Starting phenix.real_space_refine on Wed Feb 14 08:09:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/02_2024/8bm0_16116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/02_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_16116/02_2024/8bm0_16116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/02_2024/8bm0_16116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/02_2024/8bm0_16116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bm0_16116/02_2024/8bm0_16116_updated.pdb" } 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 Residue "I PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 257": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 435": "OD1" <-> "OD2" Residue "A GLU 76": "OE1" <-> "OE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 140": "OD1" <-> "OD2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "D PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 304": "OE1" <-> "OE2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 63": "OE1" <-> "OE2" Residue "H TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 308": "OE1" <-> "OE2" Residue "H GLU 408": "OE1" <-> "OE2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 428": "OD1" <-> "OD2" Residue "L GLU 308": "OE1" <-> "OE2" Residue "O ASP 5": "OD1" <-> "OD2" Residue "O PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 308": "OE1" <-> "OE2" Residue "O GLU 408": "OE1" <-> "OE2" Residue "O TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 386": "OE1" <-> "OE2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Residue "R GLU 408": "OE1" <-> "OE2" Residue "S PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 255": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 22.27, per 1000 atoms: 0.37 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.79 Conformation dependent library (CDL) restraints added in 8.2 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... running ksdssp... Secondary structure from input PDB file: 255 helices and 107 sheets defined 47.8% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.06 Creating SS restraints... Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.876A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 65 through 84 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 89 through 108 Processing helix chain 'I' and resid 113 through 134 Processing helix chain 'I' and resid 141 through 152 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 256 through 268 Processing helix chain 'I' and resid 285 through 296 Processing helix chain 'I' and resid 339 through 355 Processing helix chain 'I' and resid 359 through 372 Processing helix chain 'I' and resid 386 through 409 Processing helix chain 'I' and resid 417 through 428 removed outlier: 3.558A pdb=" N ALA I 427 " --> pdb=" O ALA I 423 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N ASP I 428 " --> pdb=" O SER I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 434 through 458 removed outlier: 3.689A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA I 449 " --> pdb=" O ARG I 445 " (cutoff:3.500A) Proline residue: I 450 - end of helix Processing helix chain 'I' and resid 462 through 471 Processing helix chain 'I' and resid 497 through 515 Processing helix chain 'G' and resid 9 through 30 removed outlier: 5.075A pdb=" N THR G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 65 through 84 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 89 through 108 Processing helix chain 'G' and resid 113 through 134 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 156 through 168 Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 230 through 239 Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 283 through 296 Processing helix chain 'G' and resid 339 through 355 Processing helix chain 'G' and resid 359 through 374 Processing helix chain 'G' and resid 386 through 408 Processing helix chain 'G' and resid 417 through 426 removed outlier: 3.615A pdb=" N LEU G 426 " --> pdb=" O VAL G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 458 removed outlier: 3.772A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA G 449 " --> pdb=" O ARG G 445 " (cutoff:3.500A) Proline residue: G 450 - end of helix Processing helix chain 'G' and resid 462 through 471 Processing helix chain 'G' and resid 497 through 514 Processing helix chain 'A' and resid 9 through 30 removed outlier: 3.900A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 84 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 89 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 285 through 296 Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 372 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.718A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.858A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 30 removed outlier: 4.974A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 84 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 89 through 108 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 138 through 141 No H-bonds generated for 'chain 'C' and resid 138 through 141' Processing helix chain 'C' and resid 144 through 152 Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 230 through 241 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 374 Processing helix chain 'C' and resid 386 through 408 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'C' and resid 434 through 458 removed outlier: 3.793A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Proline residue: C 450 - end of helix Processing helix chain 'C' and resid 462 through 471 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.988A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 30 removed outlier: 3.908A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 65 through 84 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 89 through 108 Processing helix chain 'D' and resid 113 through 134 Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 156 through 169 Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 231 through 243 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 296 Processing helix chain 'D' and resid 339 through 355 Processing helix chain 'D' and resid 359 through 372 Processing helix chain 'D' and resid 386 through 409 Processing helix chain 'D' and resid 417 through 425 Processing helix chain 'D' and resid 434 through 458 removed outlier: 3.737A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Proline residue: D 450 - end of helix Processing helix chain 'D' and resid 462 through 471 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.835A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 30 removed outlier: 4.962A pdb=" N THR F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 65 through 84 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 89 through 108 Processing helix chain 'F' and resid 113 through 134 Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 156 through 168 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 231 through 243 Proline residue: F 235 - end of helix removed outlier: 3.668A pdb=" N LYS F 242 " --> pdb=" O GLU F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 266 Processing helix chain 'F' and resid 283 through 296 Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 374 Processing helix chain 'F' and resid 386 through 408 Processing helix chain 'F' and resid 417 through 426 Processing helix chain 'F' and resid 434 through 458 removed outlier: 3.776A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA F 449 " --> pdb=" O ARG F 445 " (cutoff:3.500A) Proline residue: F 450 - end of helix Processing helix chain 'F' and resid 462 through 471 Processing helix chain 'F' and resid 497 through 514 Processing helix chain 'H' and resid 9 through 30 removed outlier: 3.929A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 84 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 89 through 108 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 156 through 169 Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 256 through 268 Processing helix chain 'H' and resid 285 through 296 Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 372 Processing helix chain 'H' and resid 386 through 409 Processing helix chain 'H' and resid 417 through 425 Processing helix chain 'H' and resid 434 through 458 removed outlier: 3.691A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA H 449 " --> pdb=" O ARG H 445 " (cutoff:3.500A) Proline residue: H 450 - end of helix Processing helix chain 'H' and resid 462 through 471 Processing helix chain 'H' and resid 488 through 491 No H-bonds generated for 'chain 'H' and resid 488 through 491' Processing helix chain 'H' and resid 497 through 515 Processing helix chain 'K' and resid 9 through 30 removed outlier: 5.081A pdb=" N THR K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 65 through 84 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 89 through 108 Processing helix chain 'K' and resid 113 through 134 Processing helix chain 'K' and resid 138 through 141 No H-bonds generated for 'chain 'K' and resid 138 through 141' Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'K' and resid 156 through 168 Processing helix chain 'K' and resid 230 through 242 Proline residue: K 235 - end of helix removed outlier: 3.978A pdb=" N LYS K 242 " --> pdb=" O GLU K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 266 Processing helix chain 'K' and resid 283 through 296 Processing helix chain 'K' and resid 339 through 355 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 386 through 