Starting phenix.real_space_refine on Tue Jun 25 13:20:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bl2_16100/06_2024/8bl2_16100_updated.pdb" } resolution = 2.3 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= 0.007 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 13770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 57128 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: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 212 Classifications: {'water': 212} Link IDs: {None: 211} Chain: "A" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 187 Classifications: {'water': 187} Link IDs: {None: 186} Chain: "B" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Classifications: {'water': 200} Link IDs: {None: 199} Chain: "C" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Classifications: {'water': 209} Link IDs: {None: 208} Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 178 Classifications: {'water': 178} Link IDs: {None: 177} Chain: "F" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "H" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "I" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 192 Classifications: {'water': 192} Link IDs: {None: 191} Chain: "J" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 203 Classifications: {'water': 203} Link IDs: {None: 202} Chain: "K" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "L" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 202 Classifications: {'water': 202} Link IDs: {None: 201} Chain: "M" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} 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: 23.51, per 1000 atoms: 0.41 Number of scatterers: 57128 At special positions: 0 Unit cell: (150.72, 151.68, 161.28, 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 13770 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 - 3.50 Amino acid : False - 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: 20.31 Conformation dependent library (CDL) restraints added in 8.1 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... running ksdssp... Secondary structure from input PDB file: 280 helices and 112 sheets defined 52.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 Creating SS restraints... Processing helix chain 'G' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 138 through 141 No H-bonds generated for 'chain 'G' and resid 138 through 141' Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 156 through 169 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 231 through 241 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 283 through 296 Processing helix chain 'G' and resid 309 through 311 No H-bonds generated for 'chain 'G' and resid 309 through 311' Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 386 through 409 Processing helix chain 'G' and resid 417 through 425 Processing helix chain 'G' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.809A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 138 through 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 231 through 241 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 260 through 266 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 108 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 138 through 141 No H-bonds generated for 'chain 'B' and resid 138 through 141' Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 241 Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 260 through 266 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 359 through 374 Processing helix chain 'B' and resid 386 through 409 Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 30 removed outlier: 4.701A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 108 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 231 through 241 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.792A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 85 removed outlier: 3.809A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 138 through 141 No H-bonds generated for 'chain 'D' and resid 138 through 141' Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 241 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 260 through 266 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 359 through 374 Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.792A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 108 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 138 through 141 No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 156 through 169 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 231 through 241 Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 260 through 266 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 374 Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 138 through 141 No H-bonds generated for 'chain 'F' and resid 138 through 141' Processing helix chain 'F' and resid 144 through 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 231 through 241 Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 260 through 266 Processing helix chain 'F' and resid 283 through 296 Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'F' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 30 removed outlier: 4.701A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 85 removed outlier: 3.809A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 138 through 141 No H-bonds generated for 'chain 'H' and resid 138 through 141' Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 231 through 241 Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 260 through 266 Processing helix chain 'H' and resid 283 through 296 Processing helix chain 'H' and resid 309 through 311 No H-bonds generated for 'chain 'H' and resid 309 through 311' Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 