Starting phenix.real_space_refine on Mon Mar 11 19:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmo_16119/03_2024/8bmo_16119_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmo_16119/03_2024/8bmo_16119.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/8bmo_16119/03_2024/8bmo_16119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmo_16119/03_2024/8bmo_16119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmo_16119/03_2024/8bmo_16119_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmo_16119/03_2024/8bmo_16119_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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 42 5.49 5 Mg 14 5.21 5 S 287 5.16 5 C 36771 2.51 5 N 10234 2.21 5 O 11998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 408": "OE1" <-> "OE2" Residue "I PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 58": "OD1" <-> "OD2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 435": "OD1" <-> "OD2" Residue "E ASP 121": "OD1" <-> "OD2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 328": "OD1" <-> "OD2" Residue "F ASP 435": "OD1" <-> "OD2" Residue "F TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "K TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 328": "OD1" <-> "OD2" Residue "M ASP 435": "OD1" <-> "OD2" Residue "N GLU 39": "OE1" <-> "OE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "P PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 328": "OD1" <-> "OD2" Residue "Q TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59346 Number of models: 1 Model: "" Number of chains: 35 Chain: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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: "E" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" 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: "H" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" 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: "L" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" 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: "O" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" 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: "R" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3849 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3851 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.93, per 1000 atoms: 0.40 Number of scatterers: 59346 At special positions: 0 Unit cell: (154.56, 153.6, 210.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 287 16.00 P 42 15.00 Mg 14 11.99 O 11998 8.00 N 10234 7.00 C 36771 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: 19.97 Conformation dependent library (CDL) restraints added in 8.6 seconds 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14476 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 278 helices and 105 sheets defined 48.9% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.53 Creating SS restraints... Processing helix chain 'C' and resid 10 through 30 removed outlier: 4.909A pdb=" N THR C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 65 through 85 Processing helix chain 'C' and resid 89 through 109 Processing helix chain 'C' and resid 113 through 134 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 156 through 168 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.563A pdb=" N MET C 267 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 339 through 355 Processing helix chain 'C' and resid 359 through 373 Processing helix chain 'C' and resid 386 through 409 Processing helix chain 'C' and resid 417 through 425 Processing helix chain 'C' and resid 434 through 458 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 Processing helix chain 'I' and resid 9 through 30 removed outlier: 3.705A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 5.083A 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: 3.791A pdb=" N GLU I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 4.018A 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 151 Processing helix chain 'I' and resid 156 through 169 Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 257 through 268 Processing helix chain 'I' and resid 285 through 295 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 425 Processing helix chain 'I' and resid 434 through 457 removed outlier: 3.937A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) removed outlier: 4.075A 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 'W' and resid 29 through 31 No H-bonds generated for 'chain 'W' and resid 29 through 31' Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'A' and resid 10 through 30 removed outlier: 4.877A pdb=" N THR A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 85 Processing helix chain 'A' and resid 89 through 109 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 151 Processing helix chain 'A' and resid 156 through 168 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 256 through 268 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 309 through 311 No H-bonds generated for 'chain 'A' and resid 309 through 311' Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 386 through 409 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 434 through 458 Proline residue: A 450 - end of helix Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 497 through 515 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.710A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 84 removed outlier: 4.069A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 108 Processing helix chain 'B' and resid 113 through 134 Processing helix chain 'B' and resid 141 through 151 Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.578A pdb=" N LEU B 234 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.507A pdb=" N GLU B 238 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 285 through 296 Processing helix chain 'B' and resid 339 through 355 Processing helix chain 'B' and resid 359 through 372 Processing helix chain 'B' and resid 386 through 409 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 434 through 458 removed outlier: 3.925A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 10 through 30 removed outlier: 4.881A pdb=" N THR E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 65 through 85 Processing helix chain 'E' and resid 89 through 109 Processing helix chain 'E' and resid 113 through 134 Processing helix chain 'E' and resid 141 through 151 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 339 through 355 Processing helix chain 'E' and resid 359 through 373 Processing helix chain 'E' and resid 386 through 409 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 434 through 458 Proline residue: E 450 - end of helix Processing helix chain 'E' and resid 462 through 471 Processing helix chain 'E' and resid 497 through 515 Processing helix chain 'F' and resid 9 through 30 removed outlier: 3.716A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 5.009A 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: 4.062A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.973A 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 151 Processing helix chain 'F' and resid 156 through 169 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 234 through 243 Processing helix chain 'F' and resid 257 through 268 Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 339 through 355 Processing helix chain 'F' and resid 359 through 372 Processing helix chain 'F' and resid 386 through 409 Processing helix chain 'F' and resid 417 through 425 Processing helix chain 'F' and resid 434 through 458 removed outlier: 3.940A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) removed outlier: 4.044A 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 515 Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'H' and resid 9 through 30 removed outlier: 4.944A pdb=" N THR H 30 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 65 through 85 Processing helix chain 'H' and resid 89 through 109 Processing helix chain 'H' and resid 113 through 134 Processing helix chain 'H' and resid 141 through 151 Processing helix chain 'H' and resid 156 through 168 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 257 through 268 Processing helix chain 'H' and resid 283 through 296 Processing helix chain 'H' and resid 309 through 311 No H-bonds generated for 'chain 'H' and resid 309 through 311' Processing helix chain 'H' and resid 339 through 355 Processing helix chain 'H' and resid 359 through 373 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 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 'J' and resid 9 through 30 removed outlier: 3.729A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N THR J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 65 through 84 removed outlier: 4.164A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 108 Processing helix chain 'J' and resid 113 through 134 Processing helix chain 'J' and resid 141 through 151 Processing helix chain 'J' and resid 156 through 169 Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 234 through 243 Processing helix chain 'J' and resid 257 through 268 Processing helix chain 'J' and resid 285 through 296 Processing helix chain 'J' and resid 339 through 355 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 386 through 409 Processing helix chain 'J' and resid 417 through 425 Processing helix chain 'J' and resid 434 through 458 removed outlier: 3.937A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA J 449 " --> pdb=" O ARG J 445 " (cutoff:3.500A) Proline residue: J 450 - end of helix Processing helix chain 'J' and resid 462 through 471 Processing helix chain 'J' and resid 497 through 515 Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'L' and resid 10 through 30 removed outlier: 4.910A 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 85 Processing helix chain 'L' and resid 89 through 109 Processing helix chain 'L' and resid 113 through 134 Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 156 through 169 Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 234 through 243 Processing helix chain 'L' and resid 257 through 268 Processing helix chain 'L' and resid 283 through 296 Processing helix chain 'L' and resid 309 through 311 No H-bonds generated for 'chain 'L' and resid 309 through 311' Processing helix chain 'L' and resid 339 through 355 Processing helix chain 'L' and resid 359 through 374 Processing helix chain 'L' and resid 386 through 409 Processing helix chain 'L' and resid 417 through 425 Processing helix chain 'L' and resid 434 through 458 Proline residue: L 450 - end of helix Processing helix chain 'L' and resid 462 through 471 Processing helix chain 'L' and resid 497 through 516 Processing helix chain 'M' and resid 9 through 30 removed outlier: 3.718A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 65 through 84 removed outlier: 4.026A pdb=" N VAL M 77 " --> pdb=" O MET M 73 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 108 Processing helix chain 'M' and resid 113 through 134 Processing helix chain 'M' and resid 141 through 151 Processing helix chain 'M' and resid 156 through 169 Processing helix chain 'M' and resid 202 through 204 No H-bonds generated for 'chain 'M' and resid 202 through 204' Processing helix chain 'M' and resid 234 through 243 Processing helix chain 'M' and resid 257 through 268 Processing helix chain 'M' and resid 285 through 295 Processing helix chain 'M' and resid 339 through 355 Processing helix chain 'M' and resid 359 through 372 Processing helix chain 'M' and resid 386 through 409 Processing helix chain 'M' and resid 417 through 425 Processing helix chain 'M' and resid 434 through 458 removed outlier: 3.983A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA M 449 " --> pdb=" O ARG M 445 " (cutoff:3.500A) Proline residue: M 450 - end of helix Processing helix chain 'M' and resid 462 through 471 Processing helix chain 'M' and resid 497 through 515 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'O' and resid 9 through 30 removed outlier: 4.951A 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 85 Processing helix chain 'O' and resid 89 through 109 Processing helix chain 'O' and resid 113 through 134 Processing helix chain 'O' and resid 141 through 151 Processing helix chain 'O' and resid 156 through 168 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 removed outlier: 4.321A pdb=" N THR O 261 " --> pdb=" O ALA O 258 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 296 Processing helix chain 'O' and resid 309 through 311 No H-bonds generated for 'chain 'O' and resid 309 through 311' Processing helix chain 'O' and resid 339 through 355 Processing helix chain 'O' and resid 359 through 374 Processing helix chain 'O' and resid 386 through 409 Processing helix chain 'O' and resid 417 through 425 Processing helix chain 'O' and resid 434 through 458 Proline residue: O 450 - end of helix Processing helix chain 'O' and resid 462 through 471 Processing helix chain 'O' and resid 488 through 491 No H-bonds generated for 'chain 'O' and resid 488 through 491' Processing helix chain 'O' and resid 497 through 516 Processing helix chain 'P' and resid 9 through 30 removed outlier: 3.682A pdb=" N VAL P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR P 30 " --> pdb=" O ALA P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 