Starting phenix.real_space_refine on Wed Sep 25 14:36:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmd_16118/09_2024/8bmd_16118.cif" } resolution = 2.8 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 12174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 55532 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 84 Classifications: {'water': 84} Link IDs: {None: 83} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 75 Classifications: {'water': 75} Link IDs: {None: 74} Chain: "B" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "F" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 82 Classifications: {'water': 82} Link IDs: {None: 81} Chain: "H" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 87 Classifications: {'water': 87} Link IDs: {None: 86} Chain: "I" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "J" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Chain: "K" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "M" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "N" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} 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: 25.11, per 1000 atoms: 0.45 Number of scatterers: 55532 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 12174 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: 10.87 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: 290 helices and 85 sheets defined 58.3% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.905A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.843A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.825A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 241 removed outlier: 4.590A pdb=" N VAL G 236 " --> pdb=" O GLU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 265 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 374 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 459 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 60 Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.943A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.536A pdb=" N PHE A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.524A pdb=" N GLU A 232 " --> pdb=" O ASN A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.627A 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 338 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.547A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) 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 459 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 60 Processing helix chain 'B' and resid 64 through 85 removed outlier: 4.051A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.882A 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 169 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.555A pdb=" N PHE B 204 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 4.001A 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 265 Processing helix chain 'B' and resid 282 through 297 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 425 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 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 60 Processing helix chain 'C' and resid 64 through 85 removed outlier: 4.044A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.973A 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 169 Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.926A pdb=" N ILE C 205 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 244 removed outlier: 4.242A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.637A 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 515 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.529A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.823A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.918A 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 169 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.522A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.854A 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 removed outlier: 3.735A pdb=" N MET D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) 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 86 removed outlier: 3.969A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.901A 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 167 Processing helix chain 'E' and resid 201 through 205 removed outlier: 4.004A pdb=" N ILE E 205 " --> pdb=" O PRO E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 242 removed outlier: 4.094A 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 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 459 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 Processing helix chain 'F' and resid 64 through 86 removed outlier: 3.834A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.949A 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 170 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.557A pdb=" N PHE F 204 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 201 through 205' 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 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 497 through 515 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: 3.869A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.911A 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 169 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.504A pdb=" N PHE H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE H 205 " --> pdb=" O PRO H 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 201 through 205' Processing helix chain 'H' and resid 229 through 242 removed outlier: 3.814A pdb=" N MET H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 259 through 267 removed outlier: 3.593A 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 86 removed outlier: 3.972A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.945A 