374 Processing helix chain 'H' and resid 386 through 409 Processing helix chain 'H' and resid 417 through 425 Processing helix chain 'H' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA I 78 " --> pdb=" O VAL I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 138 through 141 No H-bonds generated for 'chain 'I' and resid 138 through 141' Processing helix chain 'I' and resid 144 through 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 231 through 241 Proline residue: I 235 - end of helix Processing helix chain 'I' and resid 260 through 266 Processing helix chain 'I' and resid 283 through 296 Processing helix chain 'I' and resid 309 through 311 No H-bonds generated for 'chain 'I' and resid 309 through 311' Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 374 Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 425 Processing helix chain 'I' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.792A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 85 removed outlier: 3.810A 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 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 138 through 141 No H-bonds generated for 'chain 'J' and resid 138 through 141' Processing helix chain 'J' and resid 144 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 231 through 241 Proline residue: J 235 - end of helix Processing helix chain 'J' and resid 260 through 266 Processing helix chain 'J' and resid 283 through 296 Processing helix chain 'J' and resid 309 through 311 No H-bonds generated for 'chain 'J' and resid 309 through 311' Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 359 through 374 Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 425 Processing helix chain 'J' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.792A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 156 through 169 Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 231 through 241 Proline residue: K 235 - end of helix Processing helix chain 'K' and resid 260 through 266 Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 309 through 311 No H-bonds generated for 'chain 'K' and resid 309 through 311' Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 409 Processing helix chain 'K' and resid 417 through 425 Processing helix chain 'K' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 138 through 141 No H-bonds generated for 'chain 'L' and resid 138 through 141' Processing helix chain 'L' and resid 144 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 231 through 241 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 260 through 266 Processing helix chain 'L' and resid 283 through 296 Processing helix chain 'L' and resid 309 through 311 No H-bonds generated for 'chain 'L' and resid 309 through 311' Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 374 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 425 Processing helix chain 'L' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 30 removed outlier: 4.699A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 138 through 141 No H-bonds generated for 'chain 'M' and resid 138 through 141' Processing helix chain 'M' and resid 144 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 231 through 241 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 260 through 266 Processing helix chain 'M' and resid 283 through 296 Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'M' and resid 339 through 355 Processing helix chain 'M' and resid 359 through 374 Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 417 through 425 Processing helix chain 'M' and resid 434 through 457 removed outlier: 3.698A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 30 removed outlier: 4.700A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 85 removed outlier: 3.810A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 138 through 141 No H-bonds generated for 'chain 'N' and resid 138 through 141' Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 231 through 241 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 260 through 266 Processing helix chain 'N' and resid 283 through 296 Processing helix chain 'N' and resid 309 through 311 No H-bonds generated for 'chain 'N' and resid 309 through 311' Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 409 Processing helix chain 'N' and resid 417 through 425 Processing helix chain 'N' and resid 434 through 457 removed outlier: 3.699A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 497 through 516 removed outlier: 3.793A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'G' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= G, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= H, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= I, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= L, first strand: chain 'A' and resid 193 through 195 Processing sheet with id= M, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= N, first strand: chain 'A' and resid 219 through 222 Processing sheet with id= O, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= P, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= Q, first strand: chain 'B' and resid 4 through 8 Processing sheet with id= R, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= S, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= T, first strand: chain 'B' and resid 193 through 195 Processing sheet with id= U, first strand: chain 'B' and resid 213 through 216 Processing sheet with id= V, first strand: chain 'B' and resid 219 through 222 Processing sheet with id= W, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= X, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= Y, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= Z, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= AA, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= AB, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AC, first