Starting phenix.real_space_refine on Sun Dec 29 06:57:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.map" model { file = "/net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8blc_16106/12_2024/8blc_16106.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 7 Type Number sf(0) Gaussians K 14 8.98 5 P 42 5.49 5 Mg 14 5.21 5 S 280 5.16 5 C 33628 2.51 5 N 9380 2.21 5 O 12288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 55646 Number of models: 1 Model: "" Number of chains: 42 Chain: "G" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "F" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "H" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "J" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "N" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 91 Classifications: {'water': 91} Link IDs: {None: 90} Residues with excluded nonbonded symmetry interactions: 14 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG A 601 " occ=0.00 residue: pdb="MG MG B 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG D 601 " occ=0.00 residue: pdb="MG MG E 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG H 601 " occ=0.00 residue: pdb="MG MG I 601 " occ=0.00 residue: pdb="MG MG J 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG L 601 " occ=0.00 ... (remaining 2 not shown) Time building chain proxies: 25.75, per 1000 atoms: 0.46 Number of scatterers: 55646 At special positions: 0 Unit cell: (150.72, 152.64, 162.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 14 19.00 S 280 16.00 P 42 15.00 Mg 14 11.99 O 12288 8.00 N 9380 7.00 C 33628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.85 Conformation dependent library (CDL) restraints added in 5.8 seconds 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13244 Finding SS restraints... Secondary structure from input PDB file: 294 helices and 85 sheets defined 58.6% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 59 removed outlier: 3.535A pdb=" N GLU G 59 " --> pdb=" O SER G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.874A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 137 through 142 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 155 through 169 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.948A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 244 removed outlier: 3.934A pdb=" N GLY G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 308 through 312 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 458 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 497 through 515 Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.540A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.864A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 143 through 152 Processing helix chain 'A' and resid 155 through 169 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.969A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.584A pdb=" N ALA A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 Processing helix chain 'A' and resid 282 through 297 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.932A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.518A pdb=" N PHE B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 205 " --> pdb=" O PRO B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 233 through 243 Processing helix chain 'B' and resid 259 through 267 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.513A pdb=" N GLU C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 4.022A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.969A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 removed outlier: 4.240A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.925A pdb=" N GLY C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 Processing helix chain 'C' and resid 282 through 297 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.742A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.868A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 143 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.592A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 205 " --> pdb=" O PRO D 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 201 through 205' Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 259 through 267 Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 433 through 447 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 9 through 29 Processing helix chain 'E' and resid 52 through 60 Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.984A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 143 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 removed outlier: 3.980A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 242 removed outlier: 4.249A pdb=" N MET E 233 " --> pdb=" O ASN E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 267 removed outlier: 3.531A pdb=" N MET E 267 " --> pdb=" O VAL E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 426 Processing helix chain 'E' and resid 433 through 447 Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.758A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.502A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.882A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 143 through 152 Processing helix chain 'F' and resid 155 through 169 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.981A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 259 through 267 Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 308 through 312 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 375 Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'F' and resid 433 through 447 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.769A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 52 through 60 Processing helix chain 'H' and resid 64 through 86 removed outlier: 3.902A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 137 through 142 Processing helix chain 'H' and resid 143 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.999A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 242 Processing helix chain 'H' and resid 259 through 267 removed outlier: 3.563A pdb=" N MET H 267 " --> pdb=" O VAL H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 297 Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 426 Processing helix chain 'H' and resid 433 through 447 Processing helix chain 'H' and resid 448 through 458 Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 497 through 515 Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 52 through 60 Processing helix chain 'I' and resid 64 through 85 removed outlier: 3.908A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 137 through 142 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 4.036A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 241 Processing helix chain 'I' and resid 259 through 267 removed outlier: 3.602A pdb=" N MET I 267 " --> pdb=" O VAL I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 Processing helix chain 'I' and resid 308 through 312 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 458 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 52 through 59 Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.903A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 