Starting phenix.real_space_refine on Thu Sep 26 05:52:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/09_2024/8bm0_16116.cif" } resolution = 3.4 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= 0.004 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 287 5.16 5 C 36777 2.51 5 N 10255 2.21 5 O 12005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 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: 59394 Number of models: 1 Model: "" Number of chains: 35 Chain: "I" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "W" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 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: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "E" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 716 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "J" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 716 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "M" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 716 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "O" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "P" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Q" 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: "R" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "S" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 714 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "T" 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: 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: 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: "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: "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: "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: "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: "O" 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: "Q" 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: "R" 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: "T" 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} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb="MG MG G 601 " occ=0.00 residue: pdb="MG MG C 601 " occ=0.00 residue: pdb="MG MG F 601 " occ=0.00 residue: pdb="MG MG K 601 " occ=0.00 residue: pdb="MG MG N 601 " occ=0.00 residue: pdb="MG MG Q 601 " occ=0.00 residue: pdb="MG MG T 601 " occ=0.00 Time building chain proxies: 28.25, per 1000 atoms: 0.48 Number of scatterers: 59394 At special positions: 0 Unit cell: (153.6, 152.64, 208.32, 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 287 16.00 P 42 15.00 Mg 14 11.99 O 12005 8.00 N 10255 7.00 C 36777 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: 11.32 Conformation dependent library (CDL) restraints added in 6.4 seconds 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14462 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 104 sheets defined 53.3% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.876A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.817A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 removed outlier: 3.794A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.890A 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 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 removed outlier: 3.749A pdb=" N ILE I 205 " --> pdb=" O PRO I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 268 removed outlier: 3.649A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 297 Processing helix chain 'I' and resid 308 through 312 removed outlier: 3.545A pdb=" N LYS I 311 " --> pdb=" O GLU I 308 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 373 Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 427 through 429 No H-bonds generated for 'chain 'I' and resid 427 through 429' Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 497 through 516 Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.563A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.859A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.547A 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 142 through 152 Processing helix chain 'G' and resid 155 through 169 Processing helix chain 'G' and resid 201 through 205 removed outlier: 3.640A pdb=" N PHE G 204 " --> pdb=" O SER G 201 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE G 205 " --> pdb=" O PRO G 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 201 through 205' Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.955A pdb=" N MET G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 282 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 Processing helix chain 'G' and resid 385 through 409 Processing helix chain 'G' and resid 416 through 425 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 28 Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.782A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.963A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 4.022A 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 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.690A pdb=" N PHE A 204 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.872A 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 233 through 244 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 284 through 297 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 373 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 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.570A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.784A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 143 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.857A pdb=" N MET C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 4.208A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.999A pdb=" N LEU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 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 409 Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 447 Processing helix chain 'C' and resid 448 through 459 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 28 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.814A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 4.069A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.942A 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 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.609A pdb=" N PHE D 204 " --> pdb=" O SER D 201 " (cutoff:3.500A) removed outlier: 3.673A 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 255 through 268 removed outlier: 3.714A pdb=" N LEU D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 373 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 459 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 497 through 515 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.710A pdb=" N ALA E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.614A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.812A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.556A 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 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.559A pdb=" N ILE F 205 " --> pdb=" O PRO F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 232 removed outlier: 3.523A pdb=" N GLU F 232 " --> pdb=" O ASN F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 229 through 232' Processing helix chain 'F' and resid 233 through 244 removed outlier: 3.668A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 267 Processing helix chain 'F' and resid 282 through 297 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 409 Processing helix chain 'F' and resid 416 through 425 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 28 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.833A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 85 removed outlier: 3.847A pdb=" N VAL H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.906A 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 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.781A pdb=" N PHE H 204 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.857A 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 233 through 244 Processing helix chain 'H' and resid 255 through 268 removed outlier: 3.867A pdb=" N LEU H 259 " --> pdb=" O GLU H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 297 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 373 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 459 Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 497 through 516 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.574A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 85 removed outlier: 3.951A pdb=" N VAL K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.560A 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 229 through 243 removed outlier: 3.868A pdb=" N MET K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix removed outlier: 3.978A pdb=" N LYS K 242 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 243 " --> pdb=" O ALA K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 267 Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 Processing helix chain 'K' and resid 385 through 409 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 removed outlier: 3.827A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 59 removed