408 Processing helix chain 'K' and resid 417 through 426 Processing helix chain 'K' and resid 434 through 458 removed outlier: 3.782A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA K 449 " --> pdb=" O ARG K 445 " (cutoff:3.500A) Proline residue: K 450 - end of helix Processing helix chain 'K' and resid 462 through 471 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.979A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 30 removed outlier: 3.827A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR L 30 " --> pdb=" O ALA L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 58 Processing helix chain 'L' and resid 65 through 84 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 89 through 108 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 152 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 231 through 243 Proline residue: L 235 - end of helix Processing helix chain 'L' and resid 256 through 268 Processing helix chain 'L' and resid 285 through 296 Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 372 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 425 Processing helix chain 'L' and resid 434 through 458 removed outlier: 3.720A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA L 449 " --> pdb=" O ARG L 445 " (cutoff:3.500A) Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 497 through 515 Processing helix chain 'N' and resid 9 through 30 removed outlier: 4.996A pdb=" N THR N 30 " --> pdb=" O ALA N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 65 through 84 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 89 through 108 Processing helix chain 'N' and resid 113 through 134 Processing helix chain 'N' and resid 138 through 141 No H-bonds generated for 'chain 'N' and resid 138 through 141' Processing helix chain 'N' and resid 144 through 151 Processing helix chain 'N' and resid 156 through 169 Processing helix chain 'N' and resid 202 through 204 No H-bonds generated for 'chain 'N' and resid 202 through 204' Processing helix chain 'N' and resid 230 through 242 Proline residue: N 235 - end of helix Processing helix chain 'N' and resid 259 through 266 Processing helix chain 'N' and resid 283 through 296 Processing helix chain 'N' and resid 339 through 355 Processing helix chain 'N' and resid 359 through 374 Processing helix chain 'N' and resid 386 through 408 Processing helix chain 'N' and resid 417 through 426 Processing helix chain 'N' and resid 434 through 458 removed outlier: 3.821A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA N 449 " --> pdb=" O ARG N 445 " (cutoff:3.500A) Proline residue: N 450 - end of helix Processing helix chain 'N' and resid 462 through 471 Processing helix chain 'N' and resid 497 through 514 Processing helix chain 'O' and resid 9 through 30 removed outlier: 3.866A pdb=" N VAL O 29 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR O 30 " --> pdb=" O ALA O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 53 through 59 Processing helix chain 'O' and resid 65 through 84 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 89 through 108 Processing helix chain 'O' and resid 113 through 134 Processing helix chain 'O' and resid 141 through 152 Processing helix chain 'O' and resid 156 through 169 Processing helix chain 'O' and resid 202 through 204 No H-bonds generated for 'chain 'O' and resid 202 through 204' Processing helix chain 'O' and resid 234 through 243 Processing helix chain 'O' and resid 256 through 268 Processing helix chain 'O' and resid 285 through 296 Processing helix chain 'O' and resid 339 through 355 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 386 through 409 Processing helix chain 'O' and resid 417 through 428 removed outlier: 3.546A pdb=" N ALA O 427 " --> pdb=" O ALA O 423 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP O 428 " --> pdb=" O SER O 424 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 458 removed outlier: 3.708A pdb=" N GLU O 448 " --> pdb=" O LEU O 444 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA O 449 " --> pdb=" O ARG O 445 " (cutoff:3.500A) Proline residue: O 450 - end of helix Processing helix chain 'O' and resid 462 through 471 Processing helix chain 'O' and resid 497 through 515 Processing helix chain 'Q' and resid 9 through 30 removed outlier: 5.057A pdb=" N THR Q 30 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 59 Processing helix chain 'Q' and resid 65 through 84 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 89 through 108 Processing helix chain 'Q' and resid 113 through 134 Processing helix chain 'Q' and resid 138 through 141 No H-bonds generated for 'chain 'Q' and resid 138 through 141' Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 156 through 169 Processing helix chain 'Q' and resid 202 through 204 No H-bonds generated for 'chain 'Q' and resid 202 through 204' Processing helix chain 'Q' and resid 230 through 243 Proline residue: Q 235 - end of helix removed outlier: 4.194A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 260 through 266 Processing helix chain 'Q' and resid 283 through 296 Processing helix chain 'Q' and resid 339 through 355 Processing helix chain 'Q' and resid 359 through 374 Processing helix chain 'Q' and resid 386 through 408 Processing helix chain 'Q' and resid 417 through 426 Processing helix chain 'Q' and resid 434 through 458 removed outlier: 3.808A pdb=" N GLU Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA Q 449 " --> pdb=" O ARG Q 445 " (cutoff:3.500A) Proline residue: Q 450 - end of helix Processing helix chain 'Q' and resid 462 through 471 Processing helix chain 'Q' and resid 497 through 514 Processing helix chain 'R' and resid 9 through 30 removed outlier: 3.899A pdb=" N VAL R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N THR R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 65 through 84 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 89 through 108 Processing helix chain 'R' and resid 113 through 134 Processing helix chain 'R' and resid 141 through 152 Processing helix chain 'R' and resid 156 through 169 Processing helix chain 'R' and resid 202 through 204 No H-bonds generated for 'chain 'R' and resid 202 through 204' Processing helix chain 'R' and resid 234 through 243 Processing helix chain 'R' and resid 256 through 268 Processing helix chain 'R' and resid 285 through 296 Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'R' and resid 359 through 372 Processing helix chain 'R' and resid 386 through 409 Processing helix chain 'R' and resid 417 through 425 Processing helix chain 'R' and resid 434 through 458 removed outlier: 3.723A pdb=" N GLU R 448 " --> pdb=" O LEU R 444 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA R 449 " --> pdb=" O ARG R 445 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 462 through 471 Processing helix chain 'R' and resid 497 through 515 Processing helix chain 'T' and resid 9 through 30 removed outlier: 5.079A pdb=" N THR T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 59 Processing helix chain 'T' and resid 65 through 84 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 89 through 108 Processing helix chain 'T' and resid 113 through 134 Processing helix chain 'T' and resid 138 through 141 No H-bonds generated for 'chain 'T' and resid 138 through 141' Processing helix chain 'T' and resid 144 through 152 Processing helix chain 'T' and resid 156 through 168 Processing helix chain 'T' and resid 230 through 239 Proline residue: T 235 - end of helix Processing helix chain 'T' and resid 260 through 266 Processing helix chain 'T' and resid 283 through 296 Processing helix chain 'T' and resid 339 through 355 Processing helix chain 'T' and resid 359 through 374 Processing helix chain 'T' and resid 386 through 408 Processing helix chain 'T' and resid 417 through 426 Processing helix chain 'T' and resid 434 through 458 removed outlier: 3.795A pdb=" N GLU T 448 " --> pdb=" O LEU T 444 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA T 449 " --> pdb=" O ARG T 445 " (cutoff:3.500A) Proline residue: T 450 - end of helix Processing helix chain 'T' and resid 462 through 471 Processing helix chain 'T' and resid 497 through 516 removed outlier: 4.100A pdb=" N THR T 516 " --> pdb=" O GLY T 512 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'I' and resid 219 through 223 Processing sheet with id= F, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= H, 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: 6.011A pdb=" N LYS W 13 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL W 40 " --> pdb=" O LYS W 13 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 4 through 8 Processing sheet with id= J, first strand: chain 'G' and resid 38 through 40 Processing sheet with id= K, first strand: chain 'G' and resid 174 through 179 Processing sheet with id= L, first strand: chain 'G' and resid 193 through 195 Processing sheet with id= M, first strand: chain 'G' and resid 219 through 222 Processing sheet with id= N, first strand: chain 'G' and resid 411 through 413 Processing sheet with id= O, first strand: chain 'G' and resid 476 through 479 Processing sheet with id= P, first strand: chain 'A' and resid 4 through 8 Processing sheet with id= Q, first strand: chain 'A' and resid 38 through 40 Processing sheet with id= R, first strand: chain 'A' and resid 174 through 179 Processing sheet with id= S, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= T, first strand: chain 'A' and resid 219 through 223 Processing sheet with id= U, first strand: chain 'A' and resid 411 through 413 