137 through 142 Processing helix chain 'J' and resid 143 through 152 Processing helix chain 'J' and resid 155 through 169 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.794A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 242 removed outlier: 3.975A pdb=" N MET J 233 " --> pdb=" O ASN J 229 " (cutoff:3.500A) Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 259 through 267 removed outlier: 3.511A pdb=" N MET J 267 " --> pdb=" O VAL J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 308 through 312 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 375 Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 426 Processing helix chain 'J' and resid 433 through 447 Processing helix chain 'J' and resid 448 through 458 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.754A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 64 through 85 removed outlier: 3.982A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 137 through 142 Processing helix chain 'K' and resid 143 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.973A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 removed outlier: 3.506A pdb=" N GLY K 244 " --> pdb=" O VAL K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 267 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 308 through 312 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 447 Processing helix chain 'K' and resid 448 through 458 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.750A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 52 through 59 Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.995A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 137 through 142 Processing helix chain 'L' and resid 143 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.867A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 242 Processing helix chain 'L' and resid 259 through 267 Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 308 through 312 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 433 through 447 Processing helix chain 'L' and resid 448 through 458 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 497 through 515 Processing helix chain 'M' and resid 9 through 29 Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.566A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 85 removed outlier: 3.983A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 137 through 142 Processing helix chain 'M' and resid 143 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.984A pdb=" N ILE M 205 " --> pdb=" O PRO M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 242 Processing helix chain 'M' and resid 259 through 267 Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 308 through 312 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 375 Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 426 Processing helix chain 'M' and resid 433 through 447 Processing helix chain 'M' and resid 448 through 458 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.732A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 59 Processing helix chain 'N' and resid 64 through 85 removed outlier: 3.841A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 143 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.995A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 230 through 232 No H-bonds generated for 'chain 'N' and resid 230 through 232' Processing helix chain 'N' and resid 233 through 241 Processing helix chain 'N' and resid 259 through 267 Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 308 through 312 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 458 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 515 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 8 removed outlier: 7.363A pdb=" N VAL M 39 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET G 520 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.666A pdb=" N ASN G 37 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N VAL B 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 39 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASP B 523 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.646A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 193 through 195 removed outlier: 6.643A pdb=" N THR G 330 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 325 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE G 332 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL G 323 " --> pdb=" O ILE G 332 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASP G 334 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 219 through 222 removed outlier: 6.022A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'A' and resid 4 through 8 removed outlier: 5.744A pdb=" N ASN C 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.667A pdb=" N ASN A 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL N 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ASP N 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.681A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AB3, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.078A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 9.764A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.078A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 50 removed outlier: 7.414A pdb=" N ASN B 37 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N MET D 520 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 39 " --> pdb=" O MET D 520 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR D 522 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.618A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.625A pdb=" N THR B 330 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 325 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 332 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 323 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 334 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 275 removed outlier: 9.519A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC3, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC4, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.744A pdb=" N ASN E 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AC6, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.657A pdb=" N THR C 330 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE C 325 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE C 332 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 323 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP C 334 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 213 through 216 removed outlier: 9.675A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC9, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AD1, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.275A pdb=" N ASN D 37 " --> pdb=" O GLU F 518 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N MET F 520 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 39 " --> pdb=" O MET F 520 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N THR F 522 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.662A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.690A pdb=" N THR D 330 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 