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 169 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.901A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 244 removed outlier: 3.512A pdb=" N GLY I 244 " --> pdb=" O VAL I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 267 removed outlier: 3.795A 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 374 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 60 Processing helix chain 'J' and resid 64 through 86 removed outlier: 3.826A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.713A 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: 3.760A pdb=" N ILE J 205 " --> pdb=" O PRO J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 242 removed outlier: 3.811A 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 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 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 497 through 515 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 86 removed outlier: 3.938A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.922A 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 169 Processing helix chain 'K' and resid 201 through 205 removed outlier: 3.938A pdb=" N ILE K 205 " --> pdb=" O PRO K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 260 through 265 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 425 Processing helix chain 'K' and resid 433 through 447 Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 497 through 515 Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 52 through 60 Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.805A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.932A 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 60 removed outlier: 3.518A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 85 removed outlier: 3.978A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.916A 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 169 Processing helix chain 'M' and resid 201 through 205 removed outlier: 3.983A 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 260 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 515 Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 60 Processing helix chain 'N' and resid 64 through 85 removed outlier: 3.873A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.671A 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 169 Processing helix chain 'N' and resid 233 through 242 Processing helix chain 'N' and resid 259 through 267 removed outlier: 3.639A pdb=" N MET N 267 " --> pdb=" O VAL N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 removed outlier: 3.514A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 425 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 459 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: 7.413A pdb=" N VAL M 39 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 4.456A 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: 6.598A pdb=" N ASN G 37 " --> pdb=" O CYS B 519 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N VAL B 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL G 39 " --> pdb=" O VAL B 521 " (cutoff:3.500A) removed outlier: 8.482A 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 Processing sheet with id=AA4, first strand: chain 'G' and resid 193 through 195 Processing sheet with id=AA5, first strand: chain 'G' and resid 274 through 276 removed outlier: 6.232A pdb=" N LEU G 247 " --> pdb=" O ALA G 274 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (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: 5.512A pdb=" N ASN C 37 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.569A pdb=" N ASN A 37 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL N 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 39 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 8.456A 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 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 274 through 276 removed outlier: 5.857A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AB5, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.492A pdb=" N ASN B 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL D 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL B 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP D 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 179 Processing sheet with id=AB8, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 275 removed outlier: 6.062A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AC2, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC3, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.394A pdb=" N ASN E 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS C 519 " --> pdb=" O ASN E 37 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 174 through 179 Processing sheet with id=AC5, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AC6, first strand: chain 'C' and resid 274 through 276 removed outlier: 5.891A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC8, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC9, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.591A pdb=" N ASN D 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL F 521 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL D 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ASP F 523 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 174 through 179 Processing sheet with id=AD2, first strand: chain 'D' and resid 193 through 195 removed outlier: 6.644A pdb=" N THR D 330 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 325 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE D 332 " --> pdb=" O VAL D 323 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL D 323 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP D 334 