REVERT: F 430 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.6931 (p0) REVERT: G 57 ILE cc_start: 0.9165 (mp) cc_final: 0.8802 (mm) REVERT: G 91 LYS cc_start: 0.8977 (mttp) cc_final: 0.8449 (mtmt) REVERT: G 128 ASN cc_start: 0.8581 (p0) cc_final: 0.8326 (t0) REVERT: G 412 MET cc_start: 0.8203 (tpt) cc_final: 0.7835 (tpt) REVERT: H 82 PHE cc_start: 0.8325 (t80) cc_final: 0.7805 (t80) REVERT: H 181 ILE cc_start: 0.8677 (mp) cc_final: 0.8370 (mm) REVERT: H 201 LEU cc_start: 0.9156 (tt) cc_final: 0.8903 (tt) REVERT: I 91 LYS cc_start: 0.8726 (mttp) cc_final: 0.8215 (mtpt) REVERT: I 92 ILE cc_start: 0.8738 (mt) cc_final: 0.8434 (tt) REVERT: I 172 MET cc_start: 0.8935 (tpp) cc_final: 0.8727 (tpp) REVERT: I 181 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8375 (mm) REVERT: I 370 MET cc_start: 0.8638 (ppp) cc_final: 0.8352 (ppp) REVERT: I 371 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8249 (mm) REVERT: J 4 PHE cc_start: 0.4358 (OUTLIER) cc_final: 0.2468 (m-80) REVERT: J 156 MET cc_start: 0.8645 (tpp) cc_final: 0.7815 (tpt) REVERT: J 370 MET cc_start: 0.8481 (ppp) cc_final: 0.8229 (ppp) REVERT: J 373 ARG cc_start: 0.8929 (ttt180) cc_final: 0.8669 (ttt180) REVERT: J 380 TYR cc_start: 0.8772 (m-80) cc_final: 0.8372 (m-80) REVERT: K 206 ARG cc_start: 0.7351 (mtp180) cc_final: 0.6733 (ttp-170) REVERT: K 380 TYR cc_start: 0.9342 (m-80) cc_final: 0.9075 (m-80) REVERT: L 38 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7856 (m) REVERT: L 82 PHE cc_start: 0.7589 (t80) cc_final: 0.7172 (t80) REVERT: L 91 LYS cc_start: 0.8377 (mttp) cc_final: 0.7977 (mttt) REVERT: L 156 MET cc_start: 0.8599 (ttm) cc_final: 0.8379 (ttm) REVERT: M 91 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8649 (mtmt) REVERT: M 166 LYS cc_start: 0.8811 (ptmt) cc_final: 0.8451 (ptmt) REVERT: M 172 MET cc_start: 0.8206 (tpt) cc_final: 0.7736 (tpt) REVERT: M 371 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7476 (mt) REVERT: M 412 MET cc_start: 0.8717 (tpt) cc_final: 0.8286 (tpp) outliers start: 135 outliers final: 79 residues processed: 487 average time/residue: 0.2297 time to fit residues: 185.4201 Evaluate side-chains 425 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 337 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain E residue 29 GLU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 346 HIS Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 346 HIS Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 38 CYS Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 285 LEU Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 38 CYS Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 371 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [71, 188, 407, 501, 231, 177, 508, 194, 445, 87, 305] chunk 71 optimal weight: 0.8980 chunk 188 optimal weight: 20.0000 chunk 407 optimal weight: 9.9990 chunk 501 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 508 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 445 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 199 HIS ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 202 GLN G 346 HIS ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 199 HIS I 346 HIS K 47 GLN ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN M 378 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.111901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073135 restraints weight = 101382.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.074290 restraints weight = 64235.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.074776 restraints weight = 44452.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075146 restraints weight = 42855.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075361 restraints weight = 36662.218| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 41453 Z= 0.201 Angle : 0.604 14.911 56187 Z= 0.307 Chirality : 0.044 0.205 6516 Planarity : 0.004 0.040 7419 Dihedral : 4.171 55.406 5827 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 21.99 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.30 (0.12), residues: 5255 helix: 0.65 (0.12), residues: 2112 sheet: -0.41 (0.19), residues: 791 loop : -0.84 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 273 TYR 0.024 0.001 TYR F 237 PHE 0.018 0.001 PHE F 51 HIS 0.045 0.001 HIS G 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (41447) covalent geometry : angle 0.60351 / 0.31 (56175) SS BOND : bond 0.00322 / 0.19 ( 6) SS BOND : angle 1.16139 / 0.56 ( 12) hydrogen bonds : bond 0.04349 / 2.98 ( 1881) hydrogen bonds : angle 4.86969 / 3.41 ( 6237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 342 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ILE cc_start: 0.9314 (mm) cc_final: 0.9077 (mm) REVERT: A 402 ASP cc_start: 0.8471 (m-30) cc_final: 0.7969 (t0) REVERT: A 430 ASN cc_start: 0.8435 (m-40) cc_final: 0.7550 (p0) REVERT: B 36 ASP cc_start: 0.8640 (p0) cc_final: 0.8425 (p0) REVERT: B 306 LEU cc_start: 0.8526 (pp) cc_final: 0.8294 (tp) REVERT: B 348 ILE cc_start: 0.8886 (pt) cc_final: 0.8678 (pt) REVERT: C 91 LYS cc_start: 0.8851 (mttp) cc_final: 0.8281 (mmmm) REVERT: C 371 LEU cc_start: 0.9385 (mm) cc_final: 0.9180 (mm) REVERT: C 380 TYR cc_start: 0.8471 (m-80) cc_final: 0.8252 (m-80) REVERT: D 172 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8732 (tpt) REVERT: D 199 HIS cc_start: 0.9138 (OUTLIER) cc_final: 0.8863 (t70) REVERT: D 402 ASP cc_start: 0.8865 (m-30) cc_final: 0.8034 (t0) REVERT: E 22 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (mm) REVERT: E 93 TYR cc_start: 0.8397 (m-80) cc_final: 0.8026 (m-10) REVERT: E 172 MET cc_start: 0.8272 (tpp) cc_final: 0.8011 (tpp) REVERT: E 252 MET cc_start: 0.8877 (mmt) cc_final: 0.8624 (mmm) REVERT: E 285 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8729 (mp) REVERT: E 370 MET cc_start: 0.8780 (tmm) cc_final: 0.8502 (ptp) REVERT: F 91 LYS cc_start: 0.8414 (mttp) cc_final: 0.7775 (mtpt) REVERT: F 156 MET cc_start: 0.8292 (tpp) cc_final: 0.7588 (tpt) REVERT: F 236 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8807 (tm-30) REVERT: F 430 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.6887 (p0) REVERT: G 91 LYS cc_start: 0.8987 (mttp) cc_final: 0.8421 (mtmt) REVERT: G 388 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7743 (mmm160) REVERT: G 412 MET cc_start: 0.8262 (tpt) cc_final: 0.7915 (tpt) REVERT: H 201 LEU cc_start: 0.9200 (tt) cc_final: 0.8959 (tt) REVERT: H 309 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.4035 (tp30) REVERT: I 91 LYS cc_start: 0.8851 (mttp) cc_final: 0.8326 (mtpt) REVERT: I 92 ILE cc_start: 0.8853 (mt) cc_final: 0.8546 (tt) REVERT: I 181 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8638 (mm) REVERT: I 190 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5445 (ptp-170) REVERT: I 370 MET cc_start: 0.8760 (ppp) cc_final: 0.8543 (ppp) REVERT: I 371 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8227 (mm) REVERT: J 4 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.2392 (m-80) REVERT: J 156 MET cc_start: 0.8714 (tpp) cc_final: 0.7957 (tpt) REVERT: J 348 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8670 (pt) REVERT: J 373 ARG cc_start: 0.8943 (ttt180) cc_final: 0.8642 (ttt180) REVERT: K 84 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7210 (ttp) REVERT: K 223 GLU cc_start: 0.8489 (tt0) cc_final: 0.8129 (tp30) REVERT: K 380 TYR cc_start: 0.9323 (m-80) cc_final: 0.9070 (m-80) REVERT: L 38 CYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7912 (m) REVERT: L 82 PHE cc_start: 0.7642 (t80) cc_final: 0.7388 (t80) REVERT: L 91 LYS cc_start: 0.8431 (mttp) cc_final: 0.8203 (mtmt) REVERT: M 91 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8648 (mtmt) REVERT: M 172 MET cc_start: 0.8209 (tpt) cc_final: 0.7972 (tpt) REVERT: M 328 TYR cc_start: 0.7668 (t80) cc_final: 0.7359 (t80) REVERT: M 344 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8506 (mm) REVERT: M 371 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7594 (mt) outliers start: 194 outliers final: 129 residues processed: 499 average time/residue: 0.2245 time to fit residues: 187.1534 Evaluate side-chains 463 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 317 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 199 HIS Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 190 ARG Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 190 ARG Chi-restraints excluded: chain I residue 199 HIS Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 346 HIS Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 38 CYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [198, 244, 16, 332, 316, 481, 253, 345, 281, 421, 15] chunk 198 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 481 optimal weight: 0.0170 chunk 253 optimal weight: 0.1980 chunk 345 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN D 199 HIS D 202 GLN D 409 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 410 GLN M 359 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.111681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.074796 restraints weight = 101364.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.074737 restraints weight = 61106.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075129 restraints weight = 46326.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.075314 restraints weight = 42925.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077044 restraints weight = 37411.605| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 41453 Z= 0.171 Angle : 0.586 14.769 56187 Z= 0.294 Chirality : 0.043 0.278 6516 Planarity : 0.004 0.041 7419 Dihedral : 4.139 57.005 5827 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.39 % Allowed : 23.08 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.22 (0.12), residues: 5255 helix: 0.76 (0.12), residues: 2098 sheet: -0.45 (0.19), residues: 795 loop : -0.79 (0.13), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 373 TYR 0.021 0.001 TYR F 237 PHE 0.015 0.001 PHE I 4 HIS 0.020 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (41447) covalent geometry : angle 0.58609 / 0.29 (56175) SS BOND : bond 0.00458 / 0.29 ( 6) SS BOND : angle 0.86804 / 0.42 ( 12) hydrogen bonds : bond 0.04087 / 2.81 ( 1881) hydrogen bonds : angle 4.75644 / 3.33 ( 6237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 336 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: A 402 ASP cc_start: 0.8504 (m-30) cc_final: 0.8018 (t0) REVERT: A 430 ASN cc_start: 0.8413 (m-40) cc_final: 0.7517 (p0) REVERT: B 36 ASP cc_start: 0.8602 (p0) cc_final: 0.8374 (p0) REVERT: B 348 ILE cc_start: 0.8879 (pt) cc_final: 0.8667 (pt) REVERT: C 91 LYS cc_start: 0.8823 (mttp) cc_final: 0.8214 (mmmm) REVERT: C 172 MET cc_start: 0.8496 (mmp) cc_final: 0.8137 (mmt) REVERT: C 380 TYR cc_start: 0.8476 (m-80) cc_final: 0.8260 (m-80) REVERT: D 172 MET cc_start: 0.9086 (tpp) cc_final: 0.8744 (tpt) REVERT: D 402 ASP cc_start: 0.8874 (m-30) cc_final: 0.8064 (t0) REVERT: E 22 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8047 (mm) REVERT: E 172 MET cc_start: 0.8262 (tpp) cc_final: 0.7991 (tpp) REVERT: E 252 MET cc_start: 0.8871 (mmt) cc_final: 0.8627 (mmm) REVERT: E 370 MET cc_start: 0.8837 (tmm) cc_final: 0.8556 (ptm) REVERT: F 91 LYS cc_start: 0.8304 (mttp) cc_final: 0.7704 (mtpt) REVERT: F 156 MET cc_start: 0.8366 (tpp) cc_final: 0.7764 (tpt) REVERT: F 170 MET cc_start: 0.7887 (mmm) cc_final: 0.6854 (tmm) REVERT: F 236 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8828 (tm-30) REVERT: F 430 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.6927 (p0) REVERT: G 91 LYS cc_start: 0.8955 (mttp) cc_final: 0.8383 (mtmt) REVERT: G 172 MET cc_start: 0.8867 (mmm) cc_final: 0.8620 (mmm) REVERT: G 388 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7754 (mmm160) REVERT: G 412 MET cc_start: 0.8146 (tpt) cc_final: 0.7923 (tpt) REVERT: I 91 LYS cc_start: 0.8839 (mttp) cc_final: 0.8266 (mtpt) REVERT: I 92 ILE cc_start: 0.8839 (mt) cc_final: 0.8499 (tt) REVERT: I 170 MET cc_start: 0.9101 (mmt) cc_final: 0.8842 (mmp) REVERT: I 181 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8630 (mm) REVERT: I 354 LYS cc_start: 0.9279 (tppp) cc_final: 0.9036 (tppt) REVERT: I 370 MET cc_start: 0.8830 (ppp) cc_final: 0.8625 (ppp) REVERT: I 371 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8160 (mm) REVERT: J 4 PHE cc_start: 0.4391 (OUTLIER) cc_final: 0.2373 (m-80) REVERT: J 156 MET cc_start: 0.8724 (tpp) cc_final: 0.7966 (tpt) REVERT: J 348 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8645 (pt) REVERT: J 373 ARG cc_start: 0.8967 (ttt180) cc_final: 0.8645 (ttt180) REVERT: K 84 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (ttp) REVERT: K 223 GLU cc_start: 0.8475 (tt0) cc_final: 0.8092 (tp30) REVERT: K 318 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8376 (tm-30) REVERT: K 380 TYR cc_start: 0.9350 (m-80) cc_final: 0.9076 (m-80) REVERT: L 38 CYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7926 (m) REVERT: L 82 PHE cc_start: 0.7514 (t80) cc_final: 0.7287 (t80) REVERT: L 91 LYS cc_start: 0.8379 (mttp) cc_final: 0.7915 (mttt) REVERT: M 166 LYS cc_start: 0.8928 (ptmt) cc_final: 0.8703 (ptmt) REVERT: M 172 MET cc_start: 0.8198 (tpt) cc_final: 0.7776 (tpt) REVERT: M 328 TYR cc_start: 0.7664 (t80) cc_final: 0.7331 (t80) REVERT: M 344 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8349 (mm) REVERT: M 371 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7669 (mt) REVERT: M 412 MET cc_start: 0.8572 (tpt) cc_final: 0.8229 (tpp) outliers start: 190 outliers final: 131 residues processed: 490 average time/residue: 0.2243 time to fit residues: 183.6912 Evaluate side-chains 463 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 319 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 32 LEU Chi-restraints excluded: chain L residue 38 CYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain L residue 430 ASN Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [120, 122, 479, 13, 356, 344, 313, 395, 473, 260, 69] chunk 120 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 356 optimal weight: 7.9990 chunk 344 optimal weight: 5.9990 chunk 313 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 473 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 202 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 400 ASN I 346 HIS ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.109377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.070211 restraints weight = 102124.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071527 restraints weight = 63648.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.072213 restraints weight = 43662.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072976 restraints weight = 39291.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.072983 restraints weight = 35135.480| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 41453 Z= 0.242 Angle : 0.648 14.818 56187 Z= 0.327 Chirality : 0.045 0.173 6516 Planarity : 0.004 0.043 7419 Dihedral : 4.404 58.913 5827 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.04 % Allowed : 23.22 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.32 (0.12), residues: 5255 helix: 0.74 (0.12), residues: 2091 sheet: -0.62 (0.19), residues: 810 loop : -0.86 (0.13), residues: 2354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 119 TYR 0.022 0.002 TYR F 237 PHE 0.026 0.002 PHE M 280 HIS 0.005 0.001 HIS I 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (41447) covalent geometry : angle 0.64787 / 0.33 (56175) SS BOND : bond 0.00421 / 0.25 ( 6) SS BOND : angle 0.79703 / 0.37 ( 12) hydrogen bonds : bond 0.04611 / 3.15 ( 1881) hydrogen bonds : angle 4.81051 / 3.37 ( 6237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 332 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 402 ASP cc_start: 0.8521 (m-30) cc_final: 0.8079 (t0) REVERT: B 243 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (ptmt) REVERT: C 91 LYS cc_start: 0.8872 (mttp) cc_final: 0.8304 (mmmm) REVERT: C 172 MET cc_start: 0.8495 (mmp) cc_final: 0.8268 (mmt) REVERT: C 268 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: C 273 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7594 (ptm160) REVERT: C 380 TYR cc_start: 0.8414 (m-80) cc_final: 0.8211 (m-80) REVERT: D 172 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8733 (tpt) REVERT: D 402 ASP cc_start: 0.8905 (m-30) cc_final: 0.8116 (t0) REVERT: E 172 MET cc_start: 0.8296 (tpp) cc_final: 0.8017 (tpp) REVERT: E 190 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.4067 (mmt180) REVERT: E 223 GLU cc_start: 0.9249 (tp30) cc_final: 0.8935 (tp30) REVERT: E 252 MET cc_start: 0.8952 (mmt) cc_final: 0.8677 (mmm) REVERT: E 285 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8714 (mp) REVERT: E 302 TYR cc_start: 0.8152 (m-10) cc_final: 0.7819 (m-10) REVERT: E 370 MET cc_start: 0.8920 (tmm) cc_final: 0.8659 (ptm) REVERT: F 91 LYS cc_start: 0.8300 (mttp) cc_final: 0.7631 (mtmt) REVERT: F 156 MET cc_start: 0.8414 (tpp) cc_final: 0.7826 (tpt) REVERT: F 236 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: F 430 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.6954 (p0) REVERT: G 91 LYS cc_start: 0.8961 (mttp) cc_final: 0.8375 (mtmt) REVERT: G 388 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7732 (mmm160) REVERT: H 82 PHE cc_start: 0.8585 (t80) cc_final: 0.7972 (t80) REVERT: H 129 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9180 (tt) REVERT: H 309 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.4004 (tp30) REVERT: I 91 LYS cc_start: 0.8926 (mttp) cc_final: 0.8294 (mtpt) REVERT: I 92 ILE cc_start: 0.8906 (mt) cc_final: 0.8504 (tt) REVERT: I 170 MET cc_start: 0.9082 (mmt) cc_final: 0.8831 (mmp) REVERT: I 172 MET cc_start: 0.8955 (mmm) cc_final: 0.8638 (mmp) REVERT: I 181 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8832 (mm) REVERT: I 354 LYS cc_start: 0.9359 (tppp) cc_final: 0.9012 (tppt) REVERT: I 371 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8179 (mm) REVERT: J 4 PHE cc_start: 0.4467 (OUTLIER) cc_final: 0.2321 (m-80) REVERT: J 156 MET cc_start: 0.8829 (tpp) cc_final: 0.8198 (tpt) REVERT: J 201 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8892 (tt) REVERT: J 348 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8681 (pt) REVERT: J 370 MET cc_start: 0.8515 (ppp) cc_final: 0.8314 (ppp) REVERT: J 373 ARG cc_start: 0.8996 (ttt180) cc_final: 0.8646 (ttt90) REVERT: K 223 GLU cc_start: 0.8574 (tt0) cc_final: 