325 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE D 332 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL D 323 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP D 334 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.869A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD7, first strand: chain 'E' and resid 4 through 8 removed outlier: 7.343A pdb=" N VAL H 39 " --> pdb=" O GLU E 518 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N MET E 520 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.724A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.652A pdb=" N THR E 330 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE E 325 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE E 332 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL E 323 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASP E 334 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 213 through 216 removed outlier: 9.703A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE3, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE4, first strand: chain 'F' and resid 48 through 50 removed outlier: 7.335A pdb=" N ASN F 37 " --> pdb=" O GLU I 518 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N MET I 520 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL F 39 " --> pdb=" O MET I 520 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR I 522 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 174 through 179 Processing sheet with id=AE6, first strand: chain 'F' and resid 193 through 195 removed outlier: 6.614A pdb=" N THR F 330 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE F 325 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE F 332 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 323 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP F 334 " --> pdb=" O LYS F 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 213 through 216 removed outlier: 9.750A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE9, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 8 removed outlier: 5.733A pdb=" N ASN J 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS H 519 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 174 through 179 Processing sheet with id=AF3, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.638A pdb=" N THR H 330 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE H 325 " --> pdb=" O THR H 330 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE H 332 " --> pdb=" O VAL H 323 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP H 334 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 213 through 216 removed outlier: 9.699A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF6, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AF7, first strand: chain 'I' and resid 48 through 50 removed outlier: 7.329A pdb=" N ASN I 37 " --> pdb=" O GLU K 518 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N MET K 520 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL I 39 " --> pdb=" O MET K 520 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR K 522 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 174 through 179 Processing sheet with id=AF9, first strand: chain 'I' and resid 193 through 195 removed outlier: 6.673A pdb=" N THR I 330 " --> pdb=" O ILE I 325 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE I 325 " --> pdb=" O THR I 330 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE I 332 " --> pdb=" O VAL I 323 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL I 323 " --> pdb=" O ILE I 332 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASP I 334 " --> pdb=" O LYS I 321 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 219 through 222 removed outlier: 6.032A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AG4, first strand: chain 'J' and resid 4 through 8 removed outlier: 5.707A pdb=" N ASN L 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 174 through 179 Processing sheet with id=AG6, first strand: chain 'J' and resid 193 through 195 removed outlier: 6.660A pdb=" N THR J 330 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE J 325 " --> pdb=" O THR J 330 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE J 332 " --> pdb=" O VAL J 323 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP J 334 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 213 through 216 removed outlier: 9.744A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AG9, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'K' and resid 48 through 50 removed outlier: 7.341A pdb=" N ASN K 37 " --> pdb=" O GLU M 518 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET M 520 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL K 39 " --> pdb=" O MET M 520 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR M 522 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AH3, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.664A pdb=" N THR K 330 " --> pdb=" O ILE K 325 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE K 325 " --> pdb=" O THR K 330 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE K 332 " --> pdb=" O VAL K 323 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL K 323 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP K 334 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 213 through 216 removed outlier: 9.603A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AH6, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AH7, first strand: chain 'L' and resid 4 through 8 removed outlier: 5.790A pdb=" N ASN N 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS L 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.757A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.642A pdb=" N THR L 330 " --> pdb=" O ILE L 325 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE L 325 " --> pdb=" O THR L 330 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE L 332 " --> pdb=" O VAL L 323 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL L 323 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP L 334 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 213 through 216 removed outlier: 9.722A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AI3, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AI4, first strand: chain 'M' and resid 174 through 179 Processing sheet with id=AI5, first strand: chain 'M' and resid 193 through 195 removed outlier: 4.220A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR M 330 " --> pdb=" O ILE M 325 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE M 325 " --> pdb=" O THR M 330 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE M 332 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL M 323 " --> pdb=" O ILE M 332 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP M 334 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 219 through 222 removed outlier: 6.127A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AI8, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AI9, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.675A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.680A pdb=" N THR N 330 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE N 325 " --> pdb=" O THR N 330 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE N 332 " --> pdb=" O VAL N 323 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL N 323 " --> pdb=" O ILE N 332 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP N 334 " --> pdb=" O LYS N 321 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 213 through 216 removed outlier: 9.734A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'N' and resid 476 through 479 3610 hydrogen bonds defined for protein. 