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.943A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD5, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD6, first strand: chain 'E' and resid 4 through 8 removed outlier: 5.513A pdb=" N ASN H 37 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 174 through 179 Processing sheet with id=AD8, first strand: chain 'E' and resid 193 through 195 Processing sheet with id=AD9, first strand: chain 'E' and resid 273 through 276 removed outlier: 6.132A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 273 through 276 removed outlier: 6.132A pdb=" N LEU E 247 " --> pdb=" O ALA E 274 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (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: 6.581A pdb=" N ASN F 37 " --> pdb=" O CYS I 519 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N VAL I 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL F 39 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASP I 523 " --> 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: 6.646A pdb=" N THR F 330 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE F 325 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE F 332 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 323 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP F 334 " --> pdb=" O LYS F 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 193 through 195 removed outlier: 6.646A pdb=" N THR F 330 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE F 325 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE F 332 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 323 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP F 334 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (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: 5.880A pdb=" N ASN J 37 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 3.564A 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 Processing sheet with id=AF4, first strand: chain 'H' and resid 274 through 276 removed outlier: 6.212A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (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: 6.506A pdb=" N ASN I 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N VAL K 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL I 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASP K 523 " --> 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 Processing sheet with id=AG1, first strand: chain 'I' and resid 274 through 276 removed outlier: 6.145A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 7.073A 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: 5.835A pdb=" N ASN L 37 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS J 519 " --> pdb=" O ASN L 37 " (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: 3.508A pdb=" N VAL J 323 " --> pdb=" O LEU J 215 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 274 through 276 removed outlier: 6.203A pdb=" N LEU J 247 " --> pdb=" O ALA J 274 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (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: 7.312A pdb=" N ASN K 37 " --> pdb=" O GLU M 518 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N MET M 520 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL K 39 " --> pdb=" O MET M 520 " (cutoff:3.500A) removed outlier: 5.346A 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 Processing sheet with id=AH4, first strand: chain 'K' and resid 274 through 276 removed outlier: 6.249A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (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: 5.556A pdb=" N ASN N 37 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 3.635A 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 Processing sheet with id=AH9, first strand: chain 'L' and resid 193 through 195 Processing sheet with id=AI1, first strand: chain 'L' and resid 274 through 277 removed outlier: 6.028A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (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: 4.232A pdb=" N MET M 193 " --> pdb=" O ILE M 332 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 274 through 276 removed outlier: 6.117A pdb=" N LEU M 247 " --> pdb=" O ALA M 274 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL M 276 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE M 249 " --> pdb=" O VAL M 276 " (cutoff:3.500A) 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 Processing sheet with id=AJ1, first strand: chain 'N' and resid 193 through 195 removed outlier: 3.505A pdb=" N VAL N 323 " --> pdb=" O LEU N 215 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 273 through 276 removed outlier: 6.173A pdb=" N LEU N 247 " --> pdb=" O ALA N 274 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (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 3617 hydrogen bonds defined for protein. 10422 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: 26.33 Time building geometry restraints manager: 12.95 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: 18825 1.34 - 1.46: 9552 1.46 - 1.58: 25804 1.58 - 1.70: 27 1.70 - 1.82: 518 Bond restraints: 54726 Sorted by residual: bond pdb=" CG1 ILE A 353 " pdb=" CD1 ILE A 353 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CB VAL L 74 " pdb=" CG2 VAL L 74 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 bond pdb=" SD MET H 520 " pdb=" CE MET H 520 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.16e+00 bond pdb=" C LEU E 494 " pdb=" N ASP E 495 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.14e+00 bond pdb=" CA MET J 267 " pdb=" CB MET J 267 " ideal model delta sigma weight residual 1.534 1.568 -0.034 2.47e-02 1.64e+03 1.86e+00 ... (remaining 54721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 73579 2.83 - 5.66: 344 5.66 - 8.49: 41 8.49 - 11.32: 17 11.32 - 14.15: 9 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 