0.8103 (tp30) REVERT: K 318 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8342 (tm-30) REVERT: K 380 TYR cc_start: 0.9342 (m-80) cc_final: 0.9061 (m-80) REVERT: K 404 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8321 (mt) REVERT: L 38 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8051 (m) REVERT: L 91 LYS cc_start: 0.8394 (mttp) cc_final: 0.7917 (mttt) REVERT: M 172 MET cc_start: 0.8183 (tpt) cc_final: 0.7826 (tpt) REVERT: M 328 TYR cc_start: 0.7716 (t80) cc_final: 0.7267 (t80) REVERT: M 344 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8305 (mm) REVERT: M 371 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7657 (mt) REVERT: M 412 MET cc_start: 0.8647 (tpt) cc_final: 0.7999 (tpp) outliers start: 218 outliers final: 158 residues processed: 511 average time/residue: 0.2274 time to fit residues: 193.5424 Evaluate side-chains 488 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 309 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 366 LYS Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 190 ARG Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 262 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain I residue 412 MET Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 234 MET Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain K residue 404 ILE Chi-restraints excluded: chain L residue 38 CYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 181 ILE Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [418, 364, 126, 74, 441, 171, 377, 10, 338, 124, 118] chunk 418 optimal weight: 4.9990 chunk 364 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 441 optimal weight: 6.9990 chunk 171 optimal weight: 0.6980 chunk 377 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS F 152 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 GLN ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.110304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.073429 restraints weight = 101431.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073690 restraints weight = 59252.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.074461 restraints weight = 45296.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.074919 restraints weight = 40333.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075283 restraints weight = 35793.877| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41453 Z= 0.167 Angle : 0.598 15.114 56187 Z= 0.300 Chirality : 0.043 0.181 6516 Planarity : 0.004 0.042 7419 Dihedral : 4.250 57.655 5827 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.46 % Allowed : 23.70 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.21 (0.12), residues: 5255 helix: 0.87 (0.12), residues: 2082 sheet: -0.64 (0.18), residues: 815 loop : -0.80 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 119 TYR 0.021 0.001 TYR F 237 PHE 0.021 0.001 PHE E 82 HIS 0.009 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (41447) covalent geometry : angle 0.59812 / 0.30 (56175) SS BOND : bond 0.00359 / 0.20 ( 6) SS BOND : angle 0.75883 / 0.34 ( 12) hydrogen bonds : bond 0.04034 / 2.76 ( 1881) hydrogen bonds : angle 4.65318 / 3.26 ( 6237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 329 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8371 (mp) cc_final: 0.7915 (tt) REVERT: A 193 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: A 243 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8648 (mtpt) REVERT: A 402 ASP cc_start: 0.8502 (m-30) cc_final: 0.8097 (t0) REVERT: B 344 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 366 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9288 (tttm) REVERT: B 373 ARG cc_start: 0.9214 (ptt90) cc_final: 0.8882 (ptt-90) REVERT: C 91 LYS cc_start: 0.8849 (mttp) cc_final: 0.8387 (mmmm) REVERT: C 268 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: C 273 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7514 (ptm160) REVERT: C 366 LYS cc_start: 0.8536 (pttt) cc_final: 0.8303 (tmmt) REVERT: D 172 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8719 (tpt) REVERT: D 402 ASP cc_start: 0.8894 (m-30) cc_final: 0.8115 (t0) REVERT: E 45 LYS cc_start: 0.9254 (mmmm) cc_final: 0.9022 (mmmt) REVERT: E 147 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8214 (mt) REVERT: E 190 ARG cc_start: 0.5425 (OUTLIER) cc_final: 0.4094 (mmt180) REVERT: E 223 GLU cc_start: 0.9259 (tp30) cc_final: 0.8891 (tp30) REVERT: E 252 MET cc_start: 0.8949 (mmt) cc_final: 0.8692 (mmm) REVERT: E 285 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 302 TYR cc_start: 0.8086 (m-10) cc_final: 0.7780 (m-10) REVERT: F 91 LYS cc_start: 0.8245 (mttp) cc_final: 0.7570 (mtpt) REVERT: F 156 MET cc_start: 0.8413 (tpp) cc_final: 0.7836 (tpt) REVERT: F 236 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.8810 (tm-30) REVERT: F 430 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.6960 (p0) REVERT: G 91 LYS cc_start: 0.8953 (mttp) cc_final: 0.8346 (mtmt) REVERT: G 371 LEU cc_start: 0.9694 (OUTLIER) cc_final: 0.9485 (mt) REVERT: G 388 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7708 (mmm160) REVERT: H 129 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9182 (tt) REVERT: H 309 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.3959 (tp30) REVERT: H 315 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7875 (tp) REVERT: I 91 LYS cc_start: 0.8932 (mttp) cc_final: 0.8290 (mtpt) REVERT: I 92 ILE cc_start: 0.8864 (mt) cc_final: 0.8468 (tt) REVERT: I 170 MET cc_start: 0.9031 (mmt) cc_final: 0.8813 (mmp) REVERT: I 172 MET cc_start: 0.8866 (mmm) cc_final: 0.8504 (mmp) REVERT: I 181 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8703 (mm) REVERT: I 354 LYS cc_start: 0.9334 (tppp) cc_final: 0.9012 (tppt) REVERT: I 370 MET cc_start: 0.8457 (ppp) cc_final: 0.8223 (ppp) REVERT: I 371 LEU cc_start: 0.8509 (mm) cc_final: 0.8295 (mm) REVERT: J 4 PHE cc_start: 0.4369 (OUTLIER) cc_final: 0.2337 (m-80) REVERT: J 156 MET cc_start: 0.8789 (tpp) cc_final: 0.8073 (tpt) REVERT: J 201 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8811 (tt) REVERT: J 348 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8674 (pt) REVERT: K 84 