Processing sheet with id= V, first strand: chain 'A' and resid 476 through 479 Processing sheet with id= W, first strand: chain 'B' and resid 74 through 78 removed outlier: 7.825A pdb=" N GLU B 82 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG B 14 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYS B 13 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL B 40 " --> pdb=" O LYS B 13 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 93 " --> pdb=" O ILE B 66 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= Y, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= Z, first strand: chain 'C' and resid 174 through 180 Processing sheet with id= AA, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= AB, first strand: chain 'C' and resid 219 through 222 removed outlier: 7.031A pdb=" N ALA C 274 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA C 251 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL C 276 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= AD, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= AE, first strand: chain 'D' and resid 4 through 8 Processing sheet with id= AF, first strand: chain 'D' and resid 38 through 40 Processing sheet with id= AG, first strand: chain 'D' and resid 174 through 179 Processing sheet with id= AH, 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) Processing sheet with id= AI, first strand: chain 'D' and resid 219 through 222 Processing sheet with id= AJ, first strand: chain 'D' and resid 411 through 413 Processing sheet with id= AK, first strand: chain 'D' and resid 476 through 479 Processing sheet with id= AL, first strand: chain 'E' and resid 74 through 78 removed outlier: 7.793A pdb=" N GLU E 82 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG E 14 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS E 13 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL E 40 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 93 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AN, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AO, first strand: chain 'F' and resid 174 through 180 Processing sheet with id= AP, 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= AQ, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.865A pdb=" N ALA F 274 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA F 251 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL F 276 " --> pdb=" O ALA F 251 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AS, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AT, first strand: chain 'H' and resid 4 through 8 Processing sheet with id= AU, first strand: chain 'H' and resid 38 through 40 Processing sheet with id= AV, first strand: chain 'H' and resid 174 through 179 Processing sheet with id= AW, first strand: chain 'H' and resid 213 through 216 Processing sheet with id= AX, first strand: chain 'H' and resid 219 through 223 Processing sheet with id= AY, first strand: chain 'H' and resid 411 through 413 Processing sheet with id= AZ, first strand: chain 'H' and resid 476 through 479 Processing sheet with id= BA, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.921A pdb=" N GLU J 82 " --> pdb=" O ARG J 14 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ARG J 14 " --> pdb=" O GLU J 82 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS J 13 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N VAL J 40 " --> pdb=" O LYS J 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA J 93 " --> pdb=" O ILE J 66 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 4 through 8 Processing sheet with id= BC, first strand: chain 'K' and resid 38 through 40 Processing sheet with id= BD, first strand: chain 'K' and resid 174 through 179 Processing sheet with id= BE, first strand: chain 'K' and resid 193 through 195 Processing sheet with id= BF, 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) Processing sheet with id= BG, first strand: chain 'K' and resid 219 through 222 removed outlier: 7.106A pdb=" N ALA K 274 " --> pdb=" O ILE K 249 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA K 251 " --> pdb=" O ALA K 274 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL K 276 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'K' and resid 411 through 413 Processing sheet with id= BI, first strand: chain 'K' and resid 476 through 479 Processing sheet with id= BJ, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BK, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BL, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= BM, first strand: chain 'L' and resid 213 through 216 Processing sheet with id= BN, first strand: chain 'L' and resid 219 through 223 Processing sheet with id= BO, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= BP, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= BQ, first strand: chain 'M' and resid 74 through 78 removed outlier: 7.840A pdb=" N GLU M 82 " --> pdb=" O ARG M 14 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG M 14 " --> pdb=" O GLU M 82 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS M 13 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL M 40 " --> pdb=" O LYS M 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 93 " --> pdb=" O ILE M 66 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'N' and resid 4 through 8 Processing sheet with id= BS, first strand: chain 'N' and resid 38 through 40 Processing sheet with id= BT, first strand: chain 'N' and resid 174 through 179 Processing sheet with id= BU, first strand: chain 'N' and resid 193 through 195 Processing sheet with id= BV, first strand: chain 'N' and resid 213 through 216 Processing sheet with id= BW, first strand: chain 'N' and resid 219 through 222 Processing sheet with id= BX, first strand: chain 'N' and resid 411 through 413 Processing sheet with id= BY, first strand: chain 'N' and resid 476 through 479 Processing sheet with id= BZ, first strand: chain 'O' and resid 4 through 8 Processing sheet with id= CA, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= CB, first strand: chain 'O' and resid 174 through 179 Processing sheet with id= CC, first strand: chain 'O' and resid 213 through 216 Processing sheet with id= CD, first strand: chain 'O' and resid 219 through 223 Processing sheet with id= CE, first strand: chain 'O' and resid 411 through 413 Processing sheet with id= CF, first strand: chain 'O' and resid 476 through 479 Processing sheet with id= CG, first strand: chain 'P' and resid 74 through 78 removed outlier: 7.735A pdb=" N GLU P 82 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG P 14 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS P 13 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL P 40 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id= CI, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id= CJ, first strand: chain 'Q' and resid 174 through 179 Processing sheet with id= CK, 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= CL, first strand: chain 'Q' and resid 219 through 222 removed outlier: 7.231A pdb=" N ALA Q 274 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ALA Q 251 " --> pdb=" O ALA Q 274 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Q 276 " --> pdb=" O ALA Q 251 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'Q' and resid 411 through 413 Processing sheet with id= CN, first strand: chain 'Q' and resid 476 through 479 Processing sheet with id= CO, first strand: chain 'R' and resid 4 through 8 Processing sheet with id= CP, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= CQ, first strand: chain 'R' and resid 174 through 179 Processing sheet with id= CR, first strand: chain 'R' and resid 213 through 216 Processing sheet with id= CS, first strand: chain 'R' and resid 219 through 223 Processing sheet with id= CT, first strand: chain 'R' and resid 411 through 413 Processing sheet with id= CU, first strand: chain 'R' and resid 476 through 479 Processing sheet with id= CV, first strand: chain 'S' and resid 74 through 78 removed outlier: 7.644A pdb=" N GLU S 82 " --> pdb=" O ARG S 14 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG S 14 " --> pdb=" O GLU S 82 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LYS S 13 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL S 40 " --> pdb=" O LYS S 13 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'T' and resid 4 through 8 Processing sheet with id= CX, first strand: chain 'T' and resid 38 through 40 Processing sheet with id= CY, first strand: chain 'T' and resid 174 through 179 Processing sheet with id= CZ, first strand: chain 'T' and resid 193 through 195 Processing sheet with id= DA, first strand: chain 'T' and resid 219 through 222 removed outlier: 6.706A pdb=" N ALA T 274 " --> pdb=" O ILE T 249 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'T' and resid 411 through 413 Processing sheet with id= DC, first strand: chain 'T' and resid 476 through 479 3331 hydrogen bonds defined for protein. 