113.18 126.16 -12.98 2.37e+00 1.78e-01 3.00e+01 angle pdb=" CA MET E 233 " pdb=" CB MET E 233 " pdb=" CG MET E 233 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 angle pdb=" CB MET L 267 " pdb=" CG MET L 267 " pdb=" SD MET L 267 " ideal model delta sigma weight residual 112.70 98.55 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CB MET K 233 " pdb=" CG MET K 233 " pdb=" SD MET K 233 " ideal model delta sigma weight residual 112.70 126.68 -13.98 3.00e+00 1.11e-01 2.17e+01 angle pdb=" CB MET C 307 " pdb=" CG MET C 307 " pdb=" SD MET C 307 " ideal model delta sigma weight residual 112.70 125.09 -12.39 3.00e+00 1.11e-01 1.70e+01 ... (remaining 73985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 29647 17.99 - 35.98: 3337 35.98 - 53.96: 965 53.96 - 71.95: 132 71.95 - 89.94: 79 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 180.00 134.57 45.43 0 5.00e+00 4.00e-02 8.26e+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 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+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 -158.69 -21.31 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 34157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 7211 0.050 - 0.101: 1424 0.101 - 0.151: 336 0.151 - 0.201: 1 0.201 - 0.251: 2 Chirality restraints: 8974 Sorted by residual: chirality pdb=" CG LEU M 295 " pdb=" CB LEU M 295 " pdb=" CD1 LEU M 295 " pdb=" CD2 LEU M 295 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE B 250 " pdb=" CA ILE B 250 " pdb=" CG1 ILE B 250 " pdb=" CG2 ILE B 250 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL L 271 " pdb=" N VAL L 271 " pdb=" C VAL L 271 " pdb=" CB VAL L 271 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 8971 not shown) Planarity restraints: 9618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 234 " -0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO L 235 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO L 235 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO L 235 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 234 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO J 235 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO J 235 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO J 235 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 234 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO H 235 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 235 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 235 " -0.026 5.00e-02 4.00e+02 ... (remaining 9615 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.65: 1202 2.65 - 3.27: 59520 3.27 - 3.90: 121706 3.90 - 4.52: 161672 4.52 - 5.14: 243056 Nonbonded interactions: 587156 Sorted by model distance: nonbonded pdb="MG MG G 601 " pdb=" O2A ATP G 602 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR M 90 " pdb=" O1G ATP M 602 " model vdw 2.234 3.040 nonbonded pdb="MG MG A 601 " pdb=" O2A ATP A 602 " model vdw 2.234 2.170 nonbonded pdb=" OG1 THR C 90 " pdb=" O1G ATP C 602 " model vdw 2.246 3.040 nonbonded pdb="MG MG K 601 " pdb=" O2A ATP K 602 " model vdw 2.247 2.170 ... (remaining 587151 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 1.720 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 106.120 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 54726 Z= 0.259 Angle : 0.599 14.147 73990 Z= 0.314 Chirality : 0.042 0.251 8974 Planarity : 0.004 0.060 9618 Dihedral : 16.852 89.938 20916 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.77 % Favored : 98.22 % Rotamer: Outliers : 1.77 % Allowed : 19.30 % Favored : 78.93 % 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: 0.48 (0.09), residues: 7294 helix: 1.14 (0.08), residues: 4102 sheet: -0.33 (0.13), residues: 1218 loop : -0.83 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.030 0.001 PHE J 195 TYR 0.010 0.001 TYR M 478 ARG 0.002 0.000 ARG K 404 *********************** 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 362 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 262 time to evaluate : 4.584 Fit side-chains revert: symmetry clash REVERT: D 307 MET cc_start: 0.5834 (tpp) cc_final: 0.3584 (ttt) REVERT: E 114 MET cc_start: 0.8925 (tpp) cc_final: 0.8717 (tpp) REVERT: H 307 MET cc_start: 0.5921 (tpt) cc_final: 0.3363 (tmt) REVERT: K 114 MET cc_start: 0.8928 (tpp) cc_final: 0.8711 (tpp) REVERT: L 288 MET cc_start: 0.6082 (mmt) cc_final: 0.4943 (ptm) REVERT: L 307 MET cc_start: 0.4240 (tmm) cc_final: 0.3944 (tmm) REVERT: M 111 MET cc_start: 0.8866 (mtp) cc_final: 0.8657 (mtp) REVERT: M 288 MET cc_start: 0.5818 (ptm) cc_final: 0.5479 (ptt) outliers start: 100 outliers final: 81 residues processed: 355 average time/residue: 1.2600 time to fit residues: 585.0505 Evaluate side-chains 341 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 260 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 329 THR Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 358 SER Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 300 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 0.8980 chunk 551 optimal weight: 30.0000 chunk 306 optimal weight: 1.9990 chunk 188 optimal weight: 30.0000 chunk 372 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 570 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 346 optimal weight: 30.0000 chunk 424 optimal weight: 2.9990 chunk 661 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 ASN A 37 ASN B 37 ASN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN E 37 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN K 37 ASN L 37 ASN ** L 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54726 Z= 0.180 Angle : 0.488 11.821 73990 Z= 0.264 Chirality : 0.040 0.159 8974 Planarity : 0.003 0.056 9618 Dihedral : 9.168 81.662 8299 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.08 % Favored : 98.90 % Rotamer: Outliers : 2.75 % Allowed : 18.56 % Favored : 78.70 % 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: 0.96 (0.10), residues: 7294 helix: 1.60 (0.08), residues: 4116 sheet: -0.24 (0.14), residues: 1218 loop : -0.73 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 401 PHE 0.014 0.001 PHE A 44 TYR 0.008 0.001 TYR M 478 ARG 0.005 0.000 ARG N 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 fitting. rotamer outliers: 155 poor density : 261 time to evaluate : 4.600 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: D 307 MET cc_start: 0.6286 (tpp) cc_final: 0.5878 (tpt) REVERT: E 114 MET cc_start: 0.8943 (tpp) cc_final: 0.8743 (tpp) REVERT: H 307 MET cc_start: 0.6133 (tpt) cc_final: 0.3143 (ttt) REVERT: H 461 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: H 514 MET cc_start: 0.9220 (mtp) cc_final: 0.9005 (mtm) REVERT: I 447 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9037 (mtm) REVERT: K 213 VAL cc_start: 0.1092 (OUTLIER) cc_final: 0.0794 (m) REVERT: L 10 ASN cc_start: 0.8787 (OUTLIER) cc_final: 0.8373 (t0) REVERT: L 226 LYS cc_start: 0.2091 (OUTLIER) cc_final: 0.1367 (tptt) outliers start: 155 outliers final: 68 residues processed: 395 average time/residue: 1.2874 time to fit residues: 659.4708 Evaluate side-chains 335 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 261 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 520 MET Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 157 THR Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 226 LYS Chi-restraints excluded: chain M residue 10 ASN Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 138 CYS Chi-restraints excluded: chain N residue 157 THR Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU 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: 0.9980 chunk 550 optimal weight: 2.9990 chunk 450 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 662 optimal weight: 2.9990 chunk 715 optimal weight: 0.7980 chunk 589 optimal weight: 0.5980 chunk 656 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 531 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54726 Z= 0.247 Angle : 0.494 11.667 73990 Z= 0.266 Chirality : 0.040 0.157 8974 Planarity : 0.003 0.052 9618 Dihedral : 8.883 83.891 8244 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.22 % Favored : 98.77 % Rotamer: Outliers : 2.73 % Allowed : 18.66 % Favored : 78.61 % 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: 1.05 (0.10), residues: 7294 helix: 1.67 (0.08), residues: 4116 sheet: -0.22 (0.14), residues: 1218 loop : -0.70 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.014 0.001 PHE M 44 TYR 0.009 0.001 TYR M 478 ARG 0.003 0.000 ARG B 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 414 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 260 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 222 LEU cc_start: 0.1826 (OUTLIER) cc_final: 0.1458 (mp) REVERT: B 233 MET cc_start: 0.1450 (tmm) cc_final: 0.1202 (tmm) REVERT: D 307 MET cc_start: 0.6350 (tpp) cc_final: 0.5914 (tpp) REVERT: E 114 MET cc_start: 0.8935 (tpp) cc_final: 0.8720 (tpp) REVERT: H 307 MET cc_start: 0.6017 (tpt) cc_final: 0.3135 (ttt) REVERT: H 461 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: H 514 MET cc_start: 0.9253 (mtp) cc_final: 0.8978 (mtm) REVERT: I 514 MET cc_start: 0.9282 (mtp) cc_final: 0.9064 (mtm) REVERT: L 10 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8404 (t0) REVERT: L 194 GLN cc_start: 0.7496 (pm20) cc_final: 0.7250 (pm20) outliers start: 154 outliers final: 77 residues processed: 392 average time/residue: 1.2625 time to fit residues: 643.5929 Evaluate side-chains 341 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 261 time to evaluate : 4.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 520 MET Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 442 VAL Chi-restraints excluded: chain H residue 461 GLU Chi-restraints excluded: chain H residue 491 MET Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 6.9990 chunk 497 optimal weight: 50.0000 chunk 343 optimal weight: 40.0000 chunk 73 optimal weight: 0.6980 chunk 316 optimal weight: 0.2980 chunk 444 optimal weight: 7.9990 chunk 664 optimal weight: 0.9990 chunk 703 optimal weight: 9.9990 chunk 347 optimal weight: 30.0000 chunk 629 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 54726 Z= 0.336 Angle : 0.527 12.634 73990 Z= 0.282 Chirality : 0.042 0.147 8974 Planarity : 0.003 0.049 9618 Dihedral : 9.045 87.683 8235 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.12 % Favored : 98.86 % Rotamer: Outliers : 3.12 % Allowed : 18.47 % Favored : 78.41 % 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: 0.93 (0.09), residues: 7294 helix: 1.56 (0.08), residues: 4116 sheet: -0.41 (0.14), residues: 1106 loop : -0.60 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.017 0.001 PHE N 195 TYR 0.011 0.002 TYR M 478 ARG 0.003 0.000 ARG F 13 *********************** 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 442 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 266 time to evaluate : 4.