outlier: 3.771A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.957A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) removed outlier: 3.906A 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 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.678A pdb=" N PHE L 204 " --> pdb=" O SER L 201 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE L 205 " --> pdb=" O PRO L 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 201 through 205' Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 255 through 268 removed outlier: 3.863A pdb=" N LEU L 259 " --> pdb=" O GLU L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 297 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 373 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 459 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 28 through 33 Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.587A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 85 removed outlier: 3.770A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 137 through 142 Processing helix chain 'N' and resid 143 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 removed outlier: 3.509A pdb=" N ILE N 205 " --> pdb=" O PRO N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 243 removed outlier: 4.088A pdb=" N MET N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 258 through 267 removed outlier: 4.043A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (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 Processing helix chain 'N' and resid 385 through 409 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 helix chain 'O' and resid 9 through 29 removed outlier: 3.866A pdb=" N VAL O 29 " --> pdb=" O ASP O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 60 removed outlier: 3.812A pdb=" N VAL O 56 " --> pdb=" O ASP O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 85 removed outlier: 3.920A pdb=" N VAL O 77 " --> pdb=" O MET O 73 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA O 78 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 109 Processing helix chain 'O' and resid 112 through 135 Processing helix chain 'O' and resid 140 through 152 Processing helix chain 'O' and resid 155 through 170 Processing helix chain 'O' and resid 201 through 205 removed outlier: 3.671A pdb=" N PHE O 204 " --> pdb=" O SER O 201 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE O 205 " --> pdb=" O PRO O 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 201 through 205' Processing helix chain 'O' and resid 233 through 244 Processing helix chain 'O' and resid 255 through 268 removed outlier: 3.785A pdb=" N LEU O 259 " --> pdb=" O GLU O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 297 Processing helix chain 'O' and resid 338 through 356 Processing helix chain 'O' and resid 358 through 373 Processing helix chain 'O' and resid 385 through 410 Processing helix chain 'O' and resid 416 through 426 Processing helix chain 'O' and resid 427 through 429 No H-bonds generated for 'chain 'O' and resid 427 through 429' Processing helix chain 'O' and resid 433 through 447 Processing helix chain 'O' and resid 448 through 459 Processing helix chain 'O' and resid 461 through 472 Processing helix chain 'O' and resid 497 through 516 Processing helix chain 'P' and resid 28 through 32 Processing helix chain 'Q' and resid 9 through 29 Processing helix chain 'Q' and resid 52 through 60 removed outlier: 3.589A pdb=" N VAL Q 56 " --> pdb=" O ASP Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 85 removed outlier: 3.728A pdb=" N VAL Q 77 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Q 78 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 109 Processing helix chain 'Q' and resid 112 through 135 Processing helix chain 'Q' and resid 137 through 142 Processing helix chain 'Q' and resid 143 through 152 Processing helix chain 'Q' and resid 155 through 170 Processing helix chain 'Q' and resid 201 through 205 removed outlier: 3.868A pdb=" N PHE Q 204 " --> pdb=" O SER Q 201 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE Q 205 " --> pdb=" O PRO Q 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 201 through 205' Processing helix chain 'Q' and resid 229 through 232 Processing helix chain 'Q' and resid 233 through 244 removed outlier: 4.194A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY Q 244 " --> pdb=" O VAL Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 267 Processing helix chain 'Q' and resid 282 through 297 Processing helix chain 'Q' and resid 338 through 356 Processing helix chain 'Q' and resid 358 through 375 Processing helix chain 'Q' and resid 385 through 409 Processing helix chain 'Q' and resid 416 through 425 Processing helix chain 'Q' and resid 433 through 447 Processing helix chain 'Q' and resid 448 through 459 Processing helix chain 'Q' and resid 461 through 472 Processing helix chain 'Q' and resid 497 through 515 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 29 through 31 No H-bonds generated for 'chain 'R' and resid 29 through 31' Processing helix chain 'R' and resid 52 through 60 removed outlier: 3.808A pdb=" N VAL R 56 " --> pdb=" O ASP R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 85 removed outlier: 3.975A pdb=" N VAL R 77 " --> pdb=" O MET R 73 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA R 78 " --> pdb=" O VAL R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 109 Processing helix chain 'R' and resid 112 through 135 Processing helix chain 'R' and resid 140 through 152 Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 201 through 205 removed outlier: 3.751A pdb=" N PHE R 204 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE R 205 " --> pdb=" O PRO R 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 205' Processing helix chain 'R' and resid 233 through 244 Processing helix chain 'R' and resid 255 through 268 removed outlier: 3.694A pdb=" N LEU R 259 " --> pdb=" O GLU R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 297 Processing helix chain 'R' and resid 338 through 356 Processing helix chain 'R' and resid 358 through 373 Processing helix chain 'R' and resid 385 through 410 Processing helix chain 'R' and resid 416 through 426 Processing helix chain 'R' and resid 433 through 447 Processing helix chain 'R' and resid 448 through 459 Processing helix chain 'R' and resid 461 through 472 Processing helix chain 'R' and resid 497 through 516 Processing helix chain 'T' and resid 9 through 29 Processing helix chain 'T' and resid 52 through 60 removed outlier: 3.565A pdb=" N VAL T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 85 removed outlier: 3.746A pdb=" N VAL T 77 " --> pdb=" O MET T 73 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA T 78 " --> pdb=" O VAL T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 109 Processing helix chain 'T' and resid 112 through 135 Processing helix chain 'T' and resid 137 through 142 Processing helix chain 'T' and resid 143 through 152 Processing helix chain 'T' and resid 155 through 169 Processing helix chain 'T' and resid 229 through 240 removed outlier: 3.862A pdb=" N MET T 233 " --> pdb=" O ASN T 229 " (cutoff:3.500A) Proline residue: T 235 - end of helix Processing helix chain 'T' and resid 259 through 267 Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 338 through 356 Processing helix chain 'T' and resid 358 through 375 removed outlier: 3.581A pdb=" N GLY T 375 " --> pdb=" O LYS T 371 " (cutoff:3.500A) Processing helix chain 'T' and resid 385 through 409 Processing helix chain 'T' and resid 416 through 426 Processing helix chain 'T' and resid 433 through 447 Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'T' and resid 461 through 472 Processing helix chain 'T' and resid 497 through 515 Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 8 removed outlier: 5.520A pdb=" N ASN R 37 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS I 519 " --> pdb=" O ASN R 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 50 removed outlier: 6.620A pdb=" N ASN I 37 " --> pdb=" O CYS A 519 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL A 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL I 39 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP A 523 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.254A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 213 through 216 removed outlier: 6.431A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 213 through 216 removed outlier: 6.065A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AA8, first strand: chain 'W' and resid 3 through 5 removed outlier: 3.972A pdb=" N ARG W 4 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE B 94 " --> pdb=" O ARG W 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE B 66 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 94 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 64 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 11 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL B 43 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ARG B 9 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.759A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG W 9 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL W 43 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE W 11 " --> pdb=" O LEU W 41 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE W 94 " --> pdb=" O ARG S 4 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG S 4 " --> pdb=" O ILE W 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'W' and resid 47 through 48 Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 8 removed outlier: 5.808A pdb=" N ASN C 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS G 519 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 48 through 50 removed outlier: 6.563A pdb=" N ASN G 37 " --> pdb=" O CYS T 519 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL T 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL G 39 " --> pdb=" O VAL T 521 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N ASP T 523 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 174 through 179 Processing sheet with id=AB5, first strand: chain 'G' and resid 193 through 195 Processing sheet with id=AB6, first strand: chain 'G' and resid 273 through 277 removed outlier: 5.956A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 273 through 277 removed outlier: 5.956A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AB9, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AC1, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.613A pdb=" N ASN A 37 " --> pdb=" O CYS D 519 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL D 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 39 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP D 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.296A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 213 through 216 removed outlier: 8.390A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.424A pdb=" N LEU A 247 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 276 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE A 249 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AC6, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AC7, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.919A pdb=" N ARG B 4 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE E 94 " --> pdb=" O ARG B 4 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE E 66 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE E 94 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE E 64 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE E 11 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL E 43 " --> pdb=" O ARG E 9 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG E 9 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG E 14 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLU E 82 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AC9, first strand: chain 'C' and resid 4 through 8 removed outlier: 5.818A pdb=" N ASN F 37 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS C 519 " --> pdb=" O ASN F 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 174 through 180 Processing sheet with id=AD2, first strand: chain 'C' and resid 193 through 195 Processing sheet with id=AD3, first strand: chain 'C' and resid 274 through 277 removed outlier: 5.906A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'C' and resid 274 through 277 removed outlier: 5.906A pdb=" N LEU C 247 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 50 removed outlier: 7.486A pdb=" N ASN D 37 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N MET H 520 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL D 39 " --> pdb=" O MET H 520 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR H 522 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.299A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 193 through 195 removed outlier: 3.720A pdb=" N MET D 193 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU D 247 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 213 through 216 removed outlier: 8.295A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AE3, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AE4, first strand: chain 'E' and resid 3 through 5 removed outlier: 4.190A pdb=" N ARG E 4 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE J 94 " --> pdb=" O ARG E 4 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA J 93 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE J 64 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL J 40 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS J 13 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG J 14 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLU J 82 " --> pdb=" O ARG J 14 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain 'F' and resid 4 through 8 removed outlier: 5.812A pdb=" N ASN K 37 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS F 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 174 through 180 Processing sheet with id=AE8, first strand: chain 'F' and resid 193 through 195 removed outlier: 3.516A pdb=" N VAL F 323 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 274 through 277 removed outlier: 6.141A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 9.169A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 274 through 277 removed outlier: 6.141A pdb=" N LEU F 247 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AF3, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AF4, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.732A pdb=" N ASN H 37 " --> pdb=" O CYS L 519 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N VAL L 521 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL H 39 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ASP L 523 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.293A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 213 through 216 removed outlier: 6.628A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 213 through 216 removed outlier: 6.122A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AF9, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AG1, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.937A pdb=" N ARG J 4 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 94 " --> pdb=" O ARG J 4 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 93 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE M 64 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE M 11 " --> pdb=" O LEU M 41 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL M 43 " --> pdb=" O ARG M 9 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG M 9 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 47 through 48 Processing sheet with id=AG3, first strand: chain 'K' and resid 4 through 8 removed outlier: 5.825A pdb=" N ASN N 37 " --> pdb=" O THR K 517 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS K 519 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 174 through 179 Processing sheet with id=AG5, first strand: chain 'K' and resid 193 through 195 removed outlier: 6.668A pdb=" N THR K 330 " --> pdb=" O ILE K 325 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE K 325 " --> pdb=" O THR K 330 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE K 332 " --> pdb=" O VAL K 323 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL K 323 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP K 334 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU K 247 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 213 through 216 removed outlier: 3.527A pdb=" N VAL K 323 " --> pdb=" O LEU K 215 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AG8, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AG9, first strand: chain 'L' and resid 48 through 50 removed outlier: 5.557A pdb=" N ASN L 37 " --> pdb=" O THR O 517 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS O 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.282A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 213 through 216 removed outlier: 6.377A pdb=" N LEU L 247 " --> pdb=" O ALA L 274 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 213 through 216 removed outlier: 5.988A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AH5, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AH6, first strand: chain 'M' and resid 3 through 5 removed outlier: 4.361A pdb=" N ARG M 4 " --> pdb=" O ILE P 94 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE P 94 " --> pdb=" O ARG M 4 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE P 64 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL P 40 " --> pdb=" O LYS P 13 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS P 13 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AH8, first strand: chain 'N' and resid 4 through 8 removed outlier: 5.832A pdb=" N ASN Q 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS N 519 " --> pdb=" O ASN Q 37 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 174 through 179 Processing sheet with id=AI1, first strand: chain 'N' and resid 193 through 195 Processing sheet with id=AI2, first strand: chain 'N' and resid 273 through 276 removed outlier: 5.944A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 273 through 276 removed outlier: 5.944A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AI5, first strand: chain 'N' and resid 476 through 479 Processing