59 Processing helix chain 'P' and resid 65 through 84 removed outlier: 4.163A pdb=" N VAL P 77 " --> pdb=" O MET P 73 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA P 78 " --> pdb=" O VAL P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 108 Processing helix chain 'P' and resid 113 through 134 Processing helix chain 'P' and resid 141 through 151 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'P' and resid 202 through 204 No H-bonds generated for 'chain 'P' and resid 202 through 204' Processing helix chain 'P' and resid 234 through 243 Processing helix chain 'P' and resid 256 through 268 Processing helix chain 'P' and resid 285 through 296 Processing helix chain 'P' and resid 339 through 355 Processing helix chain 'P' and resid 359 through 372 Processing helix chain 'P' and resid 386 through 409 Processing helix chain 'P' and resid 417 through 425 Processing helix chain 'P' and resid 434 through 458 removed outlier: 3.946A pdb=" N GLU P 448 " --> pdb=" O LEU P 444 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA P 449 " --> pdb=" O ARG P 445 " (cutoff:3.500A) Proline residue: P 450 - end of helix Processing helix chain 'P' and resid 462 through 471 Processing helix chain 'P' and resid 497 through 515 Processing helix chain 'Q' and resid 29 through 31 No H-bonds generated for 'chain 'Q' and resid 29 through 31' Processing helix chain 'Q' and resid 88 through 90 No H-bonds generated for 'chain 'Q' and resid 88 through 90' Processing helix chain 'R' and resid 10 through 30 removed outlier: 4.851A 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 85 Processing helix chain 'R' and resid 89 through 109 Processing helix chain 'R' and resid 113 through 134 Processing helix chain 'R' and resid 141 through 151 Processing helix chain 'R' and resid 156 through 168 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 257 through 268 Processing helix chain 'R' and resid 283 through 296 Processing helix chain 'R' and resid 309 through 311 No H-bonds generated for 'chain 'R' and resid 309 through 311' Processing helix chain 'R' and resid 339 through 355 Processing helix chain 'R' and resid 359 through 374 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 Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 462 through 471 Processing helix chain 'R' and resid 488 through 491 No H-bonds generated for 'chain 'R' and resid 488 through 491' Processing helix chain 'R' and resid 497 through 516 Processing helix chain 'S' and resid 9 through 30 removed outlier: 3.737A pdb=" N VAL S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR S 30 " --> pdb=" O ALA S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 59 Processing helix chain 'S' and resid 65 through 84 removed outlier: 3.788A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL S 77 " --> pdb=" O MET S 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 108 Processing helix chain 'S' and resid 113 through 134 Processing helix chain 'S' and resid 141 through 151 Processing helix chain 'S' and resid 156 through 169 Processing helix chain 'S' and resid 202 through 204 No H-bonds generated for 'chain 'S' and resid 202 through 204' Processing helix chain 'S' and resid 234 through 243 Processing helix chain 'S' and resid 256 through 268 Processing helix chain 'S' and resid 285 through 296 Processing helix chain 'S' and resid 309 through 311 No H-bonds generated for 'chain 'S' and resid 309 through 311' Processing helix chain 'S' and resid 339 through 355 Processing helix chain 'S' and resid 359 through 372 Processing helix chain 'S' and resid 386 through 409 Processing helix chain 'S' and resid 417 through 425 Processing helix chain 'S' and resid 434 through 457 removed outlier: 3.929A pdb=" N GLU S 448 " --> pdb=" O LEU S 444 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA S 449 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Proline residue: S 450 - end of helix Processing helix chain 'S' and resid 462 through 471 Processing helix chain 'S' and resid 488 through 491 No H-bonds generated for 'chain 'S' and resid 488 through 491' Processing helix chain 'S' and resid 497 through 515 Processing helix chain 'T' and resid 29 through 31 No H-bonds generated for 'chain 'T' and resid 29 through 31' Processing helix chain 'T' and resid 88 through 90 No H-bonds generated for 'chain 'T' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'C' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'C' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'C' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'C' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'C' and resid 219 through 221 Processing sheet with id= F, first strand: chain 'C' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'C' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'I' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'I' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'I' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'I' and resid 213 through 216 Processing sheet with id= L, first strand: chain 'I' and resid 219 through 223 removed outlier: 3.608A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'I' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'W' and resid 74 through 78 removed outlier: 7.910A pdb=" N GLU W 82 " --> pdb=" O ARG W 14 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG W 14 " --> pdb=" O GLU W 82 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS W 13 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL W 40 " --> pdb=" O LYS W 13 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE W 64 " --> pdb=" O VAL W 95 " (cutoff:3.500A) 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 193 through 195 Processing sheet with id= T, first strand: chain 'A' and resid 219 through 221 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 4 through 8 Processing sheet with id= X, first strand: chain 'B' and resid 38 through 40 Processing sheet with id= Y, first strand: chain 'B' and resid 174 through 179 Processing sheet with id= Z, first strand: chain 'B' and resid 213 through 216 Processing sheet with id= AA, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.567A pdb=" N ALA B 251 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 411 through 413 Processing sheet with id= AC, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= AD, first strand: chain 'D' and resid 74 through 77 removed outlier: 7.780A pdb=" N GLU D 82 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG D 14 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS D 13 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL D 40 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 4 