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.7605 (pm20) cc_final: 0.7191 (pm20) REVERT: A 323 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7060 (t) REVERT: B 222 LEU cc_start: 0.1811 (OUTLIER) cc_final: 0.1408 (mp) REVERT: D 10 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8309 (t0) REVERT: D 307 MET cc_start: 0.6651 (tpp) cc_final: 0.6218 (tpp) REVERT: E 114 MET cc_start: 0.8908 (tpp) cc_final: 0.8676 (tpp) REVERT: F 323 VAL cc_start: 0.6817 (OUTLIER) cc_final: 0.6541 (t) REVERT: H 111 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8063 (mmp) REVERT: H 514 MET cc_start: 0.9277 (mtp) cc_final: 0.9017 (mtm) REVERT: I 514 MET cc_start: 0.9279 (mtp) cc_final: 0.9025 (mtm) REVERT: J 193 MET cc_start: 0.6460 (mmm) cc_final: 0.6174 (mmm) REVERT: L 10 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8397 (t0) REVERT: N 307 MET cc_start: 0.4706 (tmm) cc_final: 0.4214 (tmm) outliers start: 176 outliers final: 108 residues processed: 414 average time/residue: 1.2354 time to fit residues: 669.1773 Evaluate side-chains 376 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 262 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain G residue 442 VAL Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 10 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 142 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 520 MET Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 491 MET Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 1.9990 chunk 399 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 523 optimal weight: 0.6980 chunk 290 optimal weight: 0.0570 chunk 600 optimal weight: 6.9990 chunk 486 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54726 Z= 0.169 Angle : 0.475 12.447 73990 Z= 0.255 Chirality : 0.039 0.163 8974 Planarity : 0.003 0.048 9618 Dihedral : 8.729 83.127 8234 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.22 % Favored : 98.77 % Rotamer: Outliers : 2.50 % Allowed : 19.32 % Favored : 78.18 % 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: 1.16 (0.10), residues: 7294 helix: 1.79 (0.08), residues: 4116 sheet: -0.20 (0.14), residues: 1218 loop : -0.70 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.014 0.001 PHE B 44 TYR 0.008 0.001 TYR M 478 ARG 0.003 0.000 ARG G 501 *********************** 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 408 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 267 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7425 (OUTLIER) cc_final: 0.7103 (t) REVERT: B 222 LEU cc_start: 0.1790 (OUTLIER) cc_final: 0.1387 (mp) REVERT: B 365 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5831 (tp) REVERT: D 193 MET cc_start: 0.5884 (mmm) cc_final: 0.5369 (mmm) REVERT: D 307 MET cc_start: 0.6613 (tpp) cc_final: 0.6258 (tpp) REVERT: E 114 MET cc_start: 0.8951 (tpp) cc_final: 0.8750 (tpp) REVERT: E 323 VAL cc_start: 0.7157 (OUTLIER) cc_final: 0.6862 (t) REVERT: F 323 VAL cc_start: 0.6718 (OUTLIER) cc_final: 0.6428 (t) REVERT: H 307 MET cc_start: 0.5916 (tpt) cc_final: 0.3173 (ttp) REVERT: H 514 MET cc_start: 0.9243 (mtp) cc_final: 0.8956 (mtm) REVERT: I 514 MET cc_start: 0.9251 (mtp) cc_final: 0.8991 (mtm) REVERT: J 193 MET cc_start: 0.6649 (mmm) cc_final: 0.6354 (mmm) REVERT: L 10 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8430 (t0) outliers start: 141 outliers final: 79 residues processed: 386 average time/residue: 1.2410 time to fit residues: 625.3002 Evaluate side-chains 346 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 261 time to evaluate : 4.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain M residue 513 LEU Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN 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: 0.6980 chunk 139 optimal weight: 10.0000 chunk 413 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 704 optimal weight: 50.0000 chunk 584 optimal weight: 0.9980 chunk 326 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 369 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1032 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= 0.229 Angle : 0.497 12.061 73990 Z= 0.264 Chirality : 0.040 0.146 8974 Planarity : 0.003 0.047 9618 Dihedral : 8.758 84.939 8231 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.23 % Favored : 98.75 % Rotamer: Outliers : 2.52 % Allowed : 19.51 % Favored : 77.97 % 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: 1.19 (0.10), residues: 7294 helix: 1.80 (0.08), residues: 4116 sheet: -0.17 (0.14), residues: 1218 loop : -0.69 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 401 PHE 0.015 0.001 PHE A 44 TYR 0.009 0.001 TYR M 478 ARG 0.002 0.000 ARG J 13 *********************** 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 405 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 263 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 MET cc_start: -0.3227 (pp-130) cc_final: -0.3452 (pp-130) REVERT: A 323 VAL cc_start: 0.7443 (OUTLIER) cc_final: 0.7122 (t) REVERT: B 233 MET cc_start: 0.1072 (tmm) cc_final: 0.0743 (tmm) REVERT: B 365 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.6095 (tp) REVERT: D 307 MET cc_start: 0.6653 (tpp) cc_final: 0.6282 (tpp) REVERT: E 114 MET cc_start: 0.8940 (tpp) cc_final: 0.8718 (tpp) REVERT: E 323 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6903 (t) REVERT: F 323 VAL cc_start: 0.6753 (OUTLIER) cc_final: 0.6474 (t) REVERT: H 307 MET cc_start: 0.5950 (tpt) cc_final: 0.3249 (ttp) REVERT: H 514 MET cc_start: 0.9264 (mtp) cc_final: 0.8964 (mtm) REVERT: I 514 MET cc_start: 0.9253 (mtp) cc_final: 0.9006 (mtm) REVERT: J 193 MET cc_start: 0.6570 (mmm) cc_final: 0.6242 (mmm) REVERT: L 10 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8420 (t0) REVERT: N 307 MET cc_start: 0.4720 (tmm) cc_final: 0.4264 (tmm) outliers start: 142 outliers final: 104 residues processed: 389 average time/residue: 1.2158 time to fit residues: 620.6574 Evaluate side-chains 370 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 261 time to evaluate : 4.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain M residue 10 ASN Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 514 optimal weight: 0.8980 chunk 398 optimal weight: 0.9980 chunk 592 optimal weight: 8.9990 chunk 393 optimal weight: 8.9990 chunk 701 optimal weight: 6.9990 chunk 439 optimal weight: 40.0000 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 319 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54726 Z= 0.210 Angle : 0.498 11.710 73990 Z= 0.264 Chirality : 0.040 0.143 8974 Planarity : 0.003 0.047 9618 Dihedral : 8.711 84.550 8231 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.28 % Favored : 98.71 % Rotamer: Outliers : 2.68 % Allowed : 19.39 % Favored : 77.93 % 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: 1.22 (0.10), residues: 7294 helix: 1.83 (0.08), residues: 4116 sheet: -0.14 (0.14), residues: 1218 loop : -0.67 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.015 0.001 PHE B 44 TYR 0.008 0.001 TYR M 478 ARG 0.002 0.000 ARG F 13 *********************** 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 413 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 262 time to evaluate : 4.