sheet with id=AI6, first strand: chain 'O' and resid 48 through 50 removed outlier: 6.648A pdb=" N ASN O 37 " --> pdb=" O CYS R 519 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL R 521 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL O 39 " --> pdb=" O VAL R 521 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASP R 523 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 174 through 179 removed outlier: 6.298A pdb=" N VAL O 174 " --> pdb=" O ALA O 377 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE O 379 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR O 176 " --> pdb=" O ILE O 379 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL O 381 " --> pdb=" O THR O 176 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU O 178 " --> pdb=" O VAL O 381 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'O' and resid 213 through 216 removed outlier: 8.480A pdb=" N ILE O 301 " --> pdb=" O ILE O 220 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU O 222 " --> pdb=" O ILE O 301 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 273 through 277 removed outlier: 6.619A pdb=" N PHE O 219 " --> pdb=" O LEU O 248 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE O 250 " --> pdb=" O PHE O 219 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU O 221 " --> pdb=" O ILE O 250 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA O 320 " --> pdb=" O GLY O 335 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLY O 335 " --> pdb=" O ALA O 320 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 411 through 413 Processing sheet with id=AJ2, first strand: chain 'O' and resid 476 through 479 Processing sheet with id=AJ3, first strand: chain 'P' and resid 3 through 5 removed outlier: 4.393A pdb=" N ARG P 4 " --> pdb=" O ILE S 94 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE S 94 " --> pdb=" O ARG P 4 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE S 64 " --> pdb=" O VAL S 95 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL S 40 " --> pdb=" O LYS S 13 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS S 13 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'P' and resid 47 through 48 Processing sheet with id=AJ5, first strand: chain 'Q' and resid 4 through 8 removed outlier: 5.850A pdb=" N ASN T 37 " --> pdb=" O THR Q 517 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS Q 519 " --> pdb=" O ASN T 37 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Q' and resid 174 through 179 Processing sheet with id=AJ7, first strand: chain 'Q' and resid 193 through 195 removed outlier: 3.529A pdb=" N VAL Q 324 " --> pdb=" O THR Q 331 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Q 323 " --> pdb=" O LEU Q 215 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 274 through 277 removed outlier: 5.846A pdb=" N LEU Q 247 " --> pdb=" O ALA Q 274 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL Q 276 " --> pdb=" O LEU Q 247 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE Q 249 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE Q 219 " --> pdb=" O LEU Q 248 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE Q 250 " --> pdb=" O PHE Q 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU Q 221 " --> pdb=" O ILE Q 250 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N ILE Q 301 " --> pdb=" O ILE Q 220 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU Q 222 " --> pdb=" O ILE Q 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ8 Processing sheet with id=AJ9, first strand: chain 'Q' and resid 274 through 277 removed outlier: 5.846A pdb=" N LEU Q 247 " --> pdb=" O ALA Q 274 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL Q 276 " --> pdb=" O LEU Q 247 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE Q 249 " --> pdb=" O VAL Q 276 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE Q 219 " --> pdb=" O LEU Q 248 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE Q 250 " --> pdb=" O PHE Q 219 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU Q 221 " --> pdb=" O ILE Q 250 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'Q' and resid 476 through 479 Processing sheet with id=AK3, first strand: chain 'R' and resid 174 through 179 removed outlier: 6.297A pdb=" N VAL R 174 " --> pdb=" O ALA R 377 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ILE R 379 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR R 176 " --> pdb=" O ILE R 379 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL R 381 " --> pdb=" O THR R 176 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU R 178 " --> pdb=" O VAL R 381 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'R' and resid 213 through 216 removed outlier: 6.504A pdb=" N LEU R 247 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL R 276 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE R 249 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'R' and resid 213 through 216 removed outlier: 6.065A pdb=" N ALA R 320 " --> pdb=" O GLY R 335 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY R 335 " --> pdb=" O ALA R 320 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'R' and resid 411 through 413 Processing sheet with id=AK7, first strand: chain 'R' and resid 476 through 479 Processing sheet with id=AK8, first strand: chain 'S' and resid 47 through 48 Processing sheet with id=AK9, first strand: chain 'T' and resid 174 through 179 Processing sheet with id=AL1, first strand: chain 'T' and resid 193 through 195 Processing sheet with id=AL2, first strand: chain 'T' and resid 274 through 276 removed outlier: 6.156A pdb=" N LEU T 247 " --> pdb=" O ALA T 274 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL T 276 " --> pdb=" O LEU T 247 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE T 249 " --> pdb=" O VAL T 276 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N ILE T 301 " --> pdb=" O ILE T 220 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU T 222 " --> pdb=" O ILE T 301 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'T' and resid 274 through 276 removed outlier: 6.156A pdb=" N LEU T 247 " --> pdb=" O ALA T 274 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL T 276 " --> pdb=" O LEU T 247 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ILE T 249 " --> pdb=" O VAL T 276 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'T' and resid 411 through 413 Processing sheet with id=AL5, first strand: chain 'T' and resid 476 through 479 3752 hydrogen bonds defined for protein. 10854 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: 30.15 Time building geometry restraints manager: 13.55 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: 20547 1.34 - 1.46: 10160 1.46 - 1.58: 28527 1.58 - 1.70: 41 1.70 - 1.82: 532 Bond restraints: 59807 Sorted by residual: bond pdb=" CB ASP D 334 " pdb=" CG ASP D 334 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.27e+00 bond pdb=" CG LEU I 262 " pdb=" CD2 LEU I 262 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" CB GLN H 194 " pdb=" CG GLN H 194 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.61e+00 bond pdb=" CD GLU I 178 " pdb=" OE1 GLU I 178 " ideal model delta sigma weight residual 1.249 1.221 0.028 1.90e-02 2.77e+03 2.15e+00 bond pdb=" CB LYS O 327 " pdb=" CG LYS O 327 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.03e+00 ... (remaining 59802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 80664 4.66 - 9.31: 154 9.31 - 13.97: 22 13.97 - 18.63: 4 18.63 - 23.28: 1 Bond angle restraints: 80845 Sorted by residual: angle pdb=" CA LEU I 262 " pdb=" CB LEU I 262 " pdb=" CG LEU I 262 " ideal model delta sigma weight residual 116.30 139.58 -23.28 3.50e+00 8.16e-02 4.43e+01 angle pdb=" CA MET D 267 " pdb=" CB MET D 267 " pdb=" CG MET D 267 " ideal model delta sigma weight residual 114.10 125.74 -11.64 2.00e+00 2.50e-01 3.39e+01 angle pdb=" CB MET C 233 " pdb=" CG MET C 233 " pdb=" SD MET C 233 " ideal model delta sigma weight residual 112.70 129.11 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CB MET C 267 " pdb=" CG MET C 267 " pdb=" SD MET C 267 " ideal model delta sigma weight residual 112.70 129.06 -16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" CA LEU R 262 " pdb=" CB LEU R 262 " pdb=" CG LEU R 262 " ideal model delta sigma weight residual 116.30 133.29 -16.99 3.50e+00 8.16e-02 2.36e+01 ... (remaining 80840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 32682 17.96 - 35.92: 3536 35.92 - 53.88: 796 53.88 - 71.84: 233 71.84 - 89.80: 66 Dihedral angle restraints: 37313 sinusoidal: 14766 harmonic: 22547 Sorted by residual: dihedral pdb=" CA MET H 288 " pdb=" C MET H 288 " pdb=" N LEU H 289 " pdb=" CA LEU H 289 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA MET L 288 " pdb=" C MET L 288 " pdb=" N LEU L 289 " pdb=" CA LEU L 289 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA MET T 514 " pdb=" C MET T 514 " pdb=" N ILE T 515 " pdb=" CA ILE T 515 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 37310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 8180 0.059 - 0.118: 1467 0.118 - 0.177: 150 0.177 - 0.236: 10 0.236 - 0.294: 3 Chirality restraints: 9810 Sorted by residual: chirality pdb=" CB ILE E 66 " pdb=" CA ILE E 66 " pdb=" CG1 ILE