through 8 Processing sheet with id= AF, first strand: chain 'E' and resid 38 through 40 Processing sheet with id= AG, first strand: chain 'E' and resid 174 through 179 Processing sheet with id= AH, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= AI, first strand: chain 'E' and resid 219 through 221 Processing sheet with id= AJ, first strand: chain 'E' and resid 411 through 413 Processing sheet with id= AK, first strand: chain 'E' and resid 476 through 479 Processing sheet with id= AL, first strand: chain 'F' and resid 4 through 8 Processing sheet with id= AM, first strand: chain 'F' and resid 38 through 40 Processing sheet with id= AN, first strand: chain 'F' and resid 174 through 179 Processing sheet with id= AO, first strand: chain 'F' and resid 213 through 216 Processing sheet with id= AP, first strand: chain 'F' and resid 219 through 223 removed outlier: 3.537A pdb=" N ALA F 251 " --> pdb=" O VAL F 276 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'F' and resid 411 through 413 Processing sheet with id= AR, first strand: chain 'F' and resid 476 through 479 Processing sheet with id= AS, first strand: chain 'G' and resid 74 through 78 removed outlier: 7.868A pdb=" N GLU G 82 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ARG G 14 " --> pdb=" O GLU G 82 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS G 13 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL G 40 " --> pdb=" O LYS G 13 " (cutoff:3.500A) 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 193 through 195 Processing sheet with id= AX, first strand: chain 'H' and resid 219 through 221 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 4 through 8 Processing sheet with id= BB, first strand: chain 'J' and resid 38 through 40 Processing sheet with id= BC, first strand: chain 'J' and resid 174 through 179 Processing sheet with id= BD, first strand: chain 'J' and resid 213 through 216 Processing sheet with id= BE, first strand: chain 'J' and resid 219 through 223 removed outlier: 3.629A pdb=" N ALA J 251 " --> pdb=" O VAL J 276 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'J' and resid 411 through 413 Processing sheet with id= BG, first strand: chain 'J' and resid 476 through 479 Processing sheet with id= BH, first strand: chain 'K' and resid 74 through 78 removed outlier: 8.008A pdb=" N GLU K 82 " --> pdb=" O ARG K 14 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ARG K 14 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS K 13 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL K 40 " --> pdb=" O LYS K 13 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'L' and resid 4 through 8 Processing sheet with id= BJ, first strand: chain 'L' and resid 38 through 40 Processing sheet with id= BK, first strand: chain 'L' and resid 174 through 179 Processing sheet with id= BL, first strand: chain 'L' and resid 193 through 195 Processing sheet with id= BM, first strand: chain 'L' and resid 219 through 222 Processing sheet with id= BN, first strand: chain 'L' and resid 411 through 413 Processing sheet with id= BO, first strand: chain 'L' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'M' and resid 4 through 8 Processing sheet with id= BQ, first strand: chain 'M' and resid 38 through 40 Processing sheet with id= BR, first strand: chain 'M' and resid 174 through 179 Processing sheet with id= BS, first strand: chain 'M' and resid 213 through 216 Processing sheet with id= BT, first strand: chain 'M' and resid 219 through 222 removed outlier: 3.602A pdb=" N ALA M 251 " --> pdb=" O VAL M 276 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'M' and resid 411 through 413 Processing sheet with id= BV, first strand: chain 'M' and resid 476 through 479 Processing sheet with id= BW, first strand: chain 'N' and resid 74 through 78 removed outlier: 7.903A pdb=" N GLU N 82 " --> pdb=" O ARG N 14 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG N 14 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS N 13 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N VAL N 40 " --> pdb=" O LYS N 13 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'O' and resid 4 through 8 Processing sheet with id= BY, first strand: chain 'O' and resid 38 through 40 Processing sheet with id= BZ, first strand: chain 'O' and resid 174 through 179 removed outlier: 3.535A pdb=" N VAL O 381 " --> pdb=" O GLU O 178 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'O' and resid 193 through 195 Processing sheet with id= CB, first strand: chain 'O' and resid 219 through 221 Processing sheet with id= CC, first strand: chain 'O' and resid 411 through 413 Processing sheet with id= CD, first strand: chain 'O' and resid 476 through 479 Processing sheet with id= CE, first strand: chain 'P' and resid 4 through 8 Processing sheet with id= CF, first strand: chain 'P' and resid 38 through 40 Processing sheet with id= CG, first strand: chain 'P' and resid 174 through 179 Processing sheet with id= CH, first strand: chain 'P' and resid 213 through 216 Processing sheet with id= CI, first strand: chain 'P' and resid 219 through 222 Processing sheet with id= CJ, first strand: chain 'P' and resid 411 through 413 Processing sheet with id= CK, first strand: chain 'P' and resid 476 through 479 Processing sheet with id= CL, first strand: chain 'Q' and resid 74 through 78 removed outlier: 7.997A pdb=" N GLU Q 82 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG Q 14 " --> pdb=" O GLU Q 82 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS Q 13 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL Q 40 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA Q 93 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'R' and resid 4 through 8 Processing sheet with id= CN, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= CO, first strand: chain 'R' and resid 174 through 179 Processing sheet with id= CP, first strand: chain 'R' and resid 213 through 216 Processing sheet with id= CQ, first strand: chain 'R' and resid 219 through 221 Processing sheet with id= CR, first strand: chain 'R' and resid 411 through 413 Processing sheet with id= CS, first strand: chain 'R' and resid 476 through 479 Processing sheet with id= CT, first strand: chain 'S' and resid 4 through 8 Processing sheet with id= CU, first strand: chain 'S' and resid 38 through 40 Processing sheet with id= CV, first strand: chain 'S' and resid 174 through 179 Processing sheet with id= CW, first strand: chain 'S' and resid 193 through 195 removed outlier: 3.833A pdb=" N MET S 193 " --> pdb=" O ILE S 332 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'S' and resid 219 through 222 Processing sheet with id= CY, first strand: chain 'S' and resid 411 through 413 Processing sheet with id= CZ, first strand: chain 'S' and resid 476 through 479 Processing sheet with id= DA, first strand: chain 'T' and resid 74 through 78 removed outlier: 7.951A pdb=" N GLU T 82 " --> pdb=" O ARG T 14 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ARG T 14 " --> pdb=" O GLU T 82 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS T 13 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL T 40 " --> pdb=" O LYS T 13 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE T 64 " --> pdb=" O VAL T 95 " (cutoff:3.500A) 3442 hydrogen bonds defined for protein. 