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 LEU cc_start: 0.1525 (OUTLIER) cc_final: 0.1195 (mp) REVERT: B 365 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6199 (tp) REVERT: D 193 MET cc_start: 0.6010 (mmm) cc_final: 0.5407 (mmm) REVERT: D 307 MET cc_start: 0.6736 (tpp) cc_final: 0.6373 (tpp) REVERT: E 114 MET cc_start: 0.8941 (tpp) cc_final: 0.8733 (tpp) REVERT: E 323 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6910 (t) REVERT: F 323 VAL cc_start: 0.6757 (OUTLIER) cc_final: 0.6481 (t) REVERT: H 307 MET cc_start: 0.6150 (tpt) cc_final: 0.3524 (ttp) REVERT: H 514 MET cc_start: 0.9259 (mtp) cc_final: 0.8964 (mtm) REVERT: I 514 MET cc_start: 0.9214 (mtp) cc_final: 0.8952 (mtm) REVERT: J 193 MET cc_start: 0.6477 (mmm) cc_final: 0.6114 (mmm) REVERT: L 10 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8432 (t0) REVERT: L 267 MET cc_start: -0.1617 (tmm) cc_final: -0.2039 (tpp) REVERT: N 307 MET cc_start: 0.4754 (tmm) cc_final: 0.4349 (tmm) outliers start: 151 outliers final: 105 residues processed: 398 average time/residue: 1.2289 time to fit residues: 639.5060 Evaluate side-chains 372 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 262 time to evaluate : 4.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 10 ASN Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 419 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 135 optimal weight: 40.0000 chunk 446 optimal weight: 9.9990 chunk 478 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 65 optimal weight: 0.0060 chunk 551 optimal weight: 30.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 ASN L 319 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54726 Z= 0.319 Angle : 0.539 11.989 73990 Z= 0.284 Chirality : 0.042 0.141 8974 Planarity : 0.003 0.045 9618 Dihedral : 8.883 87.541 8229 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.33 % Favored : 98.66 % Rotamer: Outliers : 2.78 % Allowed : 19.39 % Favored : 77.83 % 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: 1.08 (0.10), residues: 7294 helix: 1.69 (0.08), residues: 4116 sheet: -0.18 (0.14), residues: 1218 loop : -0.70 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 401 PHE 0.015 0.001 PHE A 44 TYR 0.010 0.002 TYR I 476 ARG 0.005 0.000 ARG L 284 *********************** 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 423 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 266 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7438 (OUTLIER) cc_final: 0.7189 (p) REVERT: D 307 MET cc_start: 0.6775 (tpp) cc_final: 0.6399 (tpp) REVERT: E 114 MET cc_start: 0.8910 (tpp) cc_final: 0.8696 (tpp) REVERT: E 193 MET cc_start: 0.6384 (mmm) cc_final: 0.5772 (mmm) REVERT: E 323 VAL cc_start: 0.7219 (OUTLIER) cc_final: 0.6941 (t) REVERT: F 323 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6647 (t) REVERT: H 307 MET cc_start: 0.6159 (tpt) cc_final: 0.3550 (ttp) REVERT: H 514 MET cc_start: 0.9270 (mtp) cc_final: 0.9034 (mtm) REVERT: J 193 MET cc_start: 0.6444 (mmm) cc_final: 0.6005 (mmm) REVERT: L 10 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8433 (t0) REVERT: L 267 MET cc_start: -0.1358 (tmm) cc_final: -0.1617 (tpp) REVERT: N 307 MET cc_start: 0.4774 (tmm) cc_final: 0.4347 (tmm) outliers start: 157 outliers final: 118 residues processed: 401 average time/residue: 1.2281 time to fit residues: 644.0734 Evaluate side-chains 386 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 264 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain H residue 491 MET Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain I residue 491 MET Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 230 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 142 LYS Chi-restraints excluded: chain M residue 157 THR Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 329 THR Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 1.9990 chunk 672 optimal weight: 2.9990 chunk 613 optimal weight: 1.9990 chunk 653 optimal weight: 50.0000 chunk 393 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 513 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 590 optimal weight: 0.7980 chunk 618 optimal weight: 0.7980 chunk 651 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 319 GLN ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54726 Z= 0.186 Angle : 0.509 11.952 73990 Z= 0.267 Chirality : 0.040 0.137 8974 Planarity : 0.003 0.046 9618 Dihedral : 8.622 84.047 8227 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.15 % Favored : 98.83 % Rotamer: Outliers : 2.27 % Allowed : 20.15 % Favored : 77.58 % 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: 1.23 (0.10), residues: 7294 helix: 1.77 (0.08), residues: 4200 sheet: -0.15 (0.14), residues: 1218 loop : -0.61 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 401 PHE 0.013 0.001 PHE B 44 TYR 0.009 0.001 TYR M 478 ARG 0.002 0.000 ARG B 231 *********************** 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 391 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 263 time to evaluate : 4.