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7039 (ttp) REVERT: K 223 GLU cc_start: 0.8528 (tt0) cc_final: 0.8041 (tp30) REVERT: K 318 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8275 (tm-30) REVERT: K 380 TYR cc_start: 0.9346 (m-80) cc_final: 0.9078 (m-80) REVERT: L 91 LYS cc_start: 0.8333 (mttp) cc_final: 0.7845 (mttt) REVERT: L 412 MET cc_start: 0.8853 (mmp) cc_final: 0.7968 (mmm) REVERT: M 91 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8515 (mtmm) REVERT: M 172 MET cc_start: 0.8194 (tpt) cc_final: 0.7858 (tpt) REVERT: M 328 TYR cc_start: 0.7691 (t80) cc_final: 0.7249 (t80) REVERT: M 344 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8270 (mm) REVERT: M 370 MET cc_start: 0.7870 (tmm) cc_final: 0.7151 (tpp) REVERT: M 371 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7414 (mt) REVERT: M 412 MET cc_start: 0.8504 (tpt) cc_final: 0.8208 (tpp) outliers start: 193 outliers final: 138 residues processed: 491 average time/residue: 0.2204 time to fit residues: 181.4874 Evaluate side-chains 472 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 310 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 315 ILE Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 212 LEU Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 269 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [508, 255, 328, 526, 433, 404, 165, 240, 15, 152, 154] chunk 508 optimal weight: 10.0000 chunk 255 optimal weight: 9.9990 chunk 328 optimal weight: 4.9990 chunk 526 optimal weight: 40.0000 chunk 433 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 154 optimal weight: 0.0170 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 199 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN I 400 ASN ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 GLN ** 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 = 0.3767 r_free = 0.3767 target = 0.107792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069203 restraints weight = 101552.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.070551 restraints weight = 60791.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.070827 restraints weight = 41829.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.071106 restraints weight = 41668.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.071522 restraints weight = 36025.626| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 41453 Z= 0.303 Angle : 0.718 16.087 56187 Z= 0.362 Chirality : 0.047 0.181 6516 Planarity : 0.005 0.054 7419 Dihedral : 4.614 53.918 5825 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.97 % Allowed : 23.65 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.54 (0.11), residues: 5255 helix: 0.59 (0.11), residues: 2096 sheet: -0.88 (0.18), residues: 831 loop : -0.96 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 273 TYR 0.022 0.002 TYR F 237 PHE 0.021 0.002 PHE I 4 HIS 0.038 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.30 (41447) covalent geometry : angle 0.71820 / 0.36 (56175) SS BOND : bond 0.00596 / 0.36 ( 6) SS BOND : angle 0.83174 / 0.40 ( 12) hydrogen bonds : bond 0.05040 / 3.44 ( 1881) hydrogen bonds : angle 4.92393 / 3.45 ( 6237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 307 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: A 402 ASP cc_start: 0.8547 (m-30) cc_final: 0.8122 (t0) REVERT: B 344 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8812 (mm) REVERT: B 373 ARG cc_start: 0.9209 (ptt90) cc_final: 0.8878 (ptt-90) REVERT: C 91 LYS cc_start: 0.8866 (mttp) cc_final: 0.8449 (mmmm) REVERT: C 268 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: C 366 LYS cc_start: 0.8556 (pttt) cc_final: 0.8315 (tmmt) REVERT: D 172 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8643 (tpt) REVERT: D 402 ASP cc_start: 0.8926 (m-30) cc_final: 0.8123 (t0) REVERT: E 45 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8952 (mmmm) REVERT: E 147 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8221 (mt) REVERT: E 190 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4272 (mmt180) REVERT: E 223 GLU cc_start: 0.9262 (tp30) cc_final: 0.8937 (tp30) REVERT: E 252 MET cc_start: 0.8974 (mmt) cc_final: 0.8677 (mmm) REVERT: E 285 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8764 (mp) REVERT: E 302 TYR cc_start: 0.8145 (m-10) cc_final: 0.7847 (m-10) REVERT: F 84 MET cc_start: 0.8255 (mtm) cc_final: 0.7743 (mpp) REVERT: F 91 LYS cc_start: 0.8220 (mttp) cc_final: 0.7590 (mtpt) REVERT: F 156 MET cc_start: 0.8424 (tpp) cc_final: 0.7875 (tpt) REVERT: F 236 GLU cc_start: 0.9405 (OUTLIER) cc_final: 0.8868 (tm-30) REVERT: F 268 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: F 430 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7047 (p0) REVERT: G 91 LYS cc_start: 0.8954 (mttp) cc_final: 0.8312 (mtmt) REVERT: G 371 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9404 (mt) REVERT: G 388 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7753 (mmm160) REVERT: H 82 PHE cc_start: 0.8745 (t80) cc_final: 0.8294 (t80) REVERT: H 129 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9262 (tt) REVERT: H 309 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.3935 (tp30) REVERT: I 91 LYS cc_start: 0.8982 (mttp) cc_final: 0.8306 (mtpt) REVERT: I 92 ILE cc_start: 0.8949 (mt) cc_final: 0.8520 (tt) REVERT: I 172 MET cc_start: 0.8948 (mmm) cc_final: 0.8497 (mmp) REVERT: I 181 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9000 (mm) REVERT: I 354 LYS cc_start: 0.9396 (tppp) cc_final: 0.9104 (tppt) REVERT: I 370 MET cc_start: 0.8574 (ppp) cc_final: 0.8332 (ppp) REVERT: I 371 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8416 (mm) REVERT: J 156 MET cc_start: 0.8856 (tpp) cc_final: 0.8182 (tpt) REVERT: J 201 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8925 (tt) REVERT: J 348 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8685 (pt) REVERT: K 318 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8414 (tm-30) REVERT: K 380 TYR cc_start: 0.9356 (m-80) cc_final: 0.9148 (m-80) REVERT: K 404 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8338 (mt) REVERT: L 412 MET cc_start: 0.8881 (mmp) cc_final: 0.8473 (mmm) REVERT: M 