9825 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: 23.23 Time building geometry restraints manager: 21.80 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: 20352 1.34 - 1.46: 5735 1.46 - 1.58: 33108 1.58 - 1.70: 53 1.70 - 1.82: 532 Bond restraints: 59780 Sorted by residual: bond pdb=" N GLY M 192 " pdb=" CA GLY M 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.11e+00 bond pdb=" N GLY B 192 " pdb=" CA GLY B 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.05e+00 bond pdb=" N GLY F 192 " pdb=" CA GLY F 192 " ideal model delta sigma weight residual 1.452 1.474 -0.022 1.52e-02 4.33e+03 2.04e+00 bond pdb=" CA GLY B 192 " pdb=" C GLY B 192 " ideal model delta sigma weight residual 1.514 1.534 -0.019 1.35e-02 5.49e+03 2.00e+00 bond pdb=" N GLY J 192 " pdb=" CA GLY J 192 " ideal model delta sigma weight residual 1.448 1.474 -0.026 1.88e-02 2.83e+03 1.99e+00 ... (remaining 59775 not shown) Histogram of bond angle deviations from ideal: 96.72 - 105.33: 980 105.33 - 113.95: 36266 113.95 - 122.57: 37019 122.57 - 131.18: 6505 131.18 - 139.80: 52 Bond angle restraints: 80822 Sorted by residual: angle pdb=" C THR C 266 " pdb=" N MET C 267 " pdb=" CA MET C 267 " ideal model delta sigma weight residual 120.68 113.97 6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CA MET P 267 " pdb=" CB MET P 267 " pdb=" CG MET P 267 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CA MET C 267 " pdb=" CB MET C 267 " pdb=" CG MET C 267 " ideal model delta sigma weight residual 114.10 121.65 -7.55 2.00e+00 2.50e-01 1.43e+01 angle pdb=" N ILE J 230 " pdb=" CA ILE J 230 " pdb=" C ILE J 230 " ideal model delta sigma weight residual 112.96 109.19 3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N ILE S 230 " pdb=" CA ILE S 230 " pdb=" C ILE S 230 " ideal model delta sigma weight residual 113.42 109.08 4.34 1.17e+00 7.31e-01 1.38e+01 ... (remaining 80817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 32927 17.87 - 35.74: 3219 35.74 - 53.60: 851 53.60 - 71.47: 238 71.47 - 89.34: 61 Dihedral angle restraints: 37296 sinusoidal: 14728 harmonic: 22568 Sorted by residual: dihedral pdb=" CA ILE M 230 " pdb=" C ILE M 230 " pdb=" N ARG M 231 " pdb=" CA ARG M 231 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA THR E 266 " pdb=" C THR E 266 " pdb=" N MET E 267 " pdb=" CA MET E 267 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR H 266 " pdb=" C THR H 266 " pdb=" N MET H 267 " pdb=" CA MET H 267 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 37293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 9363 0.100 - 0.200: 448 0.200 - 0.300: 2 0.300 - 0.400: 0 0.400 - 0.500: 1 Chirality restraints: 9814 Sorted by residual: chirality pdb=" CG LEU C 215 " pdb=" CB LEU C 215 " pdb=" CD1 LEU C 215 " pdb=" CD2 LEU C 215 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.25e+00 chirality pdb=" CB ILE K 25 " pdb=" CA ILE K 25 " pdb=" CG1 ILE K 25 " pdb=" CG2 ILE K 25 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA MET C 267 " pdb=" N MET C 267 " pdb=" C MET C 267 " pdb=" CB MET C 267 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 9811 not shown) Planarity restraints: 10507 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA J 260 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C ALA J 260 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA J 260 " -0.011 2.00e-02 2.50e+03 pdb=" N THR J 261 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 283 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C ASP B 283 " -0.026 2.00e-02 2.50e+03 pdb=" O ASP B 283 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 284 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 121 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" CG ASP H 121 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP H 121 " -0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP H 121 " -0.009 2.00e-02 2.50e+03 ... (remaining 10504 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 487 2.52 - 3.12: 46953 3.12 - 3.71: 101261 3.71 - 4.31: 136941 4.31 - 4.90: 229755 Nonbonded interactions: 515397 Sorted by model distance: nonbonded pdb="MG MG R 601 " pdb=" O1A ATP R 602 " model vdw 1.931 2.170 nonbonded pdb="MG MG L 601 " pdb=" O1A ATP L 602 " model vdw 1.942 2.170 nonbonded pdb="MG MG R 601 " pdb=" O1G ATP R 602 " model vdw 1.954 2.170 nonbonded pdb="MG MG H 601 " pdb=" O1A ATP H 602 " model vdw 1.956 2.170 nonbonded pdb="MG MG A 601 " pdb=" O1A ATP A 602 " model vdw 1.960 2.170 ... (remaining 515392 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 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'B' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'C' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'E' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'F' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'H' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'I' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'J' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'L' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'M' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'O' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'P' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) selection = (chain 'R' and (resid 2 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 525 or resid 601 through 602)) selection = (chain 'S' and (resid 2 through 196 or (resid 197 and (name N or name CA or name \ C or name O or name CB )) or resid 198 through 525 or resid 601 through 602)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.660 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: 13.700 Check model and map are aligned: 0.650 Set scattering table: 0.430 Process input model: 129.140 Find NCS groups from input model: 3.750 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 59780 Z= 0.243 Angle : 0.555 11.114 80822 Z= 0.298 Chirality : 0.044 0.500 9814 Planarity : 0.003 0.031 10507 Dihedral : 16.091 89.342 22820 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.13 % Allowed : 15.34 