10359 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: 26.98 Time building geometry restraints manager: 12.88 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: 18830 1.34 - 1.46: 9645 1.46 - 1.58: 25719 1.58 - 1.70: 14 1.70 - 1.82: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" SD MET F 69 " pdb=" CE MET F 69 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.06e+00 bond pdb=" SD MET J 69 " pdb=" CE MET J 69 " ideal model delta sigma weight residual 1.791 1.749 0.042 2.50e-02 1.60e+03 2.78e+00 bond pdb=" CG1 ILE A 353 " pdb=" CD1 ILE A 353 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.55e+00 bond pdb=" CG LEU G 31 " pdb=" CD2 LEU G 31 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.55e+00 bond pdb=" O3A ATP M 602 " pdb=" PA ATP M 602 " ideal model delta sigma weight residual 1.592 1.555 0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 73520 2.27 - 4.55: 416 4.55 - 6.82: 39 6.82 - 9.10: 9 9.10 - 11.37: 6 Bond angle restraints: 73990 Sorted by residual: angle pdb=" N GLY M 192 " pdb=" CA GLY M 192 " pdb=" C GLY M 192 " ideal model delta sigma weight residual 113.18 124.55 -11.37 2.37e+00 1.78e-01 2.30e+01 angle pdb=" CA MET C 233 " pdb=" CB MET C 233 " pdb=" CG MET C 233 " ideal model delta sigma weight residual 114.10 123.59 -9.49 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CA MET I 233 " pdb=" CB MET I 233 " pdb=" CG MET I 233 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CB MET D 193 " pdb=" CG MET D 193 " pdb=" SD MET D 193 " ideal model delta sigma weight residual 112.70 123.52 -10.82 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 123.07 -10.37 3.00e+00 1.11e-01 1.20e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 29666 17.84 - 35.68: 3218 35.68 - 53.53: 1039 53.53 - 71.37: 139 71.37 - 89.21: 98 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA GLU M 191 " pdb=" C GLU M 191 " pdb=" N GLY M 192 " pdb=" CA GLY M 192 " ideal model delta harmonic sigma weight residual 180.00 146.93 33.07 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA VAL M 190 " pdb=" C VAL M 190 " pdb=" N GLU M 191 " pdb=" CA GLU M 191 " ideal model delta harmonic sigma weight residual 180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLY M 192 " pdb=" C GLY M 192 " pdb=" N MET M 193 " pdb=" CA MET M 193 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 7996 0.066 - 0.132: 957 0.132 - 0.198: 20 0.198 - 0.263: 0 0.263 - 0.329: 1 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CB ILE A 353 " pdb=" CA ILE A 353 " pdb=" CG1 ILE A 353 " pdb=" CG2 ILE A 353 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA PRO A 462 " pdb=" N PRO A 462 " pdb=" C PRO A 462 " pdb=" CB PRO A 462 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA PRO C 462 " pdb=" N PRO C 462 " pdb=" C PRO C 462 " pdb=" CB PRO C 462 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET C 233 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C MET C 233 " 0.029 2.00e-02 2.50e+03 pdb=" O MET C 233 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 234 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 362 " 0.139 9.50e-02 1.11e+02 6.22e-02 2.54e+00 pdb=" NE ARG A 362 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG A 362 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 362 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 362 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 233 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C MET I 233 " -0.026 2.00e-02 2.50e+03 pdb=" O MET I 233 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU I 234 " 0.009 2.00e-02 2.50e+03 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.68: 1566 2.68 - 3.29: 63861 3.29 - 3.91: 123931 3.91 - 4.52: 164885 4.52 - 5.14: 242773 Nonbonded interactions: 597016 Sorted by model distance: nonbonded pdb=" OD1 ASP I 87 " pdb="MG MG I 601 " model vdw 2.062 2.170 nonbonded pdb=" OD1 ASP H 87 " pdb="MG MG H 601 " model vdw 2.065 2.170 nonbonded pdb=" OD1 ASP D 87 " pdb="MG MG D 601 " model vdw 2.084 2.170 nonbonded pdb=" OD1 ASP L 87 " pdb="MG MG L 601 " model vdw 2.089 2.170 nonbonded pdb=" OD1 ASP A 87 " pdb="MG MG A 601 " model vdw 2.097 2.170 ... (remaining 597011 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 1.680 Check model and map are aligned: 0.340 Set scattering table: 0.400 Process input model: 107.160 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.350 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.005 0.062 54726 Z= 0.305 Angle : 0.514 11.375 73990 Z= 0.278 Chirality : 0.042 0.329 8974 Planarity : 0.003 0.062 9618 Dihedral : 17.029 89.212 20916 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.89 % Favored : 99.10 % Rotamer: Outliers : 1.44 % Allowed : 19.41 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 7294 helix: 1.56 (0.08), residues: 4130 sheet: 0.61 (0.15), residues: 826 loop : -0.61 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 401 PHE 0.021 0.002 PHE G 44 TYR 0.011 0.001 TYR K 506 ARG 0.007 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 291 time to evaluate : 4.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1826 (pp-130) cc_final: 0.0643 (tmt) REVERT: C 233 MET cc_start: 0.5514 (tmt) cc_final: 0.4890 (pp-130) REVERT: D 185 ASP cc_start: 0.7924 (m-30) cc_final: 0.7550 (m-30) REVERT: E 288 MET cc_start: 0.6130 (mmm) cc_final: 0.4751 (pp-130) REVERT: F 193 MET cc_start: 0.5061 (OUTLIER) cc_final: 0.4809 (tmt) REVERT: I 233 MET cc_start: 0.5376 (tmt) cc_final: 0.4290 (pp-130) REVERT: I 288 MET cc_start: 0.5680 (mmp) cc_final: 0.4185 (pp-130) REVERT: L 185 ASP cc_start: 0.7836 (m-30) cc_final: 0.7480 (m-30) outliers start: 81 outliers final: 61 residues processed: 370 average time/residue: 1.2793 time to fit residues: 612.3426 Evaluate side-chains 354 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 292 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 194 GLN Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 358 SER Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain D residue 502 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 138 CYS Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 502 SER Chi-restraints excluded: chain I residue 138 CYS Chi-restraints excluded: chain I residue 502 SER Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 502 SER Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 151 SER Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Chi-restraints excluded: chain N residue 502 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 1.9990 chunk 551 optimal weight: 50.0000 chunk 306 optimal weight: 0.8980 chunk 188 optimal weight: 20.0000 chunk 372 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 chunk 570 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 346 optimal