172 MET cc_start: 0.8083 (tpt) cc_final: 0.7870 (tpt) REVERT: M 328 TYR cc_start: 0.7746 (t80) cc_final: 0.7182 (t80) REVERT: M 344 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8307 (mm) REVERT: M 370 MET cc_start: 0.7945 (tmm) cc_final: 0.7148 (tpp) REVERT: M 371 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7369 (mt) REVERT: M 412 MET cc_start: 0.8636 (tpt) cc_final: 0.8055 (tpp) outliers start: 215 outliers final: 169 residues processed: 486 average time/residue: 0.2207 time to fit residues: 181.3566 Evaluate side-chains 486 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 296 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 150 CYS Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 345 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 30 ILE Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 150 CYS Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 303 THR Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 351 VAL Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 121 ASP Chi-restraints excluded: chain J residue 129 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 234 MET Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 297 SER Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 49 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 105 ASN Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 321 SER Chi-restraints excluded: chain K residue 348 ILE Chi-restraints excluded: chain K residue 404 ILE Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [226, 301, 66, 475, 397, 149, 454, 464, 500, 441, 177] chunk 226 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 475 optimal weight: 2.9990 chunk 397 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 454 optimal weight: 9.9990 chunk 464 optimal weight: 2.9990 chunk 500 optimal weight: 20.0000 chunk 441 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 199 HIS C 362 GLN E 152 GLN F 152 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.071404 restraints weight = 101211.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.072817 restraints weight = 62183.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.073177 restraints weight = 42553.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.073895 restraints weight = 37834.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.074077 restraints weight = 33619.974| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41453 Z= 0.149 Angle : 0.624 15.559 56187 Z= 0.308 Chirality : 0.044 0.166 6516 Planarity : 0.004 0.048 7419 Dihedral : 4.262 54.206 5824 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.97 % Allowed : 24.83 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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: -0.29 (0.12), residues: 5255 helix: 0.86 (0.12), residues: 2080 sheet: -0.85 (0.18), residues: 827 loop : -0.83 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 273 TYR 0.020 0.001 TYR F 237 PHE 0.020 0.001 PHE E 82 HIS 0.020 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (41447) covalent geometry : angle 0.62419 / 0.31 (56175) SS BOND : bond 0.00353 / 0.19 ( 6) SS BOND : angle 0.79731 / 0.36 ( 12) hydrogen bonds : bond 0.03958 / 2.71 ( 1881) hydrogen bonds : angle 4.66140 / 3.27 ( 6237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 322 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8494 (mp) cc_final: 0.8021 (tt) REVERT: A 193 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 243 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8626 (mtpt) REVERT: A 402 ASP cc_start: 0.8531 (m-30) cc_final: 0.8124 (t0) REVERT: B 344 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8752 (mm) REVERT: B 366 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9249 (tttm) REVERT: B 373 ARG cc_start: 0.9203 (ptt90) cc_final: 0.8861 (ptt-90) REVERT: C 91 LYS cc_start: 0.8832 (mttp) cc_final: 0.8416 (mmmm) REVERT: C 268 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8315 (tp30) REVERT: C 273 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7565 (ptm160) REVERT: C 366 LYS cc_start: 0.8601 (pttt) cc_final: 0.8346 (tmmt) REVERT: D 172 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8646 (tpt) REVERT: D 402 ASP cc_start: 0.8924 (m-30) cc_final: 0.8136 (t0) REVERT: E 45 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8970 (mmmm) REVERT: E 147 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8218 (mt) REVERT: E 172 MET cc_start: 0.8281 (tpp) cc_final: 0.8010 (tpp) REVERT: E 190 ARG cc_start: 0.5617 (OUTLIER) cc_final: 0.4267 (mmt180) REVERT: E 223 GLU cc_start: 0.9251 (tp30) cc_final: 0.8912 (tp30) REVERT: E 252 MET cc_start: 0.8979 (mmt) cc_final: 0.8710 (mmm) REVERT: E 285 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8757 (mp) REVERT: E 302 TYR cc_start: 0.8085 (m-10) cc_final: 0.7804 (m-10) REVERT: F 91 LYS cc_start: 0.8179 (mttp) cc_final: 0.7544 (mtpt) REVERT: F 156 MET cc_start: 0.8405 (tpp) cc_final: 0.7854 (tpt) REVERT: F 236 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8846 (tm-30) REVERT: F 268 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: F 404 ILE cc_start: 0.8479 (mm) cc_final: 0.8272 (pt) REVERT: F 430 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.6864 (p0) REVERT: G 91 LYS cc_start: 0.8973 (mttp) cc_final: 0.8330 (mtmt) REVERT: G 371 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9454 (mt) REVERT: G 388 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7788 (mmm160) REVERT: H 82 PHE cc_start: 0.8727 (t80) cc_final: 0.8257 (t80) REVERT: H 129 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9233 (tt) REVERT: H 309 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.3869 (tp30) REVERT: I 91 LYS cc_start: 0.8966 (mttp) cc_final: 0.8273 (mtpt) REVERT: I 92 ILE cc_start: 0.8784 (mt) cc_final: 0.8416 (tt) REVERT: I 170 MET cc_start: 0.9080 (mmt) cc_final: 0.8815 (mmp) REVERT: I 172 MET cc_start: 0.8873 (mmm) cc_final: 0.8494 (mmp) REVERT: I 181 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8815 (mm) REVERT: I 354 LYS cc_start: 0.9347 (tppp) cc_final: 0.9064 (tppt) REVERT: I 370 MET cc_start: 0.8572 (ppp) cc_final: 0.8318 (ppp) REVERT: I 371 