9633 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: 22.92 Time building geometry restraints manager: 20.57 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: 95.65 - 104.50: 797 104.50 - 113.34: 34964 113.34 - 122.19: 34837 122.19 - 131.04: 10182 131.04 - 139.88: 65 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: 892 2.63 - 3.26: 61994 3.26 - 3.88: 130372 3.88 - 4.51: 168163 4.51 - 5.14: 261153 Nonbonded interactions: 622574 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 622569 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' 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: 3.480 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: 0.050 Extract box with map and model: 13.640 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 125.820 Find NCS groups from input model: 4.100 Set up NCS constraints: 0.240 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:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.680 ------------------------------------------------------------------------------- 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= 0.211 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 : 5.046 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: 0.5751 time to fit residues: 476.2361 Evaluate side-chains 387 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 382 time to evaluate : 5.002 ------------------------------------------------------------------------------- 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: 0.1980 chunk 404 optimal weight: 2.9990 chunk 320 optimal weight: 50.0000 chunk 619 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 376 optimal weight: 10.0000 chunk 461 optimal weight: 0.6980 chunk 718 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 479 ASN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN L 479 ASN O 479 ASN ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 59807 Z= 0.242 Angle : 0.514 14.000 80845 Z= 0.268 Chirality : 0.042 0.189 9810 Planarity : 0.003 0.067 10514 Dihedral : 8.078 89.142 8923 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.39 % Allowed : 19.09 % Favored : 79.52 % 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: 1.16 (0.09), residues: 7959 helix: 1.74 (0.08), residues: 4130 sheet: -0.13 (0.14), residues: 1211 loop : -0.24 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 7 PHE 0.016 0.001 PHE R 195 TYR 0.009 0.001 TYR T 199 ARG 0.008 0.000 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 509 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 423 time to evaluate : 5.917 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: 0.8570 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: W 2 ASN cc_start: 0.9184 (t0) cc_final: 0.8938 (t0) REVERT: W 81 GLU cc_start: 0.9364 (tm-30) cc_final: 0.9142 (tm-30) REVERT: A 194 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: A 248 LEU cc_start: 0.9285 (tp) cc_final: 0.9016 (pp) REVERT: A 288 MET cc_start: 0.8521 (ptt) cc_final: 0.8057 (ptt) REVERT: A 311 LYS cc_start: 0.8563 (pptt) cc_final: 0.8362 (pttm) REVERT: B 86 MET cc_start: 0.8459 (pmm) cc_final: 0.8206 (pmm) REVERT: D 231 ARG cc_start: 0.8775 (mmt180) cc_final: 0.8412 (mmt-90) REVERT: E 20 LYS cc_start: 0.9268 (ttpp) cc_final: 0.8966 (mppt) REVERT: E 81 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8910 (tm-30) REVERT: F 199 TYR cc_start: 0.3686 (p90) cc_final: 0.3306 (p90) REVERT: H 111 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: K 193 MET cc_start: 0.8157 (tpp) cc_final: 0.7050 (mmm) REVERT: K 288 MET cc_start: 0.7847 (mmt) cc_final: 0.6910 (ppp) REVERT: K 307 MET cc_start: 0.6471 (tmm) cc_final: 0.6084 (tmm) REVERT: M 16 GLU cc_start: 0.8637 (pm20) cc_final: 0.8341 (pp20) REVERT: M 86 MET cc_start: 0.8224 (pmm) cc_final: 0.7634 (pmm) REVERT: N 199 TYR cc_start: 0.4176 (p90) cc_final: 0.3653 (p90) REVERT: O 111 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: O 195 PHE cc_start: 0.8266 (p90) cc_final: 0.7942 (p90) REVERT: P 86 MET cc_start: 0.8244 (pmm) cc_final: 0.7941 (pmm) REVERT: R 111 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: R 142 LYS cc_start: 0.7977 (mtmm) cc_final: 0.7614 (tptp) REVERT: S 77 LYS cc_start: 0.9274 (tmtt) cc_final: 0.9024 (tmtt) REVERT: S 86 MET cc_start: 0.8092 (pmm) cc_final: 0.7768 (pmm) outliers start: 86 outliers final: 34 residues processed: 494 average time/residue: 0.6002 time to fit residues: 495.8979 Evaluate side-chains 428 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 389 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 111 MET Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 490 ASP Chi-restraints excluded: chain P residue 9 ARG Chi-restraints excluded: chain P residue 41 LEU Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 468 THR 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 131 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 597 optimal weight: 20.0000 chunk 489 optimal weight: 10.0000 chunk 198 optimal weight: 50.0000 chunk 719 optimal weight: 1.9990 chunk 777 optimal weight: 8.9990 chunk 640 optimal weight: 6.9990 chunk 713 optimal weight: 0.9990 chunk 245 optimal weight: 20.0000 chunk 577 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 GLN H 97 GLN ** Q 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 348 GLN R 97 GLN T 348 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 59807 Z= 0.314 Angle : 0.538 13.998 80845 Z= 0.280 Chirality : 0.043 0.186 9810 Planarity : 0.003 0.077 10514 Dihedral : 7.878 89.702 8911 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.87 % Allowed : 19.90 % Favored : 78.23 % 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: 1.18 (0.09), residues: 7959 helix: 1.78 (0.08), residues: 4116 sheet: -0.22 (0.14), residues: 1211 loop : -0.22 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS P 7 PHE 0.020 0.001 PHE A 195 TYR 0.014 0.001 TYR D 199 ARG 0.008 0.000 ARG E 37 *********************** 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 524 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 408 time to evaluate : 5.080 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: I 111 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8318 (mtp) REVERT: W 2 ASN cc_start: 0.9235 (t0) cc_final: 0.8983 (t0) REVERT: G 267 MET cc_start: 0.6690 (ppp) cc_final: 0.6237 (ppp) REVERT: A 111 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8212 (mtp) REVERT: A 247 LEU cc_start: 0.9367 (tp) cc_final: 0.8943 (tt) REVERT: A 248 LEU cc_start: 0.9172 (tp) cc_final: 0.8868 (pp) REVERT: A 288 MET cc_start: 0.8526 (ptt) cc_final: 0.7966 (ptt) REVERT: C 200 LEU cc_start: 0.3035 (OUTLIER) cc_final: 0.1474 (pp) REVERT: D 69 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8944 (mtp) REVERT: D 111 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8205 (mtp) REVERT: E 20 LYS cc_start: 0.9264 (ttpp) cc_final: 0.8972 (mppt) REVERT: F 199 TYR cc_start: 0.3916 (p90) cc_final: 0.3499 (p90) REVERT: H 111 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8356 (mtp) REVERT: J 86 MET cc_start: 0.6651 (pmm) cc_final: 0.6320 (pmm) REVERT: K 193 MET cc_start: 0.8204 (tpp) cc_final: 0.7037 (mmm) REVERT: M 4 ARG cc_start: 0.6821 (pmt-80) cc_final: 0.6593 (pmt-80) REVERT: M 86 MET cc_start: 0.8297 (pmm) cc_final: 0.7803 (pmm) REVERT: N 199 TYR cc_start: 0.4264 (p90) cc_final: 0.3726 (p90) REVERT: O 111 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: O 195 PHE cc_start: 0.8267 (p90) cc_final: 0.7918 (p90) REVERT: P 20 LYS cc_start: 0.9289 (tttm) cc_final: 0.9022 (mppt) REVERT: Q 73 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8485 (mtp) REVERT: Q 233 MET cc_start: 0.5408 (ppp) cc_final: 0.5005 (ppp) REVERT: R 111 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8387 (mtp) REVERT: R 142 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7676 (tptp) REVERT: S 86 MET cc_start: 0.8182 (pmm) cc_final: 0.7865 (pmm) outliers start: 116 outliers final: 70 residues processed: 504 average time/residue: 0.5653 time to fit residues: 482.2629 Evaluate side-chains 452 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 373 time to evaluate : 5.003 ------------------------------------------------------------------------------- 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 179 ASP Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 64 ILE 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 502 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 502 SER 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 236 VAL Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 307 MET 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 L residue 56 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain N residue 502 SER 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 490 ASP Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 73 MET 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 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 468 THR 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 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 502 SER 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: 6.9990 chunk 79 optimal weight: 30.0000 chunk 343 optimal weight: 5.9990 chunk 483 optimal weight: 5.9990 chunk 722 optimal weight: 0.9990 chunk 764 optimal weight: 50.0000 chunk 377 optimal weight: 0.8980 chunk 684 optimal weight: 5.9990 chunk 206 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 GLN J 2 ASN O 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 59807 Z= 0.356 Angle : 0.550 14.066 80845 Z= 0.286 Chirality : 0.044 0.173 9810 Planarity : 0.003 0.067 10514 Dihedral : 7.779 89.232 8911 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.52 % Allowed : 20.43 % Favored : 77.05 % 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: 1.10 (0.09), residues: 7959 helix: 1.71 (0.08), residues: 4109 sheet: -0.43 (0.14), residues: 1141 loop : -0.16 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 7 PHE 0.013 0.001 PHE A 195 TYR 0.017 0.002 TYR H 199 ARG 0.015 0.000 ARG J 37 *********************** 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 555 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 