weight: 50.0000 chunk 424 optimal weight: 0.9980 chunk 661 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN J 366 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 54726 Z= 0.189 Angle : 0.479 11.018 73990 Z= 0.264 Chirality : 0.040 0.141 8974 Planarity : 0.003 0.052 9618 Dihedral : 8.948 82.582 8274 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.99 % Favored : 99.00 % Rotamer: Outliers : 2.11 % Allowed : 17.90 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.10), residues: 7294 helix: 1.67 (0.08), residues: 4158 sheet: 0.27 (0.14), residues: 1176 loop : -0.34 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 401 PHE 0.032 0.001 PHE C 44 TYR 0.007 0.001 TYR B 478 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 297 time to evaluate : 4.676 Fit side-chains revert: symmetry clash REVERT: G 233 MET cc_start: 0.1345 (pp-130) cc_final: 0.0556 (tmt) REVERT: A 200 LEU cc_start: 0.1725 (OUTLIER) cc_final: 0.1502 (mt) REVERT: A 234 LEU cc_start: 0.3294 (OUTLIER) cc_final: 0.3073 (tm) REVERT: C 233 MET cc_start: 0.5532 (tmt) cc_final: 0.5026 (pp-130) REVERT: D 193 MET cc_start: 0.5137 (tpt) cc_final: 0.4369 (tmt) REVERT: E 233 MET cc_start: 0.6327 (tmt) cc_final: 0.5932 (pp-130) REVERT: E 267 MET cc_start: 0.1506 (OUTLIER) cc_final: 0.0919 (pp-130) REVERT: E 288 MET cc_start: 0.6262 (mmm) cc_final: 0.5116 (ppp) REVERT: F 111 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8270 (mtt) REVERT: F 193 MET cc_start: 0.5334 (tpt) cc_final: 0.4934 (tmt) REVERT: F 288 MET cc_start: 0.5951 (mpm) cc_final: 0.4722 (ppp) REVERT: I 233 MET cc_start: 0.5381 (tmt) cc_final: 0.4509 (pp-130) REVERT: I 358 SER cc_start: 0.3489 (OUTLIER) cc_final: 0.3182 (p) REVERT: K 76 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7939 (tt0) REVERT: L 233 MET cc_start: 0.1569 (OUTLIER) cc_final: 0.0335 (pmt) REVERT: N 111 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8082 (mtp) outliers start: 119 outliers final: 25 residues processed: 401 average time/residue: 1.3596 time to fit residues: 694.9324 Evaluate side-chains 325 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 292 time to evaluate : 4.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 chunk 550 optimal weight: 20.0000 chunk 450 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 662 optimal weight: 0.7980 chunk 715 optimal weight: 2.9990 chunk 589 optimal weight: 2.9990 chunk 656 optimal weight: 40.0000 chunk 225 optimal weight: 2.9990 chunk 531 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54726 Z= 0.283 Angle : 0.498 10.672 73990 Z= 0.273 Chirality : 0.041 0.173 8974 Planarity : 0.003 0.051 9618 Dihedral : 8.843 86.405 8208 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.03 % Favored : 98.96 % Rotamer: Outliers : 1.93 % Allowed : 17.88 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.10), residues: 7294 helix: 1.65 (0.08), residues: 4144 sheet: 0.27 (0.14), residues: 1176 loop : -0.36 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.016 0.001 PHE L 219 TYR 0.011 0.001 TYR K 506 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 295 time to evaluate : 4.583 Fit side-chains revert: symmetry clash REVERT: G 233 MET cc_start: 0.1134 (pp-130) cc_final: 0.0461 (tmt) REVERT: A 200 LEU cc_start: 0.1683 (OUTLIER) cc_final: 0.1462 (mt) REVERT: C 233 MET cc_start: 0.5554 (tmt) cc_final: 0.5135 (pp-130) REVERT: C 267 MET cc_start: -0.0241 (mtt) cc_final: -0.1923 (ppp) REVERT: D 267 MET cc_start: 0.0995 (OUTLIER) cc_final: 0.0337 (pp-130) REVERT: D 307 MET cc_start: 0.1540 (tmt) cc_final: 0.1302 (tpt) REVERT: E 233 MET cc_start: 0.6326 (tmt) cc_final: 0.5919 (pmt) REVERT: E 267 MET cc_start: 0.1421 (OUTLIER) cc_final: 0.0915 (pp-130) REVERT: E 288 MET cc_start: 0.6231 (mmm) cc_final: 0.5311 (ppp) REVERT: F 111 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8305 (mtt) REVERT: F 193 MET cc_start: 0.5497 (tpt) cc_final: 0.5189 (tmt) REVERT: F 288 MET cc_start: 0.5944 (mpm) cc_final: 0.4887 (ppp) REVERT: H 166 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8332 (mtt) REVERT: H 288 MET cc_start: 0.5862 (mmp) cc_final: 0.4454 (pp-130) REVERT: I 166 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8243 (mtt) REVERT: I 233 MET cc_start: 0.5118 (tmt) cc_final: 0.4785 (pp-130) REVERT: K 76 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: L 233 MET cc_start: 0.1547 (OUTLIER) cc_final: 0.0333 (pmt) REVERT: N 111 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7966 (mtt) REVERT: N 272 LYS cc_start: 0.3566 (OUTLIER) cc_final: 0.1713 (mttm) outliers start: 109 outliers final: 45 residues processed: 385 average time/residue: 1.2996 time to fit residues: 643.7718 Evaluate side-chains 345 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 290 time to evaluate : 4.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 138 CYS Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 138 CYS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 376 VAL Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 272 LYS Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 10.0000 chunk 497 optimal weight: 7.9990 chunk 343 optimal weight: 50.0000 chunk 73 optimal weight: 0.4980 chunk 316 optimal weight: 0.9980 chunk 444 optimal weight: 8.9990 chunk 664 optimal weight: 4.9990 chunk 703 optimal weight: 10.0000 chunk 347 optimal weight: 20.0000 chunk 629 optimal weight: 0.7980 chunk 189 optimal weight: 20.0000 overall best weight: 3.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN K 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 54726 Z= 0.408 Angle : 0.542 10.883 73990 Z= 0.296 Chirality : 0.044 0.178 8974 Planarity : 0.004 0.055 9618 Dihedral : 9.134 89.141 8207 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.22 % Favored : 98.77 % Rotamer: Outliers : 2.16 % Allowed : 17.83 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.09), residues: 7294 helix: 1.49 (0.08), residues: 4144 sheet: 0.46 (0.15), residues: 826 loop : -0.60 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 401 PHE 0.016 0.002 PHE B 44 TYR 0.013 0.002 TYR K 506 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 294 time to evaluate : 4.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1260 (pp-130) cc_final: 0.0522 (tmt) REVERT: A 200 LEU cc_start: 0.1627 (OUTLIER) cc_final: 0.1413 (mt) REVERT: C 233 MET cc_start: 0.5632 (tmt) cc_final: 0.5240 (pp-130) REVERT: C 267 MET cc_start: -0.0153 (mtt) cc_final: -0.1802 (ppp) REVERT: D 162 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (mm) REVERT: E 76 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (tt0) REVERT: E 233 MET cc_start: 0.6325 (tmt) cc_final: 0.6100 (pmt) REVERT: E 267 MET cc_start: 0.1426 (OUTLIER) cc_final: 0.0916 (pp-130) REVERT: E 288 MET cc_start: 0.6371 (mmm) cc_final: 0.5497 (ppp) REVERT: E 404 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6953 (mpt-90) REVERT: F 111 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8365 (mtt) REVERT: F 288 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.4941 (ppp) REVERT: H 288 MET cc_start: 0.5868 (mmp) cc_final: 0.4420 (pp-130) REVERT: I 166 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8320 (mtt) REVERT: I 233 MET cc_start: 0.5299 (tmt) cc_final: 0.5067 (pp-130) REVERT: J 