strand: chain 'C' and resid 213 through 216 Processing sheet with id= AD, first strand: chain 'C' and resid 219 through 222 Processing sheet with id= AE, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AF, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AG, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AH, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AJ, first strand: chain 'D' and resid 193 through 195 Processing sheet with id= AK, first strand: chain 'D' and resid 213 through 216 Processing sheet with id= AL, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AM, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AN, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AO, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AP, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AQ, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AR, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AS, first strand: chain 'E' and resid 213 through 216 Processing sheet with id= AT, first strand: chain 'E' and resid 219 through 222 Processing sheet with id= AU, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AV, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AW, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AX, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AY, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AZ, first strand: chain 'F' and resid 193 through 195 Processing sheet with id= BA, first strand: chain 'F' and resid 213 through 216 Processing sheet with id= BB, first strand: chain 'F' and resid 219 through 222 Processing sheet with id= BC, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= BD, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= BE, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= BF, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= BG, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= BH, first strand: chain 'H' and resid 193 through 195 Processing sheet with id= BI, first strand: chain 'H' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'H' and resid 219 through 222 Processing sheet with id= BK, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= BL, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BM, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= BN, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= BO, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= BP, first strand: chain 'I' and resid 193 through 195 Processing sheet with id= BQ, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= BR, first strand: chain 'I' and resid 219 through 222 Processing sheet with id= BS, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= BT, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= BU, first strand: chain 'J' and resid 4 through 8 Processing sheet with id= BV, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BW, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BX, first strand: chain 'J' and resid 193 through 195 Processing sheet with id= BY, first strand: chain 'J' and resid 213 through 216 Processing sheet with id= BZ, first strand: chain 'J' and resid 219 through 222 Processing sheet with id= CA, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= CB, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= CC, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= CD, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= CE, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= CF, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= CG, first strand: chain 'K' and resid 213 through 216 Processing sheet with id= CH, first strand: chain 'K' and resid 219 through 222 Processing sheet with id= CI, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= CJ, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= CK, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= CL, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= CM, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= CN, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= CO, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= CP, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= CQ, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= CR, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= CS, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= CT, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= CU, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= CV, first strand: chain 'M' and resid 193 through 195 Processing sheet with id= CW, first strand: chain 'M' and resid 213 through 216 Processing sheet with id= CX, first strand: chain 'M' and resid 219 through 222 Processing sheet with id= CY, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= CZ, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= DA, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= DB, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= DC, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= DD, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= DE, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= DF, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= DG, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= DH, first strand: chain 'N' and resid 476 through 479 3164 hydrogen bonds defined for protein. 