399 time to evaluate : 5.215 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: 0.8705 (OUTLIER) cc_final: 0.8336 (mtp) REVERT: I 203 TYR cc_start: 0.8552 (m-80) cc_final: 0.8204 (m-80) REVERT: I 483 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: W 2 ASN cc_start: 0.9269 (t0) cc_final: 0.9019 (t0) REVERT: G 267 MET cc_start: 0.6643 (ppp) cc_final: 0.6074 (ppp) REVERT: A 111 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: A 194 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 288 MET cc_start: 0.8546 (ptt) cc_final: 0.7945 (ptt) REVERT: B 86 MET cc_start: 0.8674 (pmm) cc_final: 0.8468 (pmm) REVERT: C 323 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6620 (p) REVERT: D 69 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8943 (mtp) REVERT: D 111 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8236 (mtp) REVERT: D 231 ARG cc_start: 0.8753 (mmt180) cc_final: 0.8502 (mmt-90) REVERT: E 20 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8965 (mppt) REVERT: E 86 MET cc_start: 0.7641 (pmm) cc_final: 0.7409 (pmm) REVERT: F 199 TYR cc_start: 0.3876 (p90) cc_final: 0.3431 (p90) REVERT: H 111 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8317 (mtp) REVERT: J 63 ASP cc_start: 0.8136 (t0) cc_final: 0.7082 (p0) REVERT: K 193 MET cc_start: 0.8228 (tpp) cc_final: 0.7058 (mmm) REVERT: K 307 MET cc_start: 0.6374 (tmm) cc_final: 0.6115 (tmm) REVERT: M 86 MET cc_start: 0.8293 (pmm) cc_final: 0.7869 (pmm) REVERT: N 193 MET cc_start: 0.7633 (mmm) cc_final: 0.7121 (mmm) REVERT: N 199 TYR cc_start: 0.4332 (p90) cc_final: 0.3726 (p90) REVERT: O 111 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8427 (mtp) REVERT: O 195 PHE cc_start: 0.8402 (p90) cc_final: 0.7980 (p90) REVERT: P 20 LYS cc_start: 0.9282 (tttm) cc_final: 0.9001 (mppt) REVERT: P 86 MET cc_start: 0.8535 (pmm) cc_final: 0.7810 (pmm) REVERT: P 91 ILE cc_start: 0.9173 (mm) cc_final: 0.8889 (mm) REVERT: R 111 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8401 (mtp) REVERT: R 142 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7714 (tptp) REVERT: R 194 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8077 (tm-30) REVERT: S 86 MET cc_start: 0.8209 (pmm) cc_final: 0.7896 (pmm) outliers start: 156 outliers final: 106 residues processed: 528 average time/residue: 0.5780 time to fit residues: 517.0648 Evaluate side-chains 489 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 372 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 97 GLN 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 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 483 GLU Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 64 ILE 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 495 ASP Chi-restraints excluded: chain G residue 502 SER 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 266 THR Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 502 SER 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 142 LYS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 139 SER Chi-restraints excluded: chain H residue 142 LYS Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain J residue 49 LEU 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 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 139 SER Chi-restraints excluded: chain L residue 174 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 229 ASN Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 234 LEU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain N residue 502 SER 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 174 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 513 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 323 VAL 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 194 GLN Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 267 MET Chi-restraints excluded: chain R residue 468 THR 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 179 ASP Chi-restraints excluded: chain T residue 495 ASP Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 3.9990 chunk 434 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 569 optimal weight: 5.9990 chunk 315 optimal weight: 30.0000 chunk 652 optimal weight: 9.9990 chunk 528 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 390 optimal weight: 0.8980 chunk 686 optimal weight: 0.6980 chunk 192 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 97 GLN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1251 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= 0.253 Angle : 0.520 15.019 80845 Z= 0.269 Chirality : 0.042 0.202 9810 Planarity : 0.003 0.077 10514 Dihedral : 7.666 89.004 8911 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.52 % Allowed : 20.85 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 7959 helix: 1.82 (0.08), residues: 4116 sheet: -0.40 (0.15), residues: 1141 loop : -0.13 (0.11), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS M 7 PHE 0.024 0.001 PHE C 44 TYR 0.012 0.001 TYR T 199 ARG 0.012 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: 156 poor density : 390 time to evaluate : 5.090 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: I 111 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: I 203 TYR cc_start: 0.8559 (m-80) cc_final: 0.8197 (m-80) REVERT: W 2 ASN cc_start: 0.9255 (t0) cc_final: 0.9008 (t0) REVERT: G 267 MET cc_start: 0.6517 (ppp) cc_final: 0.5914 (ppp) REVERT: A 111 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: A 194 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: A 288 MET cc_start: 0.8489 (ptt) cc_final: 0.7858 (ptt) REVERT: A 321 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8695 (ptmt) REVERT: D 111 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8220 (mtp) REVERT: D 231 ARG cc_start: 0.8739 (mmt180) cc_final: 0.8483 (mmt-90) REVERT: E 20 LYS cc_start: 0.9229 (ttpp) cc_final: 0.8951 (mppt) REVERT: E 86 MET cc_start: 0.7592 (pmm) cc_final: 0.7339 (pmm) REVERT: F 199 TYR cc_start: 0.3928 (p90) cc_final: 0.3482 (p90) REVERT: H 111 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: J 63 ASP cc_start: 0.8125 (t0) cc_final: 0.7073 (p0) REVERT: K 193 MET cc_start: 0.8251 (tpp) cc_final: 0.7011 (mmm) REVERT: M 86 MET cc_start: 0.8347 (pmm) cc_final: 0.8000 (pmm) REVERT: N 193 MET cc_start: 0.7703 (mmm) cc_final: 0.7177 (mmm) REVERT: N 199 TYR cc_start: 0.4389 (p90) cc_final: 0.3807 (p90) REVERT: N 200 LEU cc_start: 0.3563 (OUTLIER) cc_final: 0.3360 (mm) REVERT: N 391 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: O 111 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8403 (mtp) REVERT: P 20 LYS cc_start: 0.9270 (tttm) cc_final: 0.8979 (mppt) REVERT: Q 193 MET cc_start: 0.7956 (tmm) cc_final: 0.7255 (tpp) REVERT: Q 233 MET cc_start: 0.5270 (ppp) cc_final: 0.5040 (ppp) REVERT: R 111 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8383 (mtp) REVERT: R 142 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7737 (tptp) REVERT: R 194 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: S 86 MET cc_start: 0.8253 (pmm) cc_final: 0.7970 (pmm) outliers start: 156 outliers final: 100 residues processed: 521 average time/residue: 0.5817 time to fit residues: 517.4727 Evaluate side-chains 482 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 371 time to evaluate : 5.434 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 64 ILE 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 179 ASP 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 G residue 502 SER Chi-restraints excluded: chain A residue 111 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 179 ASP 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 A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU 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 468 THR Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 50 THR 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 F residue 502 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 174 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 307 MET 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 461 GLU Chi-restraints excluded: chain K residue 495 ASP Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 231 ARG Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 50 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 200 LEU Chi-restraints excluded: chain N residue 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain N residue 502 SER 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 179 ASP Chi-restraints excluded: chain O residue 229 ASN 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 16 MET Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 468 THR Chi-restraints excluded: chain R residue 513 LEU Chi-restraints excluded: chain S residue 9 ARG Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain T residue 11 ASP Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 179 ASP Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 495 ASP Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 10.0000 chunk 688 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 448 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 3.9990 chunk 354 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 401 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** 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: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 59807 Z= 0.257 Angle : 0.521 15.609 80845 Z= 0.269 Chirality : 0.042 0.201 9810 Planarity : 0.003 0.061 10514 Dihedral : 7.535 87.510 8911 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.73 % Allowed : 20.85 % Favored : 76.42 % 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: 1.24 (0.09), residues: 7959 helix: 1.82 (0.08), residues: 4144 sheet: -0.22 (0.15), residues: 1099 loop : -0.19 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 401 PHE 0.019 0.001 PHE C 44 TYR 0.012 0.001 TYR I 199 ARG 0.013 0.000 ARG M 9 *********************** 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 561 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 392 time to evaluate : 5.061 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: I 111 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8298 (mtp) REVERT: I 203 TYR cc_start: 0.8545 (m-80) cc_final: 0.8171 (m-80) REVERT: W 2 ASN cc_start: 0.9260 (t0) cc_final: 0.9012 (t0) REVERT: G 267 MET cc_start: 0.6536 (ppp) cc_final: 0.5893 (ppp) REVERT: A 111 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8171 (mtp) REVERT: A 194 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: A 288 MET cc_start: 0.8456 (ptt) cc_final: 0.8169 (ptp) REVERT: A 321 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8684 (ptmt) REVERT: D 111 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8200 (mtp) REVERT: D 231 ARG cc_start: 0.8736 (mmt180) cc_final: 0.8477 (mmt-90) REVERT: E 2 ASN cc_start: 0.7839 (p0) cc_final: 0.7595 (t0) REVERT: E 20 LYS cc_start: 0.9224 (ttpp) cc_final: 0.8948 (mppt) REVERT: H 111 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8297 (mtp) REVERT: J 63 ASP cc_start: 0.8124 (t0) cc_final: 0.7067 (p0) REVERT: J 86 MET cc_start: 0.6691 (pmm) cc_final: 0.6423 (pmm) REVERT: K 193 MET cc_start: 0.8243 (tpp) cc_final: 0.6990 (mmm) REVERT: K 288 MET cc_start: 0.7811 (mmt) cc_final: 0.6882 (ppp) REVERT: K 365 LEU cc_start: 0.5738 (OUTLIER) cc_final: 0.5367 (tp) REVERT: K 483 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: M 86 MET cc_start: 0.8300 (pmm) cc_final: 0.7966 (pmm) REVERT: N 193 MET cc_start: 0.7743 (mmm) cc_final: 0.7200 (mmm) REVERT: N 199 TYR cc_start: 0.4377 (p90) cc_final: 0.3787 (p90) REVERT: N 200 LEU cc_start: 0.3485 (OUTLIER) cc_final: 0.3263 (mm) REVERT: N 391 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: O 111 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: O 195 PHE cc_start: 0.8391 (p90) cc_final: 0.7904 (p90) REVERT: P 15 LYS cc_start: 0.9591 (mmmt) cc_final: 0.9362 (mmmt) REVERT: P 20 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8988 (mppt) REVERT: P 88 GLU cc_start: 0.8797 (tt0) cc_final: 0.8525 (tt0) REVERT: Q 193 MET cc_start: 0.7931 (tmm) cc_final: 0.7209 (tpp) REVERT: R 111 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8375 (mtp) REVERT: R 142 LYS cc_start: 0.8041 (mtmm) cc_final: 0.7775 (tptp) REVERT: R 194 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: S 86 MET cc_start: 0.8230 (pmm) cc_final: 0.7921 (pmm) outliers start: 169 outliers final: 123 residues processed: 539 average time/residue: 0.5597 time to fit residues: 516.2368 Evaluate side-chains 505 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 368 time to evaluate : 5.054 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 468 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 64 ILE 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 179 ASP 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 G residue 502 SER 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 179 ASP Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 502 SER 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 D residue 468 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 11 ASP 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 179 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 502 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 174 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 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 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 483 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 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 229 ASN Chi-restraints excluded: chain L residue 231 ARG Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 48 THR 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 N residue 502 SER 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 179 ASP 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 468 THR Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 179 ASP Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 468 THR 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 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 179 ASP Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 463 SER Chi-restraints excluded: chain T residue 495 ASP Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 436 optimal weight: 40.0000 chunk 558 optimal weight: 0.5980 chunk 433 optimal weight: 8.9990 chunk 644 optimal weight: 20.0000 chunk 427 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 477 optimal weight: 8.9990 chunk 464 optimal weight: 0.6980 chunk 351 optimal weight: 0.7980 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 59807 Z= 0.346 Angle : 0.564 15.993 80845 Z= 0.290 Chirality : 0.044 0.336 9810 Planarity : 0.003 0.068 10514 Dihedral : 7.580 87.815 8911 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.88 % Allowed : 21.06 % Favored : 76.06 % 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: 1.18 (0.09), residues: 7959 helix: 1.75 (0.08), residues: 4109 sheet: -0.27 (0.15), residues: 1099 loop : -0.14 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 401 PHE 0.015 0.001 PHE C 44 TYR 0.013 0.001 TYR T 199 ARG 0.018 0.000 ARG H 231 *********************** 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 563 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 385 time to evaluate : 5.404 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: 0.8693 (OUTLIER) cc_final: 0.8320 (mtp) REVERT: I 203 TYR cc_start: 0.8586 (m-80) cc_final: 0.8214 (m-80) REVERT: W 2 ASN cc_start: 0.9299 (t0) cc_final: 0.9064 (t0) REVERT: G 267 MET cc_start: 0.6497 (ppp) cc_final: 0.5847 (ppp) REVERT: A 111 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: A 194 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: A 288 MET cc_start: 0.8480 (ptt) cc_final: 0.8187 (ptp) REVERT: A 321 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8664 (ptmt) REVERT: D 111 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8225 (mtp) REVERT: E 20 LYS cc_start: 0.9224 (ttpp) cc_final: 0.8987 (mppt) REVERT: H 111 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: H 483 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: J 63 ASP cc_start: 0.8157 (t0) cc_final: 0.7119 (p0) REVERT: K 193 MET cc_start: 0.8233 (tpp) cc_final: 0.6949 (mmm) REVERT: K 365 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5530 (tp) REVERT: K 483 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: L 114 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8434 (mmm) REVERT: M 86 MET cc_start: 0.8306 (pmm) cc_final: 0.7881 (pmm) REVERT: N 193 MET cc_start: 0.7823 (mmm) cc_final: 0.7282 (mmm) REVERT: N 199 TYR cc_start: 0.4388 (p90) cc_final: 0.3788 (p90) REVERT: N 200 LEU cc_start: 0.3484 (OUTLIER) cc_final: 0.3247 (mm) REVERT: N 391 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: P 15 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9373 (mmmt) REVERT: P 20 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8958 (mppt) REVERT: P 88 GLU cc_start: 0.8833 (tt0) cc_final: 0.8555 (tt0) REVERT: Q 233 MET cc_start: 0.4691 (ppp) cc_final: 0.4401 (ppp) REVERT: R 111 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8384 (mtp) REVERT: R 142 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7796 (tptp) REVERT: R 194 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: R 247 LEU cc_start: 0.9345 (tp) cc_final: 0.8962 (tt) REVERT: S 86 MET cc_start: 0.8369 (pmm) cc_final: 0.7607 (pmm) REVERT: T 391 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7506 (tm-30) outliers start: 178 outliers final: 137 residues processed: 542 average time/residue: 0.5653 time to fit residues: 525.8000 Evaluate side-chains 520 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 367 time to evaluate : 5.095 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 468 THR Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 179 ASP 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 G residue 502 SER 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 179 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 9 ARG Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 502 SER 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 236 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE 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 179 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 502 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 142 LYS Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 483 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 131 LEU 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 483 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 229 ASN Chi-restraints excluded: chain L residue 231 ARG Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 48 THR 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 N residue 502 SER 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 179 ASP Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 283 ASP Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 468 THR Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 179 ASP Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 323 