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7211 (p) REVERT: B 233 MET cc_start: 0.0770 (tmm) cc_final: 0.0530 (tmm) REVERT: D 193 MET cc_start: 0.5854 (mmm) cc_final: 0.5411 (mmm) REVERT: D 307 MET cc_start: 0.6814 (tpp) cc_final: 0.6388 (tpp) REVERT: E 114 MET cc_start: 0.8936 (tpp) cc_final: 0.8727 (tpp) REVERT: E 193 MET cc_start: 0.6408 (mmm) cc_final: 0.5700 (mmm) REVERT: E 323 VAL cc_start: 0.7212 (OUTLIER) cc_final: 0.6925 (t) REVERT: F 323 VAL cc_start: 0.6815 (OUTLIER) cc_final: 0.6538 (t) REVERT: H 307 MET cc_start: 0.6166 (tpt) cc_final: 0.3517 (ttp) REVERT: H 514 MET cc_start: 0.9250 (mtp) cc_final: 0.9004 (mtm) REVERT: J 193 MET cc_start: 0.6511 (mmm) cc_final: 0.6097 (mmm) REVERT: L 10 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8421 (t0) REVERT: L 288 MET cc_start: 0.6277 (mmt) cc_final: 0.5037 (ptt) REVERT: N 307 MET cc_start: 0.4954 (tmm) cc_final: 0.4487 (tmm) outliers start: 128 outliers final: 99 residues processed: 381 average time/residue: 1.2607 time to fit residues: 624.9754 Evaluate side-chains 364 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 261 time to evaluate : 4.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 52 ASP Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 230 ILE Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 365 LEU Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 4.9990 chunk 691 optimal weight: 4.9990 chunk 422 optimal weight: 0.7980 chunk 328 optimal weight: 10.0000 chunk 480 optimal weight: 0.9990 chunk 725 optimal weight: 2.9990 chunk 667 optimal weight: 1.9990 chunk 577 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 446 optimal weight: 50.0000 chunk 354 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 54726 Z= 0.163 Angle : 0.508 12.462 73990 Z= 0.265 Chirality : 0.039 0.136 8974 Planarity : 0.003 0.046 9618 Dihedral : 8.447 83.520 8225 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.14 % Favored : 98.85 % Rotamer: Outliers : 1.88 % Allowed : 20.63 % Favored : 77.49 % 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: 1.33 (0.10), residues: 7294 helix: 1.85 (0.08), residues: 4200 sheet: -0.11 (0.14), residues: 1218 loop : -0.57 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS H 401 PHE 0.021 0.001 PHE J 195 TYR 0.007 0.001 TYR M 478 ARG 0.010 0.000 ARG I 284 ********************** 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 369 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 263 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7217 (p) REVERT: B 233 MET cc_start: 0.0973 (tmm) cc_final: 0.0709 (tmm) REVERT: D 193 MET cc_start: 0.5851 (mmm) cc_final: 0.5399 (mmm) REVERT: D 307 MET cc_start: 0.6919 (tpp) cc_final: 0.6427 (tpt) REVERT: E 114 MET cc_start: 0.8954 (tpp) cc_final: 0.8742 (tpp) REVERT: E 193 MET cc_start: 0.6223 (mmm) cc_final: 0.5785 (mmm) REVERT: E 323 VAL cc_start: 0.7202 (OUTLIER) cc_final: 0.6887 (p) REVERT: F 323 VAL cc_start: 0.6748 (OUTLIER) cc_final: 0.6492 (t) REVERT: H 307 MET cc_start: 0.6164 (tpt) cc_final: 0.3545 (ttp) REVERT: H 514 MET cc_start: 0.9234 (mtp) cc_final: 0.8975 (mtm) REVERT: J 193 MET cc_start: 0.6495 (mmm) cc_final: 0.6016 (mmm) REVERT: L 10 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8455 (t0) REVERT: L 288 MET cc_start: 0.6350 (mmt) cc_final: 0.5094 (ptt) REVERT: N 307 MET cc_start: 0.5111 (tmm) cc_final: 0.4654 (tmm) outliers start: 106 outliers final: 91 residues processed: 367 average time/residue: 1.2710 time to fit residues: 607.9068 Evaluate side-chains 355 residues out of total 5656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 260 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 329 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 253 ASP Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 358 SER Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 227 ILE Chi-restraints excluded: chain H residue 329 THR Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 255 GLU Chi-restraints excluded: chain I residue 257 GLU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 329 THR Chi-restraints excluded: chain J residue 387 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 181 THR Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 227 ILE Chi-restraints excluded: chain K residue 263 VAL Chi-restraints excluded: chain K residue 329 THR Chi-restraints excluded: chain L residue 10 ASN Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 227 ILE Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 174 VAL Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 263 VAL Chi-restraints excluded: chain M residue 387 VAL Chi-restraints excluded: chain N residue 43 SER Chi-restraints excluded: chain N residue 181 THR Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 329 THR Chi-restraints excluded: chain N residue 366 GLN Chi-restraints excluded: chain N residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 1.9990 chunk 615 optimal weight: 0.0870 chunk 176 optimal weight: 0.9980 chunk 532 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 578 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 593 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.166394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.104831 restraints weight = 78920.028| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.82 r_work: 0.3109 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54726 Z= 0.187 Angle : 0.516 12.590 73990 Z= 0.268 Chirality : 0.039 0.151 8974 Planarity : 0.003 0.046 9618 Dihedral : 8.453 84.698 8225 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.10 % Favored : 98.89 % Rotamer: Outliers : 1.99 % Allowed : 20.60 % Favored : 77.42 % 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: 1.34 (0.10), residues: 7294 helix: 1.84 (0.08), residues: 4200 sheet: -0.08 (0.14), residues: 1218 loop : -0.54 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 401 PHE 0.023 0.001 PHE N 195 TYR 0.008 0.001 TYR M 478 ARG 0.007 0.000 ARG I 284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12813.62 seconds wall clock time: 222 minutes 44.06 seconds (13364.06 seconds total)