9156 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: 20.79 Time building geometry restraints manager: 22.09 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: 18775 1.34 - 1.46: 5295 1.46 - 1.57: 30110 1.57 - 1.69: 28 1.69 - 1.81: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CB VAL B 74 " pdb=" CG2 VAL B 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CB VAL N 74 " pdb=" CG2 VAL N 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.94e+00 bond pdb=" CB VAL M 74 " pdb=" CG2 VAL M 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL C 74 " pdb=" CG2 VAL C 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL I 74 " pdb=" CG2 VAL I 74 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.92e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 98.24 - 106.53: 1089 106.53 - 114.82: 34456 114.82 - 123.11: 36083 123.11 - 131.40: 2320 131.40 - 139.69: 42 Bond angle restraints: 73990 Sorted by residual: angle pdb=" CB MET A 267 " pdb=" CG MET A 267 " pdb=" SD MET A 267 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET I 267 " pdb=" CG MET I 267 " pdb=" SD MET I 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET C 267 " pdb=" CG MET C 267 " pdb=" SD MET C 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET F 267 " pdb=" CG MET F 267 " pdb=" SD MET F 267 " ideal model delta sigma weight residual 112.70 124.12 -11.42 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET G 267 " pdb=" CG MET G 267 " pdb=" SD MET G 267 " ideal model delta sigma weight residual 112.70 124.11 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 29103 15.22 - 30.45: 3173 30.45 - 45.67: 1343 45.67 - 60.90: 373 60.90 - 76.12: 168 Dihedral angle restraints: 34160 sinusoidal: 13510 harmonic: 20650 Sorted by residual: dihedral pdb=" CA LYS D 4 " pdb=" C LYS D 4 " pdb=" N ASP D 5 " pdb=" CA ASP D 5 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS M 4 " pdb=" C LYS M 4 " pdb=" N ASP M 5 " pdb=" CA ASP M 5 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LYS B 4 " pdb=" C LYS B 4 " pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta harmonic sigma weight residual 180.00 160.40 19.60 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 5185 0.032 - 0.065: 2628 0.065 - 0.097: 707 0.097 - 0.130: 383 0.130 - 0.162: 71 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CA MET G 447 " pdb=" N MET G 447 " pdb=" C MET G 447 " pdb=" CB MET G 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CA MET C 447 " pdb=" N MET C 447 " pdb=" C MET C 447 " pdb=" CB MET C 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA MET E 447 " pdb=" N MET E 447 " pdb=" C MET E 447 " pdb=" CB MET E 447 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 449 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO D 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 450 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 450 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 449 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.78e+00 pdb=" N PRO E 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 450 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 450 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 449 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO K 450 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO K 450 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO K 450 " -0.019 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.53: 1158 2.53 - 3.18: 51941 3.18 - 3.83: 130882 3.83 - 4.49: 175174 4.49 - 5.14: 266077 Nonbonded interactions: 625232 Sorted by model distance: nonbonded pdb=" O PHE J 195 " pdb=" O HOH J 701 " model vdw 1.872 2.440 nonbonded pdb=" O THR J 330 " pdb=" O HOH J 701 " model vdw 2.048 2.440 nonbonded pdb="MG MG H 601 " pdb=" O1B ATP H 602 " model vdw 2.055 2.170 nonbonded pdb="MG MG L 601 " pdb=" O1B ATP L 602 " model vdw 2.055 2.170 nonbonded pdb="MG MG E 601 " pdb=" O1B ATP E 602 " model vdw 2.055 2.170 ... (remaining 625227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.370 Check model and map are aligned: 0.310 Set scattering table: 0.390 Process input model: 124.510 Find NCS groups from input model: 3.560 Set up NCS constraints: 0.450 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:10.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 0.046 54726 Z= 0.317 Angle : 0.592 11.427 73990 Z= 0.318 Chirality : 0.045 0.162 8974 Planarity : 0.003 0.034 9618 Dihedral : 16.845 76.125 20916 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.01 % Allowed : 17.88 % Favored : 81.11 % 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: 0.70 (0.09), residues: 7294 helix: 1.27 (0.08), residues: 4144 sheet: -0.12 (0.13), residues: 1148 loop : -0.74 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.006 0.001 PHE L 195 TYR 0.014 0.002 TYR N 478 ARG 0.002 0.000 ARG B 13 *********************** 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 395 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 338 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 MET cc_start: 0.8206 (mtt) cc_final: 0.7990 (mtp) REVERT: B 166 MET cc_start: 0.8301 (mtt) cc_final: 0.7991 (mtt) REVERT: C 58 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7708 (mtt-85) REVERT: C 233 MET cc_start: 0.0958 (pmt) cc_final: 0.0700 (pmm) REVERT: C 520 MET cc_start: 0.8838 (mtp) cc_final: 0.8633 (mtp) REVERT: D 166 MET cc_start: 0.8200 (mtt) cc_final: 0.7916 (mtp) REVERT: H 233 MET cc_start: 0.0062 (pmt) cc_final: -0.1182 (tmt) REVERT: I 233 MET cc_start: 0.0316 (pmt) cc_final: -0.0658 (tmt) REVERT: K 386 GLU cc_start: 0.7297 (tp30) cc_final: 0.6877 (mm-30) REVERT: L 73 MET cc_start: 0.8143 (mtm) cc_final: 0.7883 (mtm) REVERT: M 114 MET cc_start: 0.8960 (tpp) cc_final: 0.8665 (tpp) REVERT: N 233 MET cc_start: 0.0426 (pmt) cc_final: -0.0958 (tmt) outliers start: 57 outliers final: 23 residues processed: 395 average time/residue: 1.4325 time to fit residues: 716.0230 Evaluate side-chains 327 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 304 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain K residue 236 VAL 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: 30.0000 chunk 306 optimal weight: 0.0370 chunk 188 optimal weight: 0.8980 chunk 372 optimal weight: 0.9990 chunk 294 optimal weight: 9.9990 chunk 570 optimal weight: 0.7980 chunk 220 optimal weight: 0.5980 chunk 346 optimal weight: 2.9990 chunk 424 optimal weight: 1.9990 chunk 661 optimal weight: 8.