VAL Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 468 THR 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 179 ASP 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 Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 455 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 484 optimal weight: 9.9990 chunk 519 optimal weight: 4.9990 chunk 376 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 599 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 59807 Z= 0.310 Angle : 0.557 16.959 80845 Z= 0.286 Chirality : 0.043 0.307 9810 Planarity : 0.003 0.063 10514 Dihedral : 7.553 88.456 8911 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.89 % Allowed : 21.06 % Favored : 76.05 % 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: 1.18 (0.09), residues: 7959 helix: 1.75 (0.08), residues: 4109 sheet: -0.19 (0.15), residues: 1057 loop : -0.18 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS R 401 PHE 0.019 0.001 PHE O 195 TYR 0.013 0.001 TYR T 199 ARG 0.010 0.000 ARG H 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 558 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 379 time to evaluate : 5.298 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: I 111 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8333 (mtp) REVERT: I 203 TYR cc_start: 0.8592 (m-80) cc_final: 0.8204 (m-80) REVERT: W 2 ASN cc_start: 0.9297 (t0) cc_final: 0.9064 (t0) REVERT: W 86 MET cc_start: 0.7965 (pmm) cc_final: 0.7665 (pmm) REVERT: G 267 MET cc_start: 0.6455 (ppp) cc_final: 0.5823 (ppp) REVERT: A 111 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8188 (mtp) REVERT: A 194 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: A 288 MET cc_start: 0.8450 (ptt) cc_final: 0.8143 (ptp) REVERT: A 321 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8662 (ptmt) REVERT: B 88 GLU cc_start: 0.9368 (tt0) cc_final: 0.9153 (tt0) REVERT: D 111 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: E 20 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8970 (mppt) REVERT: H 111 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: H 483 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: J 63 ASP cc_start: 0.8229 (t0) cc_final: 0.7154 (p0) REVERT: J 86 MET cc_start: 0.7484 (pmm) cc_final: 0.7135 (pmm) REVERT: K 193 MET cc_start: 0.8230 (tpp) cc_final: 0.6948 (mmm) REVERT: K 365 LEU cc_start: 0.5858 (OUTLIER) cc_final: 0.5563 (tp) REVERT: K 483 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: M 63 ASP cc_start: 0.8956 (t0) cc_final: 0.7312 (p0) REVERT: M 86 MET cc_start: 0.8380 (pmm) cc_final: 0.7818 (pmm) REVERT: N 193 MET cc_start: 0.7813 (mmm) cc_final: 0.7245 (mmm) REVERT: N 391 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: O 69 MET cc_start: 0.8758 (mtt) cc_final: 0.8556 (mtt) REVERT: O 111 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8324 (mtp) REVERT: O 195 PHE cc_start: 0.8394 (p90) cc_final: 0.7938 (p90) REVERT: P 15 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9374 (mmmt) REVERT: P 20 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8952 (mppt) REVERT: P 88 GLU cc_start: 0.8791 (tt0) cc_final: 0.8534 (tt0) REVERT: Q 193 MET cc_start: 0.7995 (tmm) cc_final: 0.7417 (tpp) REVERT: R 111 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8381 (mtp) REVERT: R 142 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7803 (tptp) REVERT: R 194 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8326 (tp40) REVERT: S 84 LEU cc_start: 0.8733 (tp) cc_final: 0.8378 (tp) REVERT: S 86 MET cc_start: 0.8382 (pmm) cc_final: 0.7859 (pmm) REVERT: T 391 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7421 (tm-30) outliers start: 179 outliers final: 144 residues processed: 537 average time/residue: 0.5557 time to fit residues: 514.3650 Evaluate side-chains 526 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 367 time to evaluate : 5.023 ------------------------------------------------------------------------------- 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 174 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 261 THR Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 283 ASP Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 468 THR Chi-restraints excluded: chain I residue 500 THR Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain G residue 11 ASP Chi-restraints excluded: chain G residue 73 MET Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 174 VAL Chi-restraints excluded: chain G residue 179 ASP 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 G residue 502 SER 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 179 ASP Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 502 SER 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 174 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE 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 179 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain F residue 502 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 142 LYS 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 283 ASP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 66 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 174 VAL Chi-restraints excluded: chain K residue 365 LEU Chi-restraints excluded: chain K residue 461 GLU Chi-restraints excluded: chain K residue 483 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 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 229 ASN Chi-restraints excluded: chain L residue 231 ARG Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 48 THR Chi-restraints excluded: chain N residue 50 THR 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 391 GLU Chi-restraints excluded: chain N residue 491 MET Chi-restraints excluded: chain N residue 502 SER 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 174 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 283 ASP Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 468 THR Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 16 MET Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 179 ASP Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 283 ASP Chi-restraints excluded: chain R residue 468 THR 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 179 ASP 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 Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.9990 chunk 730 optimal weight: 20.0000 chunk 666 optimal weight: 5.9990 chunk 710 optimal weight: 7.9990 chunk 427 optimal weight: 10.0000 chunk 309 optimal weight: 50.0000 chunk 557 optimal weight: 0.8980 chunk 218 optimal weight: 0.7980 chunk 641 optimal weight: 10.0000 chunk 671 optimal weight: 0.9990 chunk 707 optimal weight: 30.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59807 Z= 0.219 Angle : 0.538 17.528 80845 Z= 0.275 Chirality : 0.042 0.231 9810 Planarity : 0.003 0.062 10514 Dihedral : 7.437 87.468 8911 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.29 % Allowed : 21.77 % Favored : 75.93 % 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: 1.32 (0.09), residues: 7959 helix: 1.86 (0.08), residues: 4137 sheet: -0.16 (0.15), residues: 1113 loop : -0.10 (0.12), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 7 PHE 0.017 0.001 PHE O 195 TYR 0.012 0.001 TYR I 199 ARG 0.007 0.000 ARG H 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 522 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 380 time to evaluate : 5.038 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: I 111 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: I 203 TYR cc_start: 0.8529 (m-80) cc_final: 0.8162 (m-80) REVERT: W 2 ASN cc_start: 0.9296 (t0) cc_final: 0.9069 (t0) REVERT: G 193 MET cc_start: 0.6864 (mmm) cc_final: 0.6388 (mmm) REVERT: G 267 MET cc_start: 0.6388 (ppp) cc_final: 0.5813 (ppp) REVERT: A 111 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: A 194 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 288 MET cc_start: 0.8414 (ptt) cc_final: 0.8108 (ptp) REVERT: A 321 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8704 (ptmt) REVERT: B 88 GLU cc_start: 0.9346 (tt0) cc_final: 0.9088 (tt0) REVERT: D 111 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8205 (mtp) REVERT: E 20 LYS cc_start: 0.9244 (ttpp) cc_final: 0.8968 (mppt) REVERT: H 111 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: H 483 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: J 20 LYS cc_start: 0.9176 (ttpp) cc_final: 0.8802 (mppt) REVERT: J 63 ASP cc_start: 0.8221 (t0) cc_final: 0.7206 (p0) REVERT: J 86 MET cc_start: 0.7404 (pmm) cc_final: 0.7106 (pmm) REVERT: K 193 MET cc_start: 0.8260 (tpp) cc_final: 0.7003 (mmm) REVERT: K 365 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5591 (tp) REVERT: M 63 ASP cc_start: 0.8955 (t0) cc_final: 0.7370 (p0) REVERT: M 86 MET cc_start: 0.8374 (pmm) cc_final: 0.7798 (pmm) REVERT: N 193 MET cc_start: 0.7877 (mmm) cc_final: 0.7337 (mmm) REVERT: N 307 MET cc_start: 0.7847 (tmm) cc_final: 0.7285 (tmm) REVERT: O 69 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8491 (mtt) REVERT: O 111 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8283 (mtp) REVERT: P 20 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9015 (mppt) REVERT: Q 193 MET cc_start: 0.7998 (tmm) cc_final: 0.7440 (tpp) REVERT: R 111 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: R 194 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8122 (tm-30) REVERT: S 84 LEU cc_start: 0.8688 (tp) cc_final: 0.8206 (tp) REVERT: S 86 MET cc_start: 0.8357 (pmm) cc_final: 0.7824 (pmm) REVERT: T 391 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7351 (tm-30) outliers start: 142 outliers final: 116 