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 7966 helix: 1.72 (0.08), residues: 4228 sheet: 1.13 (0.17), residues: 875 loop : -0.51 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 401 PHE 0.010 0.001 PHE S 195 TYR 0.011 0.001 TYR K 71 ARG 0.004 0.000 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 643 time to evaluate : 5.169 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: C 233 MET cc_start: 0.7423 (pmm) cc_final: 0.6974 (pmm) REVERT: I 267 MET cc_start: 0.7901 (mpt) cc_final: 0.7603 (mpt) REVERT: W 51 ASN cc_start: 0.8976 (p0) cc_final: 0.8676 (p0) REVERT: W 55 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8379 (ptpt) REVERT: W 76 GLU cc_start: 0.8288 (tp30) cc_final: 0.8010 (tp30) REVERT: W 87 SER cc_start: 0.8837 (m) cc_final: 0.8475 (t) REVERT: A 219 PHE cc_start: 0.9034 (m-80) cc_final: 0.8574 (m-80) REVERT: A 233 MET cc_start: 0.8996 (pmm) cc_final: 0.8658 (pmm) REVERT: D 16 GLU cc_start: 0.8302 (pp20) cc_final: 0.7705 (pp20) REVERT: D 50 GLU cc_start: 0.7476 (pm20) cc_final: 0.7147 (pm20) REVERT: D 51 ASN cc_start: 0.8696 (p0) cc_final: 0.8399 (p0) REVERT: D 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.7890 (tp30) REVERT: E 193 MET cc_start: 0.7665 (ppp) cc_final: 0.7366 (ppp) REVERT: E 233 MET cc_start: 0.8381 (pmm) cc_final: 0.7557 (pmm) REVERT: G 51 ASN cc_start: 0.8782 (p0) cc_final: 0.8458 (p0) REVERT: G 58 ASP cc_start: 0.8490 (t70) cc_final: 0.8158 (t0) REVERT: G 76 GLU cc_start: 0.8236 (tp30) cc_final: 0.7882 (tp30) REVERT: H 219 PHE cc_start: 0.8972 (m-80) cc_final: 0.8374 (m-80) REVERT: K 51 ASN cc_start: 0.8829 (p0) cc_final: 0.8442 (p0) REVERT: K 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.8004 (tp30) REVERT: L 219 PHE cc_start: 0.8952 (m-80) cc_final: 0.8440 (m-80) REVERT: N 76 GLU cc_start: 0.8445 (tp30) cc_final: 0.8017 (tp30) REVERT: N 88 GLU cc_start: 0.8476 (pp20) cc_final: 0.8228 (tm-30) REVERT: Q 39 GLU cc_start: 0.8319 (pm20) cc_final: 0.7987 (pm20) REVERT: Q 51 ASN cc_start: 0.9104 (p0) cc_final: 0.8714 (p0) REVERT: Q 60 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8652 (mmtm) REVERT: R 193 MET cc_start: 0.7947 (ppp) cc_final: 0.7468 (ppp) REVERT: R 215 LEU cc_start: 0.8714 (mp) cc_final: 0.8281 (mt) REVERT: R 219 PHE cc_start: 0.8951 (m-80) cc_final: 0.8176 (m-80) REVERT: R 389 MET cc_start: 0.2516 (mmm) cc_final: 0.2206 (mmm) REVERT: T 16 GLU cc_start: 0.8329 (pp20) cc_final: 0.7824 (pp20) REVERT: T 20 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8610 (mtpp) REVERT: T 58 ASP cc_start: 0.8629 (m-30) cc_final: 0.8283 (t70) REVERT: T 60 LYS cc_start: 0.8753 (mptt) cc_final: 0.8549 (mptt) REVERT: T 76 GLU cc_start: 0.8152 (tp30) cc_final: 0.7804 (tp30) REVERT: T 77 LYS cc_start: 0.9087 (ptmm) cc_final: 0.8816 (tttp) outliers start: 8 outliers final: 4 residues processed: 647 average time/residue: 0.6044 time to fit residues: 658.8667 Evaluate side-chains 590 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 586 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain S residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.8980 chunk 599 optimal weight: 7.9990 chunk 332 optimal weight: 0.0010 chunk 204 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 chunk 320 optimal weight: 4.9990 chunk 619 optimal weight: 3.9990 chunk 239 optimal weight: 7.9990 chunk 376 optimal weight: 10.0000 chunk 461 optimal weight: 0.9980 chunk 718 optimal weight: 9.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 ASN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 59780 Z= 0.187 Angle : 0.474 9.693 80822 Z= 0.255 Chirality : 0.042 0.222 9814 Planarity : 0.003 0.030 10507 Dihedral : 8.778 89.485 8918 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.54 % Allowed : 15.09 % Favored : 83.37 % 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: 1.42 (0.09), residues: 7966 helix: 1.93 (0.08), residues: 4214 sheet: 0.71 (0.16), residues: 1015 loop : -0.49 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 7 PHE 0.011 0.001 PHE C 219 TYR 0.016 0.001 TYR O 199 ARG 0.004 0.000 ARG W 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 617 time to evaluate : 5.220 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: C 215 LEU cc_start: 0.7252 (mm) cc_final: 0.7000 (mm) REVERT: C 233 MET cc_start: 0.7629 (pmm) cc_final: 0.7274 (pmm) REVERT: I 267 MET cc_start: 0.7962 (mpt) cc_final: 0.7559 (mpt) REVERT: I 309 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7970 (mt) REVERT: W 27 LEU cc_start: 0.8717 (mt) cc_final: 0.8506 (tp) REVERT: W 55 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8357 (ptpt) REVERT: W 76 GLU cc_start: 0.8581 (tp30) cc_final: 0.7626 (tp30) REVERT: W 87 SER cc_start: 0.8856 (m) cc_final: 0.8522 (t) REVERT: A 219 PHE cc_start: 0.9055 (m-80) cc_final: 0.8628 (m-80) REVERT: B 267 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7611 (mpt) REVERT: B 309 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7952 (mt) REVERT: D 16 GLU cc_start: 0.8486 (pp20) cc_final: 0.7774 (pp20) REVERT: D 50 GLU cc_start: 0.7473 (pm20) cc_final: 0.7152 (pm20) REVERT: D 51 ASN cc_start: 0.8619 (p0) cc_final: 0.8351 (p0) REVERT: D 76 GLU cc_start: 0.8290 (tp30) cc_final: 0.8043 (tp30) REVERT: F 267 MET cc_start: 0.7970 (mpp) cc_final: 0.7642 (mpp) REVERT: F 309 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7791 (mt) REVERT: G 20 LYS cc_start: 0.8557 (ttmm) cc_final: 0.7814 (mmmm) REVERT: G 51 ASN cc_start: 0.8775 (p0) cc_final: 0.8452 (p0) REVERT: G 58 ASP cc_start: 0.8488 (t70) cc_final: 0.8210 (t0) REVERT: G 76 GLU cc_start: 0.8380 (tp30) cc_final: 0.7827 (tp30) REVERT: G 77 LYS cc_start: 0.8976 (tttp) cc_final: 0.8741 (tttp) REVERT: H 219 PHE cc_start: 0.8970 (m-80) cc_final: 0.8380 (m-80) REVERT: H 295 LEU cc_start: 0.9287 (mt) cc_final: 0.9064 (tp) REVERT: J 309 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7810 (mp) REVERT: K 39 GLU cc_start: 0.8286 (pm20) cc_final: 0.8076 (pm20) REVERT: K 51 ASN cc_start: 0.8829 (p0) cc_final: 0.8423 (p0) REVERT: K 76 GLU cc_start: 0.8565 (tp30) cc_final: 0.7691 (tp30) REVERT: L 219 PHE cc_start: 0.8941 (m-80) cc_final: 0.8511 (m-80) REVERT: M 267 MET cc_start: 0.8005 (mpp) cc_final: 0.7593 (mpp) REVERT: N 76 GLU cc_start: 0.8680 (tp30) cc_final: 0.7814 (tp30) REVERT: N 77 LYS cc_start: 0.8819 (tttm) cc_final: 0.8440 (tptp) REVERT: P 214 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: P 229 ASN cc_start: 0.6900 (t0) cc_final: 0.6539 (t0) REVERT: Q 51 ASN cc_start: 0.9015 (p0) cc_final: 0.8629 (p0) REVERT: Q 58 ASP cc_start: 0.8375 (t0) cc_final: 0.8101 (t0) REVERT: R 219 PHE cc_start: 0.8980 (m-80) cc_final: 0.8221 (m-80) REVERT: S 267 MET cc_start: 0.7798 (mpt) cc_final: 0.7462 (mpt) REVERT: T 