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 10 ASN L 112 ASN M 10 ASN N 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54726 Z= 0.176 Angle : 0.482 9.514 73990 Z= 0.260 Chirality : 0.040 0.144 8974 Planarity : 0.003 0.029 9618 Dihedral : 7.946 76.357 8228 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.89 % Allowed : 16.11 % Favored : 81.00 % 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: 1.08 (0.10), residues: 7294 helix: 1.68 (0.08), residues: 4074 sheet: -0.25 (0.14), residues: 1162 loop : -0.54 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.018 0.001 PHE J 195 TYR 0.013 0.001 TYR I 478 ARG 0.005 0.000 ARG G 284 *********************** 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 492 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 329 time to evaluate : 4.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 MET cc_start: 0.8278 (mtt) cc_final: 0.7861 (mtp) REVERT: A 111 MET cc_start: 0.8185 (mtp) cc_final: 0.7954 (mtp) REVERT: A 114 MET cc_start: 0.9268 (tpp) cc_final: 0.8972 (tpp) REVERT: A 267 MET cc_start: -0.0747 (pmm) cc_final: -0.1040 (ptp) REVERT: B 166 MET cc_start: 0.8307 (mtt) cc_final: 0.7873 (mtt) REVERT: B 233 MET cc_start: 0.0590 (pmt) cc_final: -0.1228 (tmt) REVERT: B 514 MET cc_start: 0.8741 (mtp) cc_final: 0.8480 (mtp) REVERT: C 267 MET cc_start: 0.0108 (pmm) cc_final: -0.0121 (pmm) REVERT: C 389 MET cc_start: 0.8370 (tpp) cc_final: 0.8140 (tpp) REVERT: C 491 MET cc_start: 0.8945 (mtm) cc_final: 0.8595 (mtm) REVERT: D 166 MET cc_start: 0.8188 (mtt) cc_final: 0.7695 (mtt) REVERT: D 233 MET cc_start: 0.0611 (pmt) cc_final: -0.1061 (tmt) REVERT: E 142 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6470 (tptp) REVERT: E 237 LEU cc_start: 0.1317 (OUTLIER) cc_final: 0.0847 (mt) REVERT: F 233 MET cc_start: 0.0511 (pmt) cc_final: -0.1286 (tmt) REVERT: F 267 MET cc_start: 0.0259 (pmm) cc_final: -0.2425 (mpp) REVERT: I 166 MET cc_start: 0.7861 (mtt) cc_final: 0.7590 (mtt) REVERT: I 174 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7390 (p) REVERT: I 267 MET cc_start: 0.0454 (pmm) cc_final: -0.0444 (ptp) REVERT: K 267 MET cc_start: -0.0012 (pmm) cc_final: -0.0681 (ptp) REVERT: L 267 MET cc_start: 0.0289 (pmm) cc_final: -0.0664 (ptp) REVERT: N 267 MET cc_start: -0.0012 (pmm) cc_final: -0.1829 (tpp) outliers start: 163 outliers final: 23 residues processed: 458 average time/residue: 1.3669 time to fit residues: 800.5074 Evaluate side-chains 334 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 308 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 219 PHE Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 219 PHE Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain E residue 142 LYS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 219 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 219 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain H residue 219 PHE Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 288 MET Chi-restraints excluded: chain J residue 219 PHE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain L residue 219 PHE Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain N residue 219 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9373 > 50: distance: 87 - 190: 24.579 distance: 90 - 187: 18.160 distance: 155 - 159: 7.837 distance: 159 - 160: 16.749 distance: 160 - 161: 9.854 distance: 160 - 163: 21.262 distance: 161 - 162: 17.890 distance: 161 - 167: 23.772 distance: 163 - 164: 25.148 distance: 164 - 165: 4.817 distance: 165 - 166: 8.830 distance: 167 - 168: 25.965 distance: 168 - 169: 36.462 distance: 169 - 170: 23.185 distance: 169 - 171: 20.809 distance: 171 - 172: 9.440 distance: 172 - 173: 47.114 distance: 172 - 175: 29.404 distance: 173 - 174: 11.534 distance: 173 - 179: 25.853 distance: 175 - 176: 4.091 distance: 175 - 177: 24.984 distance: 176 - 178: 12.308 distance: 179 - 180: 21.242 distance: 180 - 181: 52.170 distance: 180 - 183: 39.099 distance: 181 - 182: 29.819 distance: 181 - 187: 17.262 distance: 183 - 184: 18.212 distance: 184 - 185: 22.901 distance: 184 - 186: 24.168 distance: 187 - 188: 6.699 distance: 188 - 189: 12.867 distance: 188 - 191: 33.119 distance: 189 - 190: 25.306 distance: 189 - 195: 19.546 distance: 191 - 192: 15.162 distance: 192 - 193: 44.354 distance: 192 - 194: 30.294 distance: 195 - 196: 8.484 distance: 195 - 201: 14.591 distance: 196 - 197: 13.078 distance: 196 - 199: 25.926 distance: 197 - 198: 18.132 distance: 197 - 202: 7.820 distance: 199 - 200: 18.253 distance: 200 - 201: 22.450 distance: 202 - 203: 7.409 distance: 203 - 204: 20.193 distance: 203 - 206: 11.834 distance: 204 - 205: 6.943 distance: 204 - 209: 12.938 distance: 205 - 232: 21.857 distance: 206 - 207: 23.798 distance: 206 - 208: 19.578 distance: 209 - 210: 10.896 distance: 210 - 211: 10.583 distance: 210 - 213: 21.464 distance: 211 - 212: 11.324 distance: 211 - 218: 16.480 distance: 212 - 242: 5.929 distance: 213 - 214: 18.297 distance: 214 - 215: 22.120 distance: 215 - 216: 25.191 distance: 216 - 217: 6.711 distance: 218 - 219: 19.184 distance: 219 - 220: 5.001 distance: 219 - 222: 17.893 distance: 220 - 221: 17.350 distance: 220 - 225: 14.813 distance: 221 - 248: 27.118 distance: 222 - 223: 27.335 distance: 222 - 224: 19.079 distance: 225 - 226: 3.802 distance: 226 - 227: 8.361 distance: 226 - 229: 22.386 distance: 227 - 228: 6.267 distance: 227 - 232: 10.395 distance: 228 - 252: 15.610 distance: 229 - 230: 13.334 distance: 229 - 231: 7.831