267 MET cc_start: 0.1053 (OUTLIER) cc_final: -0.0184 (pp-130) REVERT: K 76 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: L 233 MET cc_start: 0.1649 (OUTLIER) cc_final: 0.0411 (pmt) REVERT: N 73 MET cc_start: 0.8904 (mtm) cc_final: 0.8625 (mtm) REVERT: N 111 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8089 (mtp) REVERT: N 171 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8479 (mtpt) REVERT: N 288 MET cc_start: 0.3619 (mmp) cc_final: 0.3216 (ptt) outliers start: 122 outliers final: 52 residues processed: 389 average time/residue: 1.3499 time to fit residues: 672.7282 Evaluate side-chains 356 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 291 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 142 LYS Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 166 MET Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 366 GLN Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 233 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 73 MET Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 0.9980 chunk 399 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 523 optimal weight: 1.9990 chunk 290 optimal weight: 20.0000 chunk 600 optimal weight: 9.9990 chunk 486 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 631 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 366 GLN J 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 54726 Z= 0.229 Angle : 0.487 10.836 73990 Z= 0.266 Chirality : 0.040 0.240 8974 Planarity : 0.003 0.057 9618 Dihedral : 8.812 83.315 8207 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.19 % Favored : 98.79 % Rotamer: Outliers : 1.70 % Allowed : 18.42 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 7294 helix: 1.59 (0.08), residues: 4172 sheet: 0.19 (0.14), residues: 1176 loop : -0.42 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.015 0.001 PHE F 195 TYR 0.008 0.001 TYR I 506 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 296 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1215 (pp-130) cc_final: 0.0553 (tmt) REVERT: A 200 LEU cc_start: 0.1626 (OUTLIER) cc_final: 0.1403 (mt) REVERT: B 233 MET cc_start: 0.2803 (tmt) cc_final: 0.2477 (pp-130) REVERT: C 267 MET cc_start: 0.0244 (mtt) cc_final: -0.1520 (ppp) REVERT: D 307 MET cc_start: 0.1683 (tmt) cc_final: 0.1450 (tpt) REVERT: E 76 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: E 267 MET cc_start: 0.1304 (OUTLIER) cc_final: 0.0753 (pp-130) REVERT: E 288 MET cc_start: 0.6433 (mmm) cc_final: 0.5725 (ppp) REVERT: E 362 ARG cc_start: 0.4666 (OUTLIER) cc_final: 0.4278 (tmt-80) REVERT: E 404 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6930 (mpt-90) REVERT: F 111 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8276 (mtt) REVERT: F 288 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5043 (ppp) REVERT: H 166 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: H 288 MET cc_start: 0.5896 (mmp) cc_final: 0.4602 (pp-130) REVERT: I 233 MET cc_start: 0.5362 (tmt) cc_final: 0.5112 (pp-130) REVERT: J 76 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: J 111 MET cc_start: 0.8435 (mtp) cc_final: 0.8227 (mtt) REVERT: J 267 MET cc_start: 0.1006 (OUTLIER) cc_final: -0.0239 (pp-130) REVERT: K 76 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: K 288 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4358 (ppp) REVERT: L 288 MET cc_start: 0.5049 (mmp) cc_final: 0.4315 (ppp) REVERT: N 111 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8084 (mtp) REVERT: N 142 LYS cc_start: 0.2012 (OUTLIER) cc_final: 0.1758 (tptp) REVERT: N 171 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8466 (mtpt) REVERT: N 288 MET cc_start: 0.3471 (mmp) cc_final: 0.3242 (ptt) outliers start: 96 outliers final: 34 residues processed: 375 average time/residue: 1.3439 time to fit residues: 644.6629 Evaluate side-chains 341 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 4.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 50.0000 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 413 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 704 optimal weight: 1.9990 chunk 584 optimal weight: 0.8980 chunk 326 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 232 optimal weight: 7.9990 chunk 369 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54726 Z= 0.270 Angle : 0.495 10.991 73990 Z= 0.271 Chirality : 0.041 0.135 8974 Planarity : 0.003 0.058 9618 Dihedral : 8.847 85.866 8205 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.19 % Favored : 98.79 % Rotamer: Outliers : 1.52 % Allowed : 18.65 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.09), residues: 7294 helix: 1.63 (0.08), residues: 4158 sheet: 0.44 (0.15), residues: 826 loop : -0.65 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.019 0.001 PHE E 204 TYR 0.009 0.001 TYR K 506 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 291 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1293 (pp-130) cc_final: 0.0560 (tmt) REVERT: B 233 MET cc_start: 0.2864 (tmt) cc_final: 0.2598 (pp-130) REVERT: C 267 MET cc_start: 0.0363 (mtt) cc_final: -0.1385 (ppp) REVERT: C 288 MET cc_start: 0.5683 (mmp) cc_final: 0.4181 (pp-130) REVERT: E 76 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: E 267 MET cc_start: 0.1270 (OUTLIER) cc_final: 0.0721 (pp-130) REVERT: E 362 ARG cc_start: 0.4668 (OUTLIER) cc_final: 0.4324 (tmt-80) REVERT: E 404 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6966 (mpt-90) REVERT: F 111 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8296 (mtt) REVERT: F 288 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.4774 (pp-130) REVERT: H 288 MET cc_start: 0.5942 (mmp) cc_final: 0.4596 (pp-130) REVERT: J 76 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: J 111 MET cc_start: 0.8452 (mtp) cc_final: 0.8228 (mtt) REVERT: J 267 MET cc_start: 0.0868 (OUTLIER) cc_final: -0.0272 (pp-130) REVERT: J 307 MET cc_start: 0.2475 (tpt) cc_final: 0.2003 (tpt) REVERT: K 76 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: L 288 MET cc_start: 0.5379 (mmp) cc_final: 0.4646 (ppp) REVERT: N 111 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8129 (mtp) REVERT: N 142 LYS cc_start: 0.1931 (OUTLIER) cc_final: 0.1690 (tptp) REVERT: N 171 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8496 (mtpt) outliers start: 86 outliers final: 35 residues processed: 362 average time/residue: 1.3614 time to fit residues: 627.9675 Evaluate side-chains 337 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 204 PHE Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.5980 chunk 79 optimal weight: 40.0000 chunk 401 optimal weight: 1.9990 chunk 514 optimal weight: 0.6980 chunk 398 optimal weight: 7.9990 chunk 592 optimal weight: 20.0000 chunk 393 optimal weight: 5.9990 chunk 701 optimal weight: 50.0000 chunk 439 optimal weight: 50.0000 chunk 427 optimal weight: 2.9990 chunk 323 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 54726 Z= 0.230 Angle : 0.487 10.783 73990 Z= 0.266 Chirality : 0.040 0.354 8974 Planarity : 0.003 0.059 9618 Dihedral : 8.749 84.184 8203 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.19 % Favored : 98.79 % Rotamer: Outliers : 1.42 % Allowed : 19.07 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 7294 helix: 1.67 (0.08), residues: 4172 sheet: 0.44 (0.16), residues: 826 loop : -0.66 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.017 0.001 PHE B 44 TYR 0.016 0.001 TYR N 203 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 6.