residues processed: 502 average time/residue: 0.5484 time to fit residues: 472.6746 Evaluate side-chains 497 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 367 time to evaluate : 5.056 ------------------------------------------------------------------------------- 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 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 463 SER Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 64 ILE 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 179 ASP Chi-restraints excluded: chain G residue 254 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 179 ASP Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN 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 C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 179 ASP 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 273 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain H residue 483 GLU Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 66 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 365 LEU 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 131 LEU Chi-restraints excluded: chain L residue 139 SER Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 229 ASN Chi-restraints excluded: chain L residue 231 ARG Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 11 ASP Chi-restraints excluded: chain N residue 48 THR 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 491 MET Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain O residue 69 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 179 ASP 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 P residue 20 LYS 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 179 ASP Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 468 THR 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 91 THR Chi-restraints excluded: chain T residue 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 179 ASP 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 Chi-restraints excluded: chain T residue 502 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 6.9990 chunk 751 optimal weight: 2.9990 chunk 458 optimal weight: 0.6980 chunk 356 optimal weight: 2.9990 chunk 522 optimal weight: 0.7980 chunk 788 optimal weight: 6.9990 chunk 725 optimal weight: 5.9990 chunk 627 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 484 optimal weight: 8.9990 chunk 384 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 479 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1536 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= 0.182 Angle : 0.532 18.317 80845 Z= 0.270 Chirality : 0.042 0.207 9810 Planarity : 0.003 0.061 10514 Dihedral : 7.283 89.955 8911 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.99 % Allowed : 22.18 % Favored : 75.84 % 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: 1.43 (0.09), residues: 7959 helix: 1.98 (0.08), residues: 4144 sheet: -0.03 (0.15), residues: 1078 loop : -0.18 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 401 PHE 0.015 0.001 PHE C 44 TYR 0.013 0.001 TYR T 199 ARG 0.006 0.000 ARG R 231 ********************** REFINEMENT MACRO_CYCLE 10 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 505 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 382 time to evaluate : 5.790 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: I 111 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8248 (mtp) REVERT: I 203 TYR cc_start: 0.8485 (m-80) cc_final: 0.8119 (m-80) REVERT: W 2 ASN cc_start: 0.9279 (t0) cc_final: 0.9057 (t0) REVERT: G 193 MET cc_start: 0.6725 (mmm) cc_final: 0.6128 (mmm) REVERT: G 267 MET cc_start: 0.6576 (ppp) cc_final: 0.6057 (ppp) REVERT: A 111 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8053 (mtp) REVERT: A 194 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: A 288 MET cc_start: 0.8380 (ptt) cc_final: 0.8080 (ptp) REVERT: A 321 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8703 (ptmt) REVERT: B 88 GLU cc_start: 0.9353 (tt0) cc_final: 0.9083 (tt0) REVERT: D 111 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8144 (mtp) REVERT: E 20 LYS cc_start: 0.9225 (ttpp) cc_final: 0.8979 (mppt) REVERT: H 111 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8247 (mtp) REVERT: J 63 ASP cc_start: 0.8180 (t0) cc_final: 0.7202 (p0) REVERT: J 86 MET cc_start: 0.7378 (pmm) cc_final: 0.7068 (pmm) REVERT: K 193 MET cc_start: 0.8231 (tpp) cc_final: 0.6964 (mmm) REVERT: K 365 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5568 (tp) REVERT: L 114 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8426 (mmm) REVERT: M 63 ASP cc_start: 0.8961 (t0) cc_final: 0.7413 (p0) REVERT: M 86 MET cc_start: 0.8371 (pmm) cc_final: 0.7808 (pmm) REVERT: N 193 MET cc_start: 0.7871 (mmm) cc_final: 0.7318 (mmm) REVERT: O 69 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8426 (mtt) REVERT: O 111 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8303 (mtt) REVERT: O 195 PHE cc_start: 0.8359 (p90) cc_final: 0.7968 (p90) REVERT: P 20 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (mppt) REVERT: Q 193 MET cc_start: 0.7988 (tmm) cc_final: 0.7416 (tpp) REVERT: R 111 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: R 194 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: S 84 LEU cc_start: 0.8658 (tp) cc_final: 0.8263 (tp) REVERT: S 86 MET cc_start: 0.8322 (pmm) cc_final: 0.7875 (pmm) outliers start: 123 outliers final: 97 residues processed: 487 average time/residue: 0.5581 time to fit residues: 466.4420 Evaluate side-chains 481 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 371 time to evaluate : 5.079 ------------------------------------------------------------------------------- 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 179 ASP Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 513 LEU Chi-restraints excluded: chain W residue 64 ILE 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 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 179 ASP Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 266 THR 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 B residue 58 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 463 SER Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain F residue 11 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 179 ASP 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 273 VAL Chi-restraints excluded: chain H residue 283 ASP Chi-restraints excluded: chain H residue 307 MET Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 463 SER Chi-restraints excluded: chain H residue 468 THR Chi-restraints excluded: chain J residue 64 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain K residue 131 LEU 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 56 VAL 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 229 ASN Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 283 ASP Chi-restraints excluded: chain L residue 307 MET Chi-restraints excluded: chain L residue 372 LEU Chi-restraints excluded: chain L residue 468 THR Chi-restraints excluded: chain L residue 513 LEU Chi-restraints excluded: chain M residue 64 ILE Chi-restraints excluded: chain N residue 48 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 491 MET Chi-restraints excluded: chain N residue 495 ASP Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain O residue 69 MET Chi-restraints excluded: chain O residue 111 MET Chi-restraints excluded: chain O residue 139 SER Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain O residue 229 ASN Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 463 SER Chi-restraints excluded: chain O residue 513 LEU Chi-restraints excluded: chain P residue 20 LYS Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 131 LEU Chi-restraints excluded: chain Q residue 174 VAL Chi-restraints excluded: chain Q residue 179 ASP Chi-restraints excluded: chain Q residue 183 LEU Chi-restraints excluded: chain Q residue 420 ILE 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 194 GLN Chi-restraints excluded: chain R residue 468 THR 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 131 LEU Chi-restraints excluded: chain T residue 174 VAL Chi-restraints excluded: chain T residue 179 ASP 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 ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.1980 chunk 668 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 578 optimal weight: 1.9990 chunk 92 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 chunk 628 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 645 optimal weight: 50.0000 chunk 79 optimal weight: 0.0050 chunk 115 optimal weight: 0.2980 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 479 ASN ** G 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.060961 restraints weight = 192200.254| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.50 r_work: 0.3014 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 59807 Z= 0.193 Angle : 0.537 18.536 80845 Z= 0.272 Chirality : 0.042 0.205 9810 Planarity : 0.003 0.060 10514 Dihedral : 7.229 88.999 8911 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.92 % Allowed : 22.27 % Favored : 75.80 % 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: 1.47 (0.09), residues: 7959 helix: 2.01 (0.08), residues: 4144 sheet: -0.07 (0.15), residues: 1120 loop : -0.13 (0.12), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS S 7 PHE 0.014 0.001 PHE C 44 TYR 0.013 0.001 TYR T 199 ARG 0.006 0.000 ARG R 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11023.17 seconds wall clock time: 196 minutes 42.34 seconds (11802.34 seconds total)