E 66 " pdb=" CG2 ILE E 66 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE W 66 " pdb=" CA ILE W 66 " pdb=" CG1 ILE W 66 " pdb=" CG2 ILE W 66 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE M 11 " pdb=" N ILE M 11 " pdb=" C ILE M 11 " pdb=" CB ILE M 11 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 9807 not shown) Planarity restraints: 10514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 76 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" CD GLU A 76 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU A 76 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 76 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 9 " -0.216 9.50e-02 1.11e+02 9.71e-02 5.94e+00 pdb=" NE ARG B 9 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG B 9 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 9 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 9 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 9 " -0.200 9.50e-02 1.11e+02 8.96e-02 5.11e+00 pdb=" NE ARG E 9 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG E 9 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 9 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 9 " -0.010 2.00e-02 2.50e+03 ... (remaining 10511 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 862 2.63 - 3.26: 61665 3.26 - 3.88: 129729 3.88 - 4.51: 167624 4.51 - 5.14: 261150 Nonbonded interactions: 621030 Sorted by model distance: nonbonded pdb="MG MG Q 601 " pdb=" O3G ATP Q 602 " model vdw 2.002 2.170 nonbonded pdb="MG MG G 601 " pdb=" O3B ATP G 602 " model vdw 2.003 2.170 nonbonded pdb="MG MG C 601 " pdb=" O3B ATP C 602 " model vdw 2.004 2.170 nonbonded pdb="MG MG K 601 " pdb=" O3G ATP K 602 " model vdw 2.005 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3B ATP F 602 " model vdw 2.006 2.170 ... (remaining 621025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 524 or resid 601)) selection = (chain 'C' and (resid 2 through 524 or resid 601)) selection = (chain 'D' and (resid 2 through 524 or resid 601)) selection = (chain 'F' and (resid 2 through 524 or resid 601)) selection = (chain 'G' and (resid 2 through 524 or resid 601)) selection = (chain 'H' and (resid 2 through 524 or resid 601)) selection = (chain 'I' and (resid 2 through 524 or resid 601)) selection = (chain 'K' and (resid 2 through 524 or resid 601)) selection = (chain 'L' and (resid 2 through 524 or resid 601)) selection = (chain 'N' and (resid 2 through 524 or resid 601)) selection = (chain 'O' and (resid 2 through 524 or resid 601)) selection = (chain 'Q' and (resid 2 through 524 or resid 601)) selection = (chain 'R' and (resid 2 through 524 or resid 601)) selection = (chain 'T' and (resid 2 through 524 or resid 601)) } ncs_group { reference = chain 'B' selection = (chain 'E' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 97)) selection = (chain 'J' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 97)) selection = (chain 'M' and (resid 2 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 97)) selection = chain 'P' selection = chain 'S' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 1.850 Check model and map are aligned: 0.340 Set scattering table: 0.440 Process input model: 118.260 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.260 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.003 0.058 59807 Z= 0.207 Angle : 0.640 23.285 80845 Z= 0.330 Chirality : 0.044 0.294 9810 Planarity : 0.004 0.097 10514 Dihedral : 16.346 89.800 22851 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.11 % Allowed : 19.16 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.09), residues: 7959 helix: 1.18 (0.08), residues: 4130 sheet: 0.04 (0.14), residues: 1239 loop : -0.39 (0.11), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS S 7 PHE 0.031 0.002 PHE A 195 TYR 0.022 0.001 TYR I 478 ARG 0.008 0.000 ARG M 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 489 time to evaluate : 5.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 2 ASN cc_start: 0.9104 (t0) cc_final: 0.8869 (t0) REVERT: A 248 LEU cc_start: 0.9312 (tp) cc_final: 0.8992 (pp) REVERT: A 288 MET cc_start: 0.8576 (ptt) cc_final: 0.8282 (ptt) REVERT: B 41 LEU cc_start: 0.9467 (mt) cc_final: 0.9243 (mt) REVERT: F 199 TYR cc_start: 0.3662 (p90) cc_final: 0.3343 (p90) REVERT: K 193 MET cc_start: 0.8253 (tpp) cc_final: 0.7547 (mmm) REVERT: M 84 LEU cc_start: 0.8661 (mt) cc_final: 0.8331 (mp) REVERT: N 193 MET cc_start: 0.7345 (mmm) cc_final: 0.6645 (mmm) REVERT: N 199 TYR cc_start: 0.4229 (p90) cc_final: 0.3719 (p90) REVERT: N 226 LYS cc_start: 0.1326 (OUTLIER) cc_final: 0.0662 (tptt) REVERT: N 304 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4519 (mp0) REVERT: S 84 LEU cc_start: 0.8621 (mt) cc_final: 0.8403 (mt) outliers start: 7 outliers final: 3 residues processed: 494 average time/residue: 0.5776 time to fit residues: 480.0520 Evaluate side-chains 387 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 4.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 412 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain N residue 226 LYS Chi-restraints excluded: chain N residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 2.9990 chunk 599 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 404 optimal weight: 8.9990 chunk 320 optimal weight: 50.0000 chunk 619 optimal weight: 9.9990 chunk 239 optimal weight: 7.9990 chunk 376 optimal weight: 10.0000 chunk 461 optimal weight: 0.6980 chunk 718 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 479 ASN G 37 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN F 37 ASN F 348 GLN H 479 ASN K 37 ASN L 479 ASN N 37 ASN O 479 ASN Q 37 ASN T 37 ASN T 348 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 59807 Z= 0.440 Angle : 0.621 13.512 80845 Z= 0.324 Chirality : 0.046 0.186 9810 Planarity : 0.004 0.076 10514 Dihedral : 8.576 89.848 8923 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.57 % Allowed : 18.96 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 7959 helix: 1.38 (0.08), residues: 4179 sheet: -0.06 (0.16), residues: 980 loop : -0.50 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.012 0.001 PHE N 44 TYR 0.013 0.002 TYR I 506 ARG 0.009 0.001 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 430 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8325 (mtp) REVERT: W 2 ASN cc_start: 0.9128 (t0) cc_final: 0.8906 (t0) REVERT: A 111 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8274 (mtp) REVERT: A 247 LEU cc_start: 0.9417 (tp) cc_final: 0.9033 (tt) REVERT: A 248 LEU cc_start: 0.9304 (tp) cc_final: 0.9000 (pp) REVERT: A 288 MET cc_start: 0.8512 (ptt) cc_final: 0.8177 (ptt) REVERT: A 311 LYS cc_start: 0.8610 (pptt) cc_final: 0.8398 (pttm) REVERT: D 111 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8260 (mtp) REVERT: E 20 LYS cc_start: 0.9302 (ttpp) cc_final: 0.9046 (mppt) REVERT: E 81 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8884 (tm-30) REVERT: F 199 TYR cc_start: 0.3612 (p90) cc_final: 0.3239 (p90) REVERT: H 111 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8397 (mtp) REVERT: H 231 ARG cc_start: 0.8666 (mmt-90) cc_final: 0.7754 (mmt-90) REVERT: J 20 LYS cc_start: 0.9301 (ttpp) cc_final: 0.8991 (mppt) REVERT: J 66 ILE cc_start: 0.8430 (pt) cc_final: 0.8219 (mt) REVERT: K 193 MET cc_start: 0.8156 (tpp) cc_final: 0.7023 (mmm) REVERT: K 288 MET cc_start: 0.7756 (mmt) cc_final: 0.6814 (ppp) REVERT: K 307 MET cc_start: 0.6501 (tmm) cc_final: 0.6119 (tmm) REVERT: M 86 MET cc_start: 0.8159 (pmm) cc_final: 0.7727 (pmm) REVERT: N 199 TYR cc_start: 0.4153 (p90) cc_final: 0.3627 (p90) REVERT: O 111 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8380 (mtp) REVERT: O 195 PHE cc_start: 0.8302 (p90) cc_final: 0.7945 (p90) REVERT: O 330 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.9139 (m) REVERT: P 77 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9178 (tmtt) REVERT: Q 323 VAL cc_start: 0.5137 (OUTLIER) cc_final: 0.4342 (m) REVERT: R 111 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8408 (mtp) outliers start: 97 outliers final: 44 residues processed: 504 average time/residue: 0.5922 time to fit residues: 502.0084 Evaluate side-chains 443 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 391 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 461 GLU Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain M residue 9 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 174 VAL Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 330 THR Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 16 MET Chi-restraints excluded: chain T residue 131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 597 optimal weight: 20.0000 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 50.0000 chunk 719 optimal weight: 3.9990 chunk 777 optimal weight: 6.9990 chunk 640 optimal weight: 6.9990 chunk 713 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 577 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN H 97 GLN Q 348 GLN R 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 59807 Z= 0.421 Angle : 0.604 14.684 80845 Z= 0.314 Chirality : 0.045 0.195 9810 Planarity : 0.004 0.076 10514 Dihedral : 8.594 89.942 8912 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.31 % Allowed : 19.09 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 7959 helix: 1.40 (0.08), residues: 4179 sheet: -0.31 (0.15), residues: 980 loop : -0.45 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 7 PHE 0.018 0.001 PHE R 195 TYR 0.013 0.002 TYR R 199 ARG 0.008 0.001 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 422 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: W 2 ASN cc_start: 0.9169 (t0) cc_final: 0.8942 (t0) REVERT: G 238 GLU cc_start: 0.5532 (OUTLIER) cc_final: 0.5322 (tp30) REVERT: G 267 MET cc_start: 0.6644 (ppp) cc_final: 0.6143 (ppp) REVERT: A 111 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8282 (mtp) REVERT: A 248 LEU cc_start: 0.9227 (tp) cc_final: 0.8947 (pp) REVERT: A 288 MET cc_start: 0.8526 (ptt) cc_final: 0.7964 (ptt) REVERT: B 86 MET cc_start: 0.8439 (pmm) cc_final: 0.8040 (pmm) REVERT: C 323 VAL cc_start: 0.7040 (OUTLIER) cc_final: 0.6814 (p) REVERT: D 69 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8914 (mtp) REVERT: D 111 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8270 (mtp) REVERT: D 231 ARG cc_start: 0.8774 (mmt180) cc_final: 0.8545 (mmt-90) REVERT: E 20 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9082 (mppt) REVERT: F 199 TYR cc_start: 0.3727 (p90) cc_final: 0.3301 (p90) REVERT: H 111 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8352 (mtp) REVERT: J 20 LYS cc_start: 0.9314 (ttpp) cc_final: 0.9000 (mppt) REVERT: K 193 MET cc_start: 0.8186 (tpp) cc_final: 0.7085 (mmm) REVERT: M 53 GLU cc_start: 0.9284 (mp0) cc_final: 0.9062 (mp0) REVERT: M 86 MET cc_start: 0.8177 (pmm) cc_final: 0.7810 (pmm) REVERT: N 199 TYR cc_start: 0.4290 (p90) cc_final: 0.3640 (p90) REVERT: O 195 PHE cc_start: 0.8388 (p90) cc_final: 0.7909 (p90) REVERT: O 330 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9106 (m) REVERT: P 20 LYS cc_start: 0.9312 (tttm) cc_final: 0.9034 (mppt) REVERT: R 111 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8419 (mtp) outliers start: 143 outliers final: 89 residues processed: 535 average time/residue: 0.5678 time to fit residues: 520.3380 Evaluate side-chains 485 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 387 time to evaluate : 5.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 517 THR Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 442 VAL Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 9 ARG Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 330 THR Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 514 MET Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 400 LEU Chi-restraints excluded: chain R residue 463 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 9.9990 chunk 541 optimal weight: 50.0000 chunk 373 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 483 optimal weight: 6.9990 chunk 722 optimal weight: 0.9980 chunk 764 optimal weight: 50.0000 chunk 377 optimal weight: 2.9990 chunk 684 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 59807 Z= 0.196 Angle : 0.531 15.639 80845 Z= 0.275 Chirality : 0.042 0.180 9810 Planarity : 0.003 0.064 10514 Dihedral : 8.409 89.277 8912 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.83 % Allowed : 19.61 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 7959 helix: 1.71 (0.08), residues: 4193 sheet: -0.37 (0.15), residues: 1092 loop : -0.30 (0.11), residues: 2674 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS Q 401 PHE 0.013 0.001 PHE A 195 TYR 0.011 0.001 TYR T 199 ARG 0.007 0.000 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 417 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: I 203 TYR cc_start: 0.8572 (m-80) cc_final: 0.8341 (m-80) REVERT: G 238 GLU cc_start: 0.5398 (OUTLIER) cc_final: 0.5184 (tp30) REVERT: G 267 MET cc_start: 0.6583 (ppp) cc_final: 0.6035 (ppp) REVERT: A 194 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8145 (tm-30) REVERT: A 288 MET cc_start: 0.8505 (ptt) cc_final: 0.7879 (ptt) REVERT: A 321 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8594 (ptmt) REVERT: D 111 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: E 20 LYS cc_start: 0.9284 (ttpp) cc_final: 0.9079 (mppt) REVERT: F 199 TYR cc_start: 0.3928 (p90) cc_final: 0.3478 (p90) REVERT: H 111 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: J 20 LYS cc_start: 0.9297 (ttpp) cc_final: 0.8987 (mppt) REVERT: K 193 MET cc_start: 0.8235 (tpp) cc_final: 0.7115 (mmm) REVERT: K 307 MET cc_start: 0.6349 (tmm) cc_final: 0.6089 (tmm) REVERT: K 365 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5532 (tp) REVERT: L 321 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8830 (ptmt) REVERT: M 53 GLU cc_start: 0.9338 (mp0) cc_final: 0.9114 (mp0) REVERT: M 63 ASP cc_start: 0.8845 (t0) cc_final: 0.7019 (p0) REVERT: N 199 TYR cc_start: 0.4260 (p90) cc_final: 0.3610 (p90) REVERT: N 391 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: O 111 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: O 195 PHE cc_start: 0.8408 (p90) cc_final: 0.7917 (p90) REVERT: P 20 LYS cc_start: 0.9319 (tttm) cc_final: 0.9027 (mppt) REVERT: P 77 LYS cc_start: 0.9290 (tmtt) cc_final: 0.9044 (tmtt) REVERT: Q 219 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6044 (t80) REVERT: R 111 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8355 (mtp) REVERT: S 63 ASP cc_start: 0.8234 (p0) cc_final: 0.7942 (t0) REVERT: S 86 MET cc_start: 0.8248 (pmm) cc_final: 0.7769 (pmm) outliers start: 113 outliers final: 62 residues processed: 505 average time/residue: 0.5895 time to fit residues: 510.8852 Evaluate side-chains 465 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 391 time to evaluate : 5.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 238 GLU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 2.9990 chunk 434 optimal weight: 30.0000 chunk 11 optimal weight: 1.9990 chunk 569 optimal weight: 6.9990 chunk 315 optimal weight: 50.0000 chunk 652 optimal weight: 0.8980 chunk 528 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 390 optimal weight: 1.9990 chunk 686 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 59807 Z= 0.237 Angle : 0.539 15.947 80845 Z= 0.278 Chirality : 0.043 0.203 9810 Planarity : 0.003 0.065 10514 Dihedral : 8.223 89.825 8911 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.08 % Allowed : 19.75 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 7959 helix: 1.81 (0.08), residues: 4193 sheet: -0.23 (0.16), residues: 966 loop : -0.43 (0.11), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 7 PHE 0.013 0.001 PHE Q 44 TYR 0.012 0.001 TYR T 199 ARG 0.019 0.000 ARG M 9 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 417 time to evaluate : 5.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8257 (mtp) REVERT: I 203 TYR cc_start: 0.8556 (m-80) cc_final: 0.8311 (m-80) REVERT: G 267 MET cc_start: 0.6453 (ppp) cc_final: 0.5816 (ppp) REVERT: A 111 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: A 194 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: A 248 LEU cc_start: 0.9149 (tp) cc_final: 0.8836 (pp) REVERT: A 249 ILE cc_start: 0.9636 (OUTLIER) cc_final: 0.9435 (mm) REVERT: A 288 MET cc_start: 0.8463 (ptt) cc_final: 0.8184 (ptp) REVERT: A 321 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8602 (ptmm) REVERT: B 4 ARG cc_start: 0.7587 (pmt-80) cc_final: 0.7275 (pmt-80) REVERT: B 86 MET cc_start: 0.8329 (pmm) cc_final: 0.8116 (pmm) REVERT: C 323 VAL cc_start: 0.6871 (OUTLIER) cc_final: 0.6669 (p) REVERT: D 111 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8221 (mtp) REVERT: E 86 MET cc_start: 0.7392 (pmm) cc_final: 0.6710 (pmm) REVERT: F 199 TYR cc_start: 0.4028 (p90) cc_final: 0.3578 (p90) REVERT: H 111 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: J 20 LYS cc_start: 0.9295 (ttpp) cc_final: 0.8992 (mppt) REVERT: J 63 ASP cc_start: 0.8132 (t0) cc_final: 0.6747 (p0) REVERT: J 86 MET cc_start: 0.7293 (pmm) cc_final: 0.6997 (pmm) REVERT: K 193 MET cc_start: 0.8238 (tpp) cc_final: 0.7021 (mmm) REVERT: K 288 MET cc_start: 0.7844 (mmt) cc_final: 0.6995 (ppp) REVERT: K 365 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5469 (tp) REVERT: L 111 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8428 (mtt) REVERT: L 114 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8404 (mmm) REVERT: L 321 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (ptmt) REVERT: M 53 GLU cc_start: 0.9359 (mp0) cc_final: 0.9134 (mp0) REVERT: M 63 ASP cc_start: 0.8700 (t0) cc_final: 0.7080 (p0) REVERT: M 86 MET cc_start: 0.8275 (pmm) cc_final: 0.7564 (pmm) REVERT: N 193 MET cc_start: 0.7582 (mmm) cc_final: 0.7057 (mmm) REVERT: N 199 TYR cc_start: 0.4270 (p90) cc_final: 0.3645 (p90) REVERT: N 200 LEU cc_start: 0.3643 (OUTLIER) cc_final: 0.3421 (mm) REVERT: N 391 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7167 (tm-30) REVERT: O 111 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: O 330 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9116 (m) REVERT: P 20 LYS cc_start: 0.9316 (tttm) cc_final: 0.9033 (mppt) REVERT: P 77 LYS cc_start: 0.9327 (tmtt) cc_final: 0.9119 (tmtt) REVERT: Q 193 MET cc_start: 0.7857 (tmm) cc_final: 0.7211 (tpp) REVERT: Q 219 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6075 (t80) REVERT: R 111 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8378 (mtp) outliers start: 129 outliers final: 81 residues processed: 515 average time/residue: 0.5808 time to fit residues: 511.8701 Evaluate side-chains 483 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 384 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 461 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 366 GLN Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 16 MET Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 330 THR Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 84 LEU Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 30.0000 chunk 688 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 448 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 5.9990 chunk 354 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 253 optimal weight: 40.0000 chunk 401 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN E 7 HIS L 343 GLN O 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 59807 Z= 0.206 Angle : 0.536 16.464 80845 Z= 0.275 Chirality : 0.042 0.223 9810 Planarity : 0.003 0.062 10514 Dihedral : 8.002 89.694 8911 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.15 % Allowed : 20.11 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.09), residues: 7959 helix: 1.87 (0.08), residues: 4200 sheet: -0.20 (0.16), residues: 966 loop : -0.43 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 7 PHE 0.011 0.001 PHE A 195 TYR 0.012 0.001 TYR T 199 ARG 0.010 0.000 ARG S 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 415 time to evaluate : 5.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: I 203 TYR cc_start: 0.8538 (m-80) cc_final: 0.8291 (m-80) REVERT: G 267 MET cc_start: 0.6524 (ppp) cc_final: 0.5916 (ppp) REVERT: A 111 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8137 (mtp) REVERT: A 194 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: A 248 LEU cc_start: 0.9108 (tp) cc_final: 0.8791 (pp) REVERT: A 288 MET cc_start: 0.8455 (ptt) cc_final: 0.8179 (ptp) REVERT: A 307 MET cc_start: 0.8356 (mpp) cc_final: 0.7860 (tpt) REVERT: A 321 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8722 (ptmt) REVERT: A 514 MET cc_start: 0.9022 (mtp) cc_final: 0.8686 (ttt) REVERT: B 4 ARG cc_start: 0.7663 (pmt-80) cc_final: 0.7382 (pmt-80) REVERT: E 25 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8599 (mt) REVERT: H 111 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: J 20 LYS cc_start: 0.9295 (ttpp) cc_final: 0.8987 (mppt) REVERT: J 86 MET cc_start: 0.7353 (pmm) cc_final: 0.7062 (pmm) REVERT: K 193 MET cc_start: 0.8249 (tpp) cc_final: 0.7018 (mmm) REVERT: K 365 LEU cc_start: 0.5769 (OUTLIER) cc_final: 0.5495 (tp) REVERT: L 114 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8401 (mmm) REVERT: L 321 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8835 (ptmt) REVERT: M 63 ASP cc_start: 0.8579 (t0) cc_final: 0.6974 (p0) REVERT: M 86 MET cc_start: 0.8193 (pmm) cc_final: 0.7399 (pmm) REVERT: N 193 MET cc_start: 0.7556 (mmm) cc_final: 0.7005 (mmm) REVERT: N 199 TYR cc_start: 0.4271 (p90) cc_final: 0.3655 (p90) REVERT: N 200 LEU cc_start: 0.3663 (OUTLIER) cc_final: 0.3446 (mm) REVERT: N 391 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7229 (tm-30) REVERT: O 111 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8272 (mtp) REVERT: P 20 LYS cc_start: 0.9311 (tttm) cc_final: 0.9025 (mppt) REVERT: Q 219 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.6180 (t80) REVERT: R 111 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8366 (mtp) REVERT: T 391 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7377 (tm-30) outliers start: 133 outliers final: 85 residues processed: 521 average time/residue: 0.6086 time to fit residues: 545.7168 Evaluate side-chains 483 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 383 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 463 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 391 GLU Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 30.0000 chunk 86 optimal weight: 50.0000 chunk 436 optimal weight: 30.0000 chunk 558 optimal weight: 0.9990 chunk 433 optimal weight: 5.9990 chunk 644 optimal weight: 5.9990 chunk 427 optimal weight: 5.9990 chunk 762 optimal weight: 50.0000 chunk 477 optimal weight: 6.9990 chunk 464 optimal weight: 0.9980 chunk 351 optimal weight: 0.7980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 343 GLN J 2 ASN R 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 59807 Z= 0.289 Angle : 0.567 17.026 80845 Z= 0.290 Chirality : 0.043 0.301 9810 Planarity : 0.003 0.065 10514 Dihedral : 7.907 89.730 8911 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 20.11 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.09), residues: 7959 helix: 1.80 (0.08), residues: 4200 sheet: -0.24 (0.16), residues: 966 loop : -0.42 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 7 PHE 0.013 0.001 PHE Q 44 TYR 0.014 0.001 TYR T 199 ARG 0.007 0.000 ARG E 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 401 time to evaluate : 5.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8276 (mtp) REVERT: I 203 TYR cc_start: 0.8563 (m-80) cc_final: 0.8317 (m-80) REVERT: W 53 GLU cc_start: 0.9309 (mp0) cc_final: 0.9035 (mp0) REVERT: W 86 MET cc_start: 0.8100 (pmm) cc_final: 0.7789 (pmm) REVERT: G 267 MET cc_start: 0.6463 (ppp) cc_final: 0.5854 (ppp) REVERT: A 111 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8182 (mtp) REVERT: A 194 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: A 288 MET cc_start: 0.8485 (ptt) cc_final: 0.8201 (ptp) REVERT: A 321 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8760 (ptmt) REVERT: A 514 MET cc_start: 0.9027 (mtp) cc_final: 0.8770 (ttt) REVERT: B 4 ARG cc_start: 0.7688 (pmt-80) cc_final: 0.7486 (pmt-80) REVERT: D 111 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8246 (mtp) REVERT: H 111 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: J 63 ASP cc_start: 0.8108 (t0) cc_final: 0.6933 (p0) REVERT: K 193 MET cc_start: 0.8250 (tpp) cc_final: 0.6988 (mmm) REVERT: K 365 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5493 (tp) REVERT: L 114 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8421 (mmm) REVERT: L 321 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8853 (ptmt) REVERT: M 11 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9154 (pt) REVERT: M 86 MET cc_start: 0.8146 (pmm) cc_final: 0.7406 (pmm) REVERT: N 193 MET cc_start: 0.7648 (mmm) cc_final: 0.7096 (mmm) REVERT: N 199 TYR cc_start: 0.4273 (p90) cc_final: 0.3627 (p90) REVERT: N 200 LEU cc_start: 0.3616 (OUTLIER) cc_final: 0.3415 (mm) REVERT: N 391 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: O 111 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8354 (mtp) REVERT: O 195 PHE cc_start: 0.8311 (p90) cc_final: 0.7807 (p90) REVERT: P 20 LYS cc_start: 0.9317 (tttm) cc_final: 0.9037 (mppt) REVERT: Q 193 MET cc_start: 0.8017 (tmm) cc_final: 0.6666 (tpp) REVERT: Q 219 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6147 (t80) REVERT: Q 233 MET cc_start: 0.4476 (ppp) cc_final: 0.4174 (ppp) REVERT: R 111 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8397 (mtp) REVERT: T 391 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7491 (tm-30) outliers start: 150 outliers final: 107 residues processed: 525 average time/residue: 0.5494 time to fit residues: 498.2751 Evaluate side-chains 504 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 381 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 463 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 3 ILE Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 73 MET Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 391 GLU Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 455 optimal weight: 0.6980 chunk 229 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 484 optimal weight: 9.9990 chunk 519 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 599 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59807 Z= 0.270 Angle : 0.569 17.422 80845 Z= 0.290 Chirality : 0.043 0.293 9810 Planarity : 0.003 0.068 10514 Dihedral : 7.776 89.126 8911 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.34 % Allowed : 20.24 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.09), residues: 7959 helix: 1.80 (0.08), residues: 4200 sheet: -0.25 (0.16), residues: 966 loop : -0.42 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 401 PHE 0.010 0.001 PHE N 44 TYR 0.012 0.001 TYR T 199 ARG 0.028 0.000 ARG L 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 399 time to evaluate : 5.