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8378 (mm) REVERT: J 156 MET cc_start: 0.8800 (tpp) cc_final: 0.8049 (tpt) REVERT: J 201 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8845 (tt) REVERT: K 206 ARG cc_start: 0.7426 (mtp180) cc_final: 0.6674 (ttp-170) REVERT: K 223 GLU cc_start: 0.8606 (tt0) cc_final: 0.8186 (tp30) REVERT: K 243 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8402 (ptpt) REVERT: K 318 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8321 (tm-30) REVERT: L 412 MET cc_start: 0.8853 (mmp) cc_final: 0.8435 (mmm) REVERT: M 91 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8201 (pttm) REVERT: M 172 MET cc_start: 0.8146 (tpt) cc_final: 0.7917 (tpt) REVERT: M 328 TYR cc_start: 0.7675 (t80) cc_final: 0.7144 (t80) REVERT: M 344 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8393 (mm) REVERT: M 371 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (mt) REVERT: M 412 MET cc_start: 0.8483 (tpt) cc_final: 0.8261 (tpp) outliers start: 172 outliers final: 127 residues processed: 463 average time/residue: 0.2245 time to fit residues: 173.1961 Evaluate side-chains 450 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 300 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 344 ILE Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 371 LEU Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 388 ARG Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 285 LEU Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [120, 445, 126, 69, 455, 385, 81, 28, 113, 504, 513] chunk 120 optimal weight: 20.0000 chunk 445 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 455 optimal weight: 8.9990 chunk 385 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 513 optimal weight: 10.0000 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN C 199 HIS ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 409 GLN ** 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 = 0.3793 r_free = 0.3793 target = 0.109554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.070606 restraints weight = 102385.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.072157 restraints weight = 62881.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.072426 restraints weight = 42187.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.072966 restraints weight = 38852.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.073185 restraints weight = 34893.522| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41453 Z= 0.181 Angle : 0.646 15.613 56187 Z= 0.319 Chirality : 0.044 0.359 6516 Planarity : 0.004 0.046 7419 Dihedral : 4.247 53.203 5824 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.77 % Allowed : 25.16 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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 (0.12), residues: 5255 helix: 0.86 (0.12), residues: 2086 sheet: -0.86 (0.18), residues: 822 loop : -0.81 (0.13), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 273 TYR 0.020 0.001 TYR F 237 PHE 0.024 0.001 PHE D 248 HIS 0.013 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (41447) covalent geometry : angle 0.64591 / 0.32 (56175) SS BOND : bond 0.00387 / 0.22 ( 6) SS BOND : angle 0.71171 / 0.32 ( 12) hydrogen bonds : bond 0.04095 / 2.81 ( 1881) hydrogen bonds : angle 4.64854 / 3.26 ( 6237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10510 Ramachandran restraints generated. 5255 Oldfield, 0 Emsley, 5255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 307 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8495 (mp) cc_final: 0.8011 (tt) REVERT: A 193 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 402 ASP cc_start: 0.8538 (m-30) cc_final: 0.8148 (t0) REVERT: B 344 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8756 (mm) REVERT: B 366 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9172 (tttm) REVERT: B 373 ARG cc_start: 0.9192 (ptt90) cc_final: 0.8867 (ptt-90) REVERT: C 91 LYS cc_start: 0.8835 (mttp) cc_final: 0.8419 (mmmm) REVERT: C 172 MET cc_start: 0.8492 (mmp) cc_final: 0.8130 (mmt) REVERT: C 268 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: C 273 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7561 (ptm160) REVERT: C 366 LYS cc_start: 0.8614 (pttt) cc_final: 0.8348 (tmmt) REVERT: D 172 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8653 (tpt) REVERT: D 402 ASP cc_start: 0.8947 (m-30) cc_final: 0.8184 (t0) REVERT: E 45 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8955 (mmmm) REVERT: E 147 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (mt) REVERT: E 190 ARG cc_start: 0.5687 (OUTLIER) cc_final: 0.4363 (mmt180) REVERT: E 223 GLU cc_start: 0.9274 (tp30) cc_final: 0.8923 (tp30) REVERT: E 252 MET cc_start: 0.8949 (mmt) cc_final: 0.8683 (mmm) REVERT: E 285 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8783 (mp) REVERT: E 302 TYR cc_start: 0.8059 (m-10) cc_final: 0.7788 (m-10) REVERT: E 317 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8857 (p0) REVERT: F 84 MET cc_start: 0.7867 (mpp) cc_final: 0.7244 (mtm) REVERT: F 91 LYS cc_start: 0.8096 (mttp) cc_final: 0.7508 (mtpt) REVERT: F 156 MET cc_start: 0.8379 (tpp) cc_final: 0.7823 (tpt) REVERT: F 236 GLU cc_start: 0.9395 (OUTLIER) cc_final: 0.8867 (tm-30) REVERT: F 268 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6979 (tt0) REVERT: F 430 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.6930 (p0) REVERT: G 91 LYS cc_start: 0.8968 (mttp) cc_final: 0.8313 (mtmt) REVERT: H 129 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9240 (tt) REVERT: H 309 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.3837 (tp30) REVERT: I 91 LYS cc_start: 0.8976 (mttp) cc_final: 0.8261 (mtpt) REVERT: I 92 ILE cc_start: 0.8800 (mt) cc_final: 0.8400 (tt) REVERT: I 170 MET cc_start: 0.9112 (mmt) cc_final: 0.8824 (mmp) REVERT: I 181 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8823 (mm) REVERT: I 354 LYS cc_start: 0.9371 (tppp) cc_final: 0.9085 (tppt) REVERT: I 370 MET cc_start: 0.8604 (ppp) cc_final: 0.8337 (ppp) REVERT: I 371 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8393 (mm) REVERT: J 156 MET cc_start: 0.8775 (tpp) cc_final: 0.8007 (tpt) REVERT: J 201 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8859 (tt) REVERT: K 223 GLU cc_start: 0.8611 (tt0) cc_final: 0.8205 (tp30) REVERT: K 243 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8397 (ptpt) REVERT: K 318 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8343 (tm-30) REVERT: L 412 MET cc_start: 0.8895 (mmp) cc_final: 0.8461 (mmm) REVERT: M 91 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8361 (ptpp) REVERT: M 172 MET cc_start: 0.8109 (tpt) cc_final: 0.7895 (tpt) REVERT: M 328 TYR cc_start: 0.7610 (t80) cc_final: 0.7119 (t80) REVERT: M 344 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8396 (mm) REVERT: M 370 MET cc_start: 0.8130 (tmm) cc_final: 0.7403 (tpp) REVERT: M 371 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7653 (mt) REVERT: M 412 MET cc_start: 0.8729 (tpt) cc_final: 0.8175 (tpp) outliers start: 163 outliers final: 132 residues processed: 440 average time/residue: 0.2231 time to fit residues: 164.4363 Evaluate side-chains 455 residues out of total 4336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 302 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 PHE Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 225 CYS Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 243 LYS Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 366 LYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 225 CYS Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 234 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 348 ILE Chi-restraints excluded: chain C residue 430 ASN Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 190 ARG Chi-restraints excluded: chain E residue 225 CYS Chi-restraints excluded: chain E residue 285 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 225 CYS Chi-restraints excluded: chain F residue 236 GLU Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 430 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 135 THR Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 190 ARG Chi-restraints excluded: chain G residue 225 CYS Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 14 HIS Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 156 MET Chi-restraints excluded: chain H residue 225 CYS Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 245 VAL Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 282 GLN Chi-restraints excluded: chain H residue 309 GLU Chi-restraints excluded: chain H residue 351 VAL Chi-restraints excluded: chain H residue 403 VAL Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 184 ILE Chi-restraints excluded: chain I residue 225 CYS Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 321 SER Chi-restraints excluded: chain I residue 371 LEU Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 14 HIS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 139 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 225 CYS Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain J residue 245 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 319 ILE Chi-restraints excluded: chain J residue 371 LEU Chi-restraints excluded: chain J residue 404 ILE Chi-restraints excluded: chain K residue 11 SER Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 174 MET Chi-restraints excluded: chain K residue 190 ARG Chi-restraints excluded: chain K residue 225 CYS Chi-restraints excluded: chain K residue 232 THR Chi-restraints excluded: chain K residue 243 LYS Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain K residue 321 SER Chi-restraints excluded: chain L residue 135 THR Chi-restraints excluded: chain L residue 150 CYS Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 VAL Chi-restraints excluded: chain L residue 403 VAL Chi-restraints excluded: chain M residue 150 CYS Chi-restraints excluded: chain M residue 225 CYS Chi-restraints excluded: chain M residue 243 LYS Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain M residue 302 TYR Chi-restraints excluded: chain M residue 344 ILE Chi-restraints excluded: chain M residue 371 LEU Chi-restraints excluded: chain M residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 527 random chunks: [55, 298, 195, 36, 46, 43, 423, 175, 68, 119, 228] chunk 55 optimal weight: 0.8980 chunk 298 optimal weight: 6.9990 chunk 195 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 423 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 68 optimal weight: 0.0070 chunk 119 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 GLN ** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS C 362 GLN ** F 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 GLN ** L 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.111592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.073530 restraints weight = 100397.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.075085 restraints weight = 58140.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075591 restraints weight = 38293.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.075978 restraints weight = 35212.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.076436 restraints weight = 31896.274| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 41453 Z= 0.110 Angle : 0.622 15.326 56187 Z= 0.302 Chirality : 0.044 0.479 6516 Planarity : 0.004 0.049 7419 Dihedral : 4.013 52.901 5824 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.98 % Allowed : 26.01 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.35 % Cis-general : 0.26 % 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 (0.12), residues: 5255 helix: 0.98 (0.12), residues: 2080 sheet: -0.72 (0.18), residues: 820 loop : -0.68 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 273 TYR 0.020 0.001 TYR F 237 PHE 0.022 0.001 PHE D 248 HIS 0.020 0.001 HIS C 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (41447) covalent geometry : angle 0.62192 / 0.30 (56175) SS BOND : bond 0.00310 / 0.17 ( 6) SS BOND : angle 0.79779 / 0.34 ( 12) hydrogen bonds : bond 0.03397 / 2.35 ( 1881) hydrogen bonds : angle 4.46577 / 3.13 ( 6237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7224.55 seconds wall clock time: 125 minutes 9.77 seconds (7509.77 seconds total)