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1268 (pp-130) cc_final: 0.0578 (tmt) REVERT: C 207 LYS cc_start: 0.0907 (OUTLIER) cc_final: 0.0387 (ttpp) REVERT: C 267 MET cc_start: 0.0349 (mtt) cc_final: -0.1383 (ppp) REVERT: C 288 MET cc_start: 0.5628 (mmp) cc_final: 0.4398 (ppp) REVERT: D 193 MET cc_start: 0.5048 (tpt) cc_final: 0.4786 (tmt) REVERT: D 307 MET cc_start: 0.1740 (tmt) cc_final: 0.1477 (tpt) REVERT: E 76 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: E 233 MET cc_start: 0.2594 (OUTLIER) cc_final: 0.1636 (pmt) REVERT: E 267 MET cc_start: 0.1273 (OUTLIER) cc_final: 0.0720 (pp-130) REVERT: E 288 MET cc_start: 0.6159 (mmm) cc_final: 0.5065 (pp-130) REVERT: E 362 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.4462 (tmt-80) REVERT: E 404 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.6966 (mpt-90) REVERT: F 111 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: F 288 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.4944 (ppp) REVERT: H 288 MET cc_start: 0.5909 (mmp) cc_final: 0.4670 (pp-130) REVERT: I 233 MET cc_start: 0.5586 (tmt) cc_final: 0.4638 (pp-130) REVERT: J 76 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: J 111 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8205 (mtt) REVERT: J 267 MET cc_start: 0.0876 (OUTLIER) cc_final: -0.0265 (pp-130) REVERT: K 76 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: K 237 LEU cc_start: 0.3434 (OUTLIER) cc_final: 0.2824 (tt) REVERT: L 233 MET cc_start: 0.1909 (pmt) cc_final: 0.1553 (pp-130) REVERT: L 267 MET cc_start: 0.1912 (OUTLIER) cc_final: 0.1324 (pp-130) REVERT: L 288 MET cc_start: 0.5182 (mmp) cc_final: 0.4563 (ppp) REVERT: N 111 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8136 (mtp) REVERT: N 142 LYS cc_start: 0.1893 (OUTLIER) cc_final: 0.1658 (tptp) outliers start: 80 outliers final: 36 residues processed: 358 average time/residue: 1.4007 time to fit residues: 638.7295 Evaluate side-chains 342 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 290 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 362 ARG Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 44 PHE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 4.9990 chunk 280 optimal weight: 9.9990 chunk 419 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 135 optimal weight: 30.0000 chunk 446 optimal weight: 7.9990 chunk 478 optimal weight: 1.9990 chunk 346 optimal weight: 50.0000 chunk 65 optimal weight: 0.3980 chunk 551 optimal weight: 20.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 54726 Z= 0.344 Angle : 0.524 11.272 73990 Z= 0.284 Chirality : 0.042 0.217 8974 Planarity : 0.003 0.059 9618 Dihedral : 8.947 86.887 8203 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.26 % Favored : 98.72 % Rotamer: Outliers : 1.40 % Allowed : 19.07 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 7294 helix: 1.59 (0.08), residues: 4158 sheet: 0.37 (0.15), residues: 826 loop : -0.68 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.016 0.001 PHE B 44 TYR 0.011 0.002 TYR M 506 ARG 0.009 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 290 time to evaluate : 4.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1236 (pp-130) cc_final: 0.0627 (tmt) REVERT: B 230 ILE cc_start: -0.2289 (OUTLIER) cc_final: -0.2711 (mm) REVERT: B 233 MET cc_start: 0.0341 (pp-130) cc_final: 0.0102 (tmt) REVERT: C 207 LYS cc_start: 0.0897 (OUTLIER) cc_final: 0.0509 (ttpp) REVERT: C 267 MET cc_start: 0.0184 (mtt) cc_final: -0.1531 (ppp) REVERT: C 288 MET cc_start: 0.5548 (mmp) cc_final: 0.4523 (ppp) REVERT: D 307 MET cc_start: 0.1798 (tmt) cc_final: 0.1552 (tpt) REVERT: E 76 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: E 233 MET cc_start: 0.2669 (OUTLIER) cc_final: 0.1773 (pmt) REVERT: E 267 MET cc_start: 0.1278 (OUTLIER) cc_final: 0.0730 (pp-130) REVERT: E 288 MET cc_start: 0.6302 (mmm) cc_final: 0.5493 (ppp) REVERT: E 404 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.6970 (mpt-90) REVERT: F 111 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8336 (mtt) REVERT: F 288 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.4948 (ppp) REVERT: H 288 MET cc_start: 0.6002 (mmp) cc_final: 0.4741 (pp-130) REVERT: I 233 MET cc_start: 0.5497 (tmt) cc_final: 0.4501 (ppp) REVERT: J 76 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: J 111 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8247 (mtt) REVERT: J 267 MET cc_start: 0.0929 (OUTLIER) cc_final: -0.0219 (pp-130) REVERT: J 307 MET cc_start: 0.2500 (tpt) cc_final: 0.2067 (tpt) REVERT: K 76 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: K 237 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.2905 (tt) REVERT: L 233 MET cc_start: 0.2041 (pmt) cc_final: 0.1614 (pp-130) REVERT: L 267 MET cc_start: 0.1926 (OUTLIER) cc_final: 0.1333 (pp-130) REVERT: L 288 MET cc_start: 0.5108 (mmp) cc_final: 0.4500 (ppp) REVERT: N 111 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8109 (mtp) REVERT: N 142 LYS cc_start: 0.2020 (OUTLIER) cc_final: 0.1783 (tptp) REVERT: N 171 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8482 (mtpt) outliers start: 79 outliers final: 40 residues processed: 354 average time/residue: 1.3923 time to fit residues: 627.0968 Evaluate side-chains 347 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 257 GLU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 44 PHE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 138 CYS Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 2.9990 chunk 672 optimal weight: 0.9980 chunk 613 optimal weight: 3.9990 chunk 653 optimal weight: 10.0000 chunk 393 optimal weight: 50.0000 chunk 284 optimal weight: 8.9990 chunk 513 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 590 optimal weight: 5.9990 chunk 618 optimal weight: 0.6980 chunk 651 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 54726 Z= 0.243 Angle : 0.493 12.186 73990 Z= 0.268 Chirality : 0.041 0.166 8974 Planarity : 0.003 0.061 9618 Dihedral : 8.769 84.000 8203 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.21 % Favored : 98.78 % Rotamer: Outliers : 1.29 % Allowed : 19.14 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.10), residues: 7294 helix: 1.63 (0.08), residues: 4186 sheet: 0.12 (0.14), residues: 1176 loop : -0.49 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.020 0.001 PHE D 44 TYR 0.009 0.001 TYR K 506 ARG 0.008 0.000 ARG E 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 293 time to evaluate : 4.