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8269 (mtp) REVERT: I 203 TYR cc_start: 0.8532 (m-80) cc_final: 0.8290 (m-80) REVERT: W 53 GLU cc_start: 0.9312 (mp0) cc_final: 0.9031 (mp0) REVERT: W 86 MET cc_start: 0.8056 (pmm) cc_final: 0.7713 (pmm) REVERT: G 267 MET cc_start: 0.6526 (ppp) cc_final: 0.5952 (ppp) REVERT: A 111 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8167 (mtp) REVERT: A 194 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: A 248 LEU cc_start: 0.9114 (tp) cc_final: 0.8837 (pp) REVERT: A 288 MET cc_start: 0.8463 (ptt) cc_final: 0.8031 (ptt) REVERT: A 307 MET cc_start: 0.8433 (mpp) cc_final: 0.7848 (tpt) REVERT: A 321 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8763 (ptmt) REVERT: A 514 MET cc_start: 0.8992 (mtp) cc_final: 0.8766 (ttt) REVERT: B 91 ILE cc_start: 0.9520 (mm) cc_final: 0.9292 (mt) REVERT: D 111 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8240 (mtp) REVERT: D 236 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9071 (p) REVERT: H 111 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: J 63 ASP cc_start: 0.8054 (t0) cc_final: 0.6941 (p0) REVERT: K 193 MET cc_start: 0.8273 (tpp) cc_final: 0.7033 (mmm) REVERT: K 365 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5567 (tp) REVERT: L 114 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: L 321 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8856 (ptmt) REVERT: M 11 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9165 (pt) REVERT: M 63 ASP cc_start: 0.8563 (t0) cc_final: 0.6986 (p0) REVERT: M 86 MET cc_start: 0.8065 (pmm) cc_final: 0.7369 (pmm) REVERT: N 193 MET cc_start: 0.7708 (mmm) cc_final: 0.7152 (mmm) REVERT: N 307 MET cc_start: 0.7908 (tmm) cc_final: 0.7398 (tmm) REVERT: N 391 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: O 111 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8374 (mtp) REVERT: P 20 LYS cc_start: 0.9306 (tttm) cc_final: 0.9022 (mppt) REVERT: Q 193 MET cc_start: 0.7967 (tmm) cc_final: 0.6658 (tpp) REVERT: Q 219 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.6123 (t80) REVERT: Q 233 MET cc_start: 0.4679 (ppp) cc_final: 0.4297 (ppp) REVERT: R 111 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8368 (mtp) REVERT: R 488 MET cc_start: 0.8838 (mmm) cc_final: 0.8554 (mtp) REVERT: T 391 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7490 (tm-30) outliers start: 145 outliers final: 116 residues processed: 521 average time/residue: 0.5573 time to fit residues: 505.3277 Evaluate side-chains 516 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 384 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 13 LYS Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 461 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 144 ILE Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 463 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 73 MET Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 391 GLU Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 7.9990 chunk 730 optimal weight: 2.9990 chunk 666 optimal weight: 8.9990 chunk 710 optimal weight: 20.0000 chunk 427 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 557 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 641 optimal weight: 10.0000 chunk 671 optimal weight: 0.7980 chunk 707 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 319 GLN ** R 343 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: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 59807 Z= 0.275 Angle : 0.577 17.650 80845 Z= 0.294 Chirality : 0.043 0.426 9810 Planarity : 0.003 0.064 10514 Dihedral : 7.724 89.143 8911 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.46 % Allowed : 20.19 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7959 helix: 1.80 (0.08), residues: 4200 sheet: -0.43 (0.15), residues: 1106 loop : -0.26 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 7 PHE 0.014 0.001 PHE Q 44 TYR 0.014 0.001 TYR T 199 ARG 0.012 0.000 ARG L 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15918 Ramachandran restraints generated. 7959 Oldfield, 0 Emsley, 7959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 394 time to evaluate : 5.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 111 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: I 203 TYR cc_start: 0.8539 (m-80) cc_final: 0.8294 (m-80) REVERT: W 53 GLU cc_start: 0.9318 (mp0) cc_final: 0.9025 (mp0) REVERT: W 86 MET cc_start: 0.8115 (pmm) cc_final: 0.7829 (pmm) REVERT: G 267 MET cc_start: 0.6496 (ppp) cc_final: 0.5984 (ppp) REVERT: A 111 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: A 194 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: A 248 LEU cc_start: 0.9121 (tp) cc_final: 0.8799 (pp) REVERT: A 288 MET cc_start: 0.8414 (ptt) cc_final: 0.7981 (ptt) REVERT: A 307 MET cc_start: 0.8430 (mpp) cc_final: 0.7917 (tpt) REVERT: A 321 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8771 (ptmt) REVERT: A 514 MET cc_start: 0.8995 (mtp) cc_final: 0.8775 (ttt) REVERT: D 111 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8243 (mtp) REVERT: D 236 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9094 (p) REVERT: H 111 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: J 63 ASP cc_start: 0.8054 (t0) cc_final: 0.6968 (p0) REVERT: K 193 MET cc_start: 0.8246 (tpp) cc_final: 0.6961 (mmm) REVERT: K 365 LEU cc_start: 0.5840 (OUTLIER) cc_final: 0.5577 (tp) REVERT: L 114 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: L 321 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8869 (ptmt) REVERT: M 11 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9229 (pt) REVERT: M 63 ASP cc_start: 0.8540 (t0) cc_final: 0.6976 (p0) REVERT: M 86 MET cc_start: 0.8035 (pmm) cc_final: 0.7355 (pmm) REVERT: N 193 MET cc_start: 0.7678 (mmm) cc_final: 0.7085 (mmm) REVERT: N 307 MET cc_start: 0.7856 (tmm) cc_final: 0.7325 (tmm) REVERT: N 391 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: O 111 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: O 195 PHE cc_start: 0.8340 (p90) cc_final: 0.7868 (p90) REVERT: P 20 LYS cc_start: 0.9297 (tttm) cc_final: 0.9016 (mppt) REVERT: Q 193 MET cc_start: 0.7954 (tmm) cc_final: 0.6685 (tpp) REVERT: Q 219 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6171 (t80) REVERT: Q 233 MET cc_start: 0.4750 (ppp) cc_final: 0.4361 (ppp) REVERT: R 36 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7778 (mtt180) REVERT: R 111 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8376 (mtp) REVERT: R 488 MET cc_start: 0.8821 (mmm) cc_final: 0.8562 (mtp) REVERT: T 391 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7493 (tm-30) outliers start: 152 outliers final: 121 residues processed: 521 average time/residue: 0.5477 time to fit residues: 494.8643 Evaluate side-chains 519 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 381 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 139 SER Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 461 GLU Chi-restraints excluded: chain G residue 495 ASP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 18 GLU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain K residue 11 ASP Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 255 GLU Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 273 VAL Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 321 LYS Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 273 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 219 PHE Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE Chi-restraints excluded: chain Q residue 461 GLU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 139 SER Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 463 SER Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 73 MET Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 391 GLU Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 495 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8794 > 50: distance: 84 - 182: 10.210 distance: 87 - 179: 8.352 distance: 147 - 151: 7.135 distance: 151 - 152: 8.837 distance: 152 - 153: 11.505 distance: 152 - 155: 11.747 distance: 153 - 154: 23.449 distance: 153 - 159: 22.970 distance: 155 - 156: 19.251 distance: 156 - 157: 6.946 distance: 157 - 158: 15.677 distance: 159 - 160: 14.483 distance: 160 - 161: 28.757 distance: 161 - 162: 23.172 distance: 161 - 163: 18.673 distance: 163 - 164: 7.499 distance: 164 - 165: 6.834 distance: 164 - 167: 14.366 distance: 165 - 166: 7.156 distance: 165 - 171: 10.418 distance: 167 - 168: 13.213 distance: 167 - 169: 7.056 distance: 168 - 170: 14.021 distance: 171 - 172: 6.252 distance: 172 - 173: 12.354 distance: 172 - 175: 8.354 distance: 173 - 174: 6.485 distance: 173 - 179: 7.238 distance: 175 - 176: 6.899 distance: 176 - 177: 9.823 distance: 176 - 178: 10.193 distance: 179 - 180: 5.757 distance: 180 - 181: 5.702 distance: 180 - 183: 8.021 distance: 181 - 182: 3.482 distance: 181 - 187: 3.301 distance: 183 - 184: 6.507 distance: 184 - 185: 7.045 distance: 184 - 186: 10.351 distance: 187 - 193: 9.558 distance: 188 - 189: 7.551 distance: 188 - 191: 6.606 distance: 189 - 190: 6.543 distance: 189 - 194: 4.173 distance: 191 - 192: 9.768 distance: 192 - 193: 12.117 distance: 194 - 195: 3.331 distance: 195 - 196: 3.239 distance: 195 - 198: 3.012 distance: 196 - 197: 3.405 distance: 197 - 224: 10.980 distance: 198 - 199: 4.558 distance: 198 - 200: 6.832 distance: 201 - 202: 5.489 distance: 202 - 203: 3.155 distance: 203 - 204: 4.566 distance: 203 - 210: 5.547 distance: 204 - 234: 8.037 distance: 205 - 206: 7.710 distance: 206 - 207: 6.744 distance: 207 - 208: 3.597 distance: 208 - 209: 7.422 distance: 210 - 211: 3.239 distance: 211 - 212: 3.018 distance: 212 - 213: 3.183 distance: 213 - 240: 7.980 distance: 214 - 215: 3.767 distance: 214 - 216: 5.539 distance: 218 - 219: 3.626 distance: 218 - 221: 5.273 distance: 219 - 220: 5.983 distance: 219 - 224: 4.048 distance: 220 - 244: 5.587 distance: 221 - 222: 7.446 distance: 221 - 223: 4.399