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 233 MET cc_start: 0.1096 (pp-130) cc_final: 0.0628 (tmt) REVERT: B 230 ILE cc_start: -0.2391 (OUTLIER) cc_final: -0.3039 (mp) REVERT: B 233 MET cc_start: 0.0321 (pp-130) cc_final: 0.0084 (tmt) REVERT: C 207 LYS cc_start: 0.1008 (OUTLIER) cc_final: 0.0571 (ttpp) REVERT: C 267 MET cc_start: 0.0304 (mtt) cc_final: -0.1437 (ppp) REVERT: C 288 MET cc_start: 0.5441 (mmp) cc_final: 0.4549 (ppp) REVERT: D 76 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8387 (tp30) REVERT: D 307 MET cc_start: 0.1775 (tmt) cc_final: 0.1531 (tpt) REVERT: E 76 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: E 233 MET cc_start: 0.2564 (OUTLIER) cc_final: 0.1680 (pmt) REVERT: E 267 MET cc_start: 0.1331 (OUTLIER) cc_final: 0.0802 (pp-130) REVERT: E 288 MET cc_start: 0.6334 (mmm) cc_final: 0.5581 (ppp) REVERT: E 404 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6971 (mpt-90) REVERT: F 111 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8281 (mtt) REVERT: F 288 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5001 (ppp) REVERT: I 233 MET cc_start: 0.5459 (tmt) cc_final: 0.4486 (ppp) REVERT: J 76 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: J 111 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8174 (mtt) REVERT: J 267 MET cc_start: 0.0924 (OUTLIER) cc_final: -0.0221 (pp-130) REVERT: J 307 MET cc_start: 0.2487 (tpt) cc_final: 0.2100 (tpt) REVERT: K 76 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: K 237 LEU cc_start: 0.3509 (OUTLIER) cc_final: 0.2923 (tt) REVERT: L 233 MET cc_start: 0.2085 (pmt) cc_final: 0.1665 (pp-130) REVERT: L 267 MET cc_start: 0.1834 (OUTLIER) cc_final: 0.1257 (pp-130) REVERT: L 288 MET cc_start: 0.5000 (mmp) cc_final: 0.4489 (ppp) REVERT: N 111 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: N 142 LYS cc_start: 0.1897 (OUTLIER) cc_final: 0.1679 (tptp) REVERT: N 171 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8490 (mtpt) REVERT: N 204 PHE cc_start: 0.0556 (OUTLIER) cc_final: -0.0167 (t80) outliers start: 73 outliers final: 37 residues processed: 351 average time/residue: 1.4284 time to fit residues: 634.5230 Evaluate side-chains 346 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 524 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 44 PHE Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 142 LYS Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 204 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 376 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 1.9990 chunk 691 optimal weight: 2.9990 chunk 422 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 480 optimal weight: 0.9980 chunk 725 optimal weight: 0.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 446 optimal weight: 3.9990 chunk 354 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54726 Z= 0.228 Angle : 0.492 13.145 73990 Z= 0.266 Chirality : 0.040 0.143 8974 Planarity : 0.003 0.060 9618 Dihedral : 8.709 83.901 8203 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.15 % Favored : 98.83 % Rotamer: Outliers : 1.12 % Allowed : 19.32 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.10), residues: 7294 helix: 1.66 (0.08), residues: 4186 sheet: 0.12 (0.14), residues: 1176 loop : -0.50 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.017 0.001 PHE B 44 TYR 0.008 0.001 TYR E 506 ARG 0.008 0.000 ARG E 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14588 Ramachandran restraints generated. 7294 Oldfield, 0 Emsley, 7294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 193 MET cc_start: 0.5144 (tpt) cc_final: 0.4744 (tmt) REVERT: G 233 MET cc_start: 0.1364 (pp-130) cc_final: 0.0744 (tmt) REVERT: B 230 ILE cc_start: -0.2465 (OUTLIER) cc_final: -0.3078 (mp) REVERT: C 207 LYS cc_start: 0.1315 (OUTLIER) cc_final: 0.0807 (ttpp) REVERT: C 267 MET cc_start: 0.0276 (mtt) cc_final: -0.1452 (ppp) REVERT: C 288 MET cc_start: 0.5380 (mmp) cc_final: 0.4553 (ppp) REVERT: D 76 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8372 (tp30) REVERT: D 267 MET cc_start: 0.1051 (OUTLIER) cc_final: 0.0542 (pp-130) REVERT: D 307 MET cc_start: 0.1893 (tmt) cc_final: 0.1654 (tpt) REVERT: E 76 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: E 233 MET cc_start: 0.2501 (OUTLIER) cc_final: 0.1627 (pmt) REVERT: E 267 MET cc_start: 0.1322 (OUTLIER) cc_final: 0.0785 (pp-130) REVERT: E 288 MET cc_start: 0.6252 (mmm) cc_final: 0.5568 (ppp) REVERT: E 404 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6969 (mpt-90) REVERT: F 111 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: F 288 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5015 (ppp) REVERT: H 288 MET cc_start: 0.5364 (mmp) cc_final: 0.4409 (pp-130) REVERT: I 193 MET cc_start: 0.4690 (tpp) cc_final: 0.4220 (tpt) REVERT: I 233 MET cc_start: 0.5389 (tmt) cc_final: 0.4553 (ppp) REVERT: J 76 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: J 111 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: J 267 MET cc_start: 0.0917 (OUTLIER) cc_final: -0.0177 (pp-130) REVERT: K 76 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: K 237 LEU cc_start: 0.3428 (OUTLIER) cc_final: 0.3067 (tt) REVERT: L 233 MET cc_start: 0.2081 (pmt) cc_final: 0.1675 (pp-130) REVERT: L 267 MET cc_start: 0.1708 (OUTLIER) cc_final: 0.1151 (pp-130) REVERT: L 288 MET cc_start: 0.4857 (mmp) cc_final: 0.4510 (ppp) REVERT: N 111 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: N 142 LYS cc_start: 0.1801 (OUTLIER) cc_final: 0.1580 (tptp) REVERT: N 171 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8497 (mtpt) REVERT: N 204 PHE cc_start: 0.0539 (OUTLIER) cc_final: -0.0195 (t80) outliers start: 63 outliers final: 33 residues processed: 339 average time/residue: 1.3941 time to fit residues: 601.3752 Evaluate side-chains 342 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 289 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 142 LYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 467 ASN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 111 MET Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 376 VAL Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 267 MET Chi-restraints excluded: chain L residue 376 VAL Chi-restraints excluded: chain L residue 467 ASN Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 230 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 171 LYS Chi-restraints excluded: chain N residue 204 PHE Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 240 VAL Chi-restraints excluded: chain N residue 467 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.1980 chunk 615 optimal weight: 0.6980 chunk 176 optimal weight: 7.9990 chunk 532 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 160 optimal weight: 0.9990 chunk 578 optimal weight: 0.6980 chunk 242 optimal weight: 50.0000 chunk 593 optimal weight: 6.9990 chunk 73 optimal weight: 0.0050 chunk 106 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.182680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.117484 restraints weight = 68479.255| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.95 r_work: 0.3164 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 54726 Z= 0.149 Angle : 0.467 12.318 73990 Z= 0.252 Chirality : 0.039 0.136 8974 Planarity : 0.003 0.059 9618 Dihedral : 8.316 76.777 8201 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.23 % Favored : 98.75 % Rotamer: Outliers : 0.83 % Allowed : 19.62 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 7294 helix: 1.72 (0.08), residues: 4284 sheet: 0.21 (0.14), residues: 1162 loop : -0.51 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.018 0.001 PHE B 44 TYR 0.006 0.001 TYR G 478 ARG 0.007 0.000 ARG E 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11732.18 seconds wall clock time: 207 minutes 4.33 seconds (12424.33 seconds total)