20 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8693 (mtpp) REVERT: T 58 ASP cc_start: 0.8606 (m-30) cc_final: 0.8355 (m-30) REVERT: T 76 GLU cc_start: 0.8319 (tp30) cc_final: 0.7431 (tp30) REVERT: T 77 LYS cc_start: 0.9087 (ptmm) cc_final: 0.8765 (tttp) REVERT: T 88 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8261 (tm-30) outliers start: 95 outliers final: 33 residues processed: 689 average time/residue: 0.5724 time to fit residues: 671.9082 Evaluate side-chains 620 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 581 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 214 GLU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 0.3980 chunk 222 optimal weight: 20.0000 chunk 597 optimal weight: 30.0000 chunk 489 optimal weight: 40.0000 chunk 198 optimal weight: 10.0000 chunk 719 optimal weight: 4.9990 chunk 777 optimal weight: 5.9990 chunk 640 optimal weight: 10.0000 chunk 713 optimal weight: 50.0000 chunk 245 optimal weight: 10.0000 chunk 577 optimal weight: 0.9990 overall best weight: 4.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN B 112 ASN B 194 GLN ** B 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN ** J 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 2 ASN ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 59780 Z= 0.479 Angle : 0.579 10.615 80822 Z= 0.309 Chirality : 0.047 0.202 9814 Planarity : 0.004 0.036 10507 Dihedral : 9.283 89.499 8911 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.51 % Allowed : 15.29 % Favored : 82.20 % 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: 0.96 (0.09), residues: 7966 helix: 1.49 (0.08), residues: 4235 sheet: 0.33 (0.17), residues: 987 loop : -0.51 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS W 7 PHE 0.010 0.001 PHE J 195 TYR 0.015 0.002 TYR S 199 ARG 0.005 0.000 ARG T 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 618 time to evaluate : 5.258 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: C 389 MET cc_start: 0.3262 (mmm) cc_final: 0.2949 (mmm) REVERT: I 267 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7626 (mpt) REVERT: I 309 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7944 (mt) REVERT: W 51 ASN cc_start: 0.9043 (p0) cc_final: 0.8611 (p0) REVERT: W 76 GLU cc_start: 0.8411 (tp30) cc_final: 0.7604 (tp30) REVERT: A 121 ASP cc_start: 0.6872 (t0) cc_final: 0.6615 (t0) REVERT: A 219 PHE cc_start: 0.9074 (m-80) cc_final: 0.8601 (m-80) REVERT: B 309 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7996 (mt) REVERT: D 15 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7657 (mtmt) REVERT: D 50 GLU cc_start: 0.7616 (pm20) cc_final: 0.7228 (pm20) REVERT: D 51 ASN cc_start: 0.8598 (p0) cc_final: 0.8333 (p0) REVERT: D 76 GLU cc_start: 0.8555 (tp30) cc_final: 0.7964 (tp30) REVERT: E 121 ASP cc_start: 0.6521 (t0) cc_final: 0.6267 (t0) REVERT: E 514 MET cc_start: 0.8481 (mtm) cc_final: 0.8170 (mtm) REVERT: F 267 MET cc_start: 0.8009 (mpp) cc_final: 0.7708 (mpp) REVERT: F 309 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7846 (mt) REVERT: G 20 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8158 (mmmm) REVERT: G 51 ASN cc_start: 0.8752 (p0) cc_final: 0.8443 (p0) REVERT: G 58 ASP cc_start: 0.8547 (t70) cc_final: 0.8217 (t0) REVERT: G 76 GLU cc_start: 0.8461 (tp30) cc_final: 0.7866 (tp30) REVERT: G 77 LYS cc_start: 0.8936 (tttp) cc_final: 0.8680 (tttp) REVERT: H 114 MET cc_start: 0.8404 (mmt) cc_final: 0.8150 (mmt) REVERT: H 219 PHE cc_start: 0.9001 (m-80) cc_final: 0.8445 (m-80) REVERT: H 447 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: J 309 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7857 (mp) REVERT: K 51 ASN cc_start: 0.8743 (p0) cc_final: 0.8440 (p0) REVERT: K 76 GLU cc_start: 0.8454 (tp30) cc_final: 0.7900 (tp30) REVERT: L 219 PHE cc_start: 0.9019 (m-80) cc_final: 0.8499 (m-80) REVERT: M 267 MET cc_start: 0.8043 (mpp) cc_final: 0.7663 (mpt) REVERT: N 76 GLU cc_start: 0.8416 (tp30) cc_final: 0.7870 (tp30) REVERT: N 77 LYS cc_start: 0.8825 (tttm) cc_final: 0.8500 (tptp) REVERT: O 195 PHE cc_start: 0.8640 (p90) cc_final: 0.8389 (p90) REVERT: O 447 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: P 214 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: Q 76 GLU cc_start: 0.8365 (tp30) cc_final: 0.7558 (tp30) REVERT: R 121 ASP cc_start: 0.6419 (t0) cc_final: 0.6212 (t0) REVERT: R 215 LEU cc_start: 0.8740 (mp) cc_final: 0.8288 (mt) REVERT: R 219 PHE cc_start: 0.9014 (m-80) cc_final: 0.8448 (m-80) REVERT: R 233 MET cc_start: 0.8975 (pmm) cc_final: 0.8725 (pmm) REVERT: R 295 LEU cc_start: 0.9351 (mt) cc_final: 0.9031 (tp) REVERT: S 267 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7515 (mpt) REVERT: S 309 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7929 (mt) REVERT: S 483 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: T 20 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8703 (mtpp) REVERT: T 58 ASP cc_start: 0.8551 (m-30) cc_final: 0.8320 (t70) REVERT: T 76 GLU cc_start: 0.8117 (tp30) cc_final: 0.7478 (tp30) outliers start: 155 outliers final: 86 residues processed: 723 average time/residue: 0.5425 time to fit residues: 674.7392 Evaluate side-chains 683 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 586 time to evaluate : 5.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 435 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 199 TYR Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 114 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 433 ASN Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 185 ASP Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 199 TYR Chi-restraints excluded: chain P residue 214 GLU Chi-restraints excluded: chain P residue 233 MET Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 64 ILE Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 233 MET Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 372 LEU Chi-restraints excluded: chain S residue 483 GLU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain T residue 75 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 6.9990 chunk 541 optimal weight: 9.9990 chunk 373 optimal weight: 40.0000 chunk 79 optimal weight: 0.0770 chunk 343 optimal weight: 0.9990 chunk 483 optimal weight: 7.9990 chunk 722 optimal weight: 0.8980 chunk 764 optimal weight: 9.9990 chunk 377 optimal weight: 6.9990 chunk 684 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 ASN ** I 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** N 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** P 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59780 Z= 0.205 Angle : 0.491 9.711 80822 Z= 0.263 Chirality : 0.043 0.200 9814 Planarity : 0.003 0.031 10507 Dihedral : 8.655 89.812 8911 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.99 % Allowed : 16.32 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7966 helix: 1.70 (0.08), residues: 4242 sheet: 0.40 (0.17), residues: 973 loop : -0.48 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 7 PHE 0.022 0.001 PHE R 219 TYR 0.015 0.001 TYR O 199 ARG 0.006 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 594 time to evaluate : 5.207 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: I 267 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7718 (mpt) REVERT: I 309 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7953 (mt) REVERT: W 27 LEU cc_start: 0.8659 (mt) cc_final: 0.8442 (tp) REVERT: W 76 GLU cc_start: 0.8249 (tp30) cc_final: 0.7761 (tp30) REVERT: W 87 SER cc_start: 0.8729 (m) cc_final: 0.8385 (t) REVERT: A 121 ASP cc_start: 0.6841 (t0) cc_final: 0.6553 (t0) REVERT: A 219 PHE cc_start: 0.9088 (m-80) cc_final: 0.8669 (m-80) REVERT: B 309 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8001 (mt) REVERT: B 483 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: D 15 LYS cc_start: 0.7846 (mtmm) cc_final: 0.7459 (mtmt) REVERT: D 50 GLU cc_start: 0.7525 (pm20) cc_final: 0.7102 (pm20) REVERT: D 51 ASN cc_start: 0.8591 (p0) cc_final: 0.8287 (p0) REVERT: D 76 GLU cc_start: 0.8302 (tp30) cc_final: 0.7987 (tp30) REVERT: E 121 ASP cc_start: 0.6449 (t0) cc_final: 0.6188 (t0) REVERT: F 194 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8520 (tm-30) REVERT: F 267 MET cc_start: 0.8069 (mpp) cc_final: 0.7615 (mpp) REVERT: F 309 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7759 (mt) REVERT: G 51 ASN cc_start: 0.8725 (p0) cc_final: 0.8397 (p0) REVERT: G 58 ASP cc_start: 0.8537 (t70) cc_final: 0.8312 (t0) REVERT: G 76 GLU cc_start: 0.8340 (tp30) cc_final: 0.7772 (tp30) REVERT: G 77 LYS cc_start: 0.8904 (tttp) cc_final: 0.8661 (tttp) REVERT: H 219 PHE cc_start: 0.8997 (m-80) cc_final: 0.8447 (m-80) REVERT: H 447 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8433 (mtp) REVERT: J 309 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7842 (mp) REVERT: K 51 ASN cc_start: 0.8731 (p0) cc_final: 0.8340 (p0) REVERT: K 76 GLU cc_start: 0.8321 (tp30) cc_final: 0.7760 (tp30) REVERT: K 84 LEU cc_start: 0.8074 (mt) cc_final: 0.7782 (mt) REVERT: L 219 PHE cc_start: 0.9010 (m-80) cc_final: 0.8521 (m-80) REVERT: L 233 MET cc_start: 0.9019 (pmm) cc_final: 0.8742 (pmm) REVERT: M 194 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: M 267 MET cc_start: 0.8032 (mpp) cc_final: 0.7659 (mpt) REVERT: N 64 ILE cc_start: 0.9094 (mp) cc_final: 0.8755 (mt) REVERT: N 76 GLU cc_start: 0.8263 (tp30) cc_final: 0.7748 (tp30) REVERT: N 77 LYS cc_start: 0.8798 (tttm) cc_final: 0.8381 (tptp) REVERT: O 447 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8062 (mpp) REVERT: P 214 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7665 (mm-30) REVERT: P 267 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7320 (mpt) REVERT: P 289 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9337 (mm) REVERT: Q 51 ASN cc_start: 0.8985 (p0) cc_final: 0.8545 (p0) REVERT: Q 76 GLU cc_start: 0.8065 (tp30) cc_final: 0.7659 (tp30) REVERT: R 215 LEU cc_start: 0.8742 (mp) cc_final: 0.8280 (mt) REVERT: R 233 MET cc_start: 0.8971 (pmm) cc_final: 0.8764 (pmm) REVERT: R 295 LEU cc_start: 0.9384 (mt) cc_final: 0.9079 (tp) REVERT: S 267 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7526 (mpt) REVERT: T 13 LYS cc_start: 0.9117 (tttp) cc_final: 0.8862 (ttmt) REVERT: T 20 LYS cc_start: 0.8848 (mtmt) cc_final: 0.8607 (mtpp) REVERT: T 76 GLU cc_start: 0.7903 (tp30) cc_final: 0.7307 (tp30) outliers start: 123 outliers final: 69 residues processed: 682 average time/residue: 0.6021 time to fit residues: 708.4149 Evaluate side-chains 644 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 561 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 75 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 84 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 214 GLU Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 10.0000 chunk 434 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 569 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 652 optimal weight: 10.0000 chunk 528 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 390 optimal weight: 0.4980 chunk 686 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 59780 Z= 0.225 Angle : 0.498 9.612 80822 Z= 0.264 Chirality : 0.043 0.197 9814 Planarity : 0.003 0.030 10507 Dihedral : 8.522 89.906 8911 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.23 % Allowed : 16.86 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 7966 helix: 1.80 (0.08), residues: 4242 sheet: 0.31 (0.16), residues: 1092 loop : -0.54 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 7 PHE 0.012 0.001 PHE C 219 TYR 0.013 0.001 TYR O 199 ARG 0.006 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 588 time to evaluate : 5.159 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: C 215 LEU cc_start: 0.7302 (mm) cc_final: 0.7092 (mm) REVERT: I 267 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7907 (mpt) REVERT: I 309 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7956 (mt) REVERT: W 76 GLU cc_start: 0.8561 (tp30) cc_final: 0.7448 (tp30) REVERT: W 87 SER cc_start: 0.8800 (m) cc_final: 0.8429 (t) REVERT: A 121 ASP cc_start: 0.6856 (t0) cc_final: 0.6534 (t0) REVERT: A 219 PHE cc_start: 0.9097 (m-80) cc_final: 0.8674 (m-80) REVERT: B 309 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8003 (mt) REVERT: B 483 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: D 15 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7524 (mtmt) REVERT: D 50 GLU cc_start: 0.7533 (pm20) cc_final: 0.7075 (pm20) REVERT: D 51 ASN cc_start: 0.8583 (p0) cc_final: 0.8276 (p0) REVERT: D 76 GLU cc_start: 0.8648 (tp30) cc_final: 0.7833 (tp30) REVERT: E 121 ASP cc_start: 0.6461 (t0) cc_final: 0.6191 (t0) REVERT: F 267 MET cc_start: 0.8085 (mpp) cc_final: 0.7599 (mpp) REVERT: F 309 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7766 (mt) REVERT: G 51 ASN cc_start: 0.8663 (p0) cc_final: 0.8326 (p0) REVERT: G 58 ASP cc_start: 0.8572 (t70) cc_final: 0.8301 (t0) REVERT: G 76 GLU cc_start: 0.8303 (tp30) cc_final: 0.7701 (tp30) REVERT: G 77 LYS cc_start: 0.8936 (tttp) cc_final: 0.8680 (tttp) REVERT: G 79 ASP cc_start: 0.8859 (p0) cc_final: 0.8621 (p0) REVERT: H 219 PHE cc_start: 0.8997 (m-80) cc_final: 0.8439 (m-80) REVERT: H 447 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8421 (mtp) REVERT: J 309 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7840 (mp) REVERT: K 51 ASN cc_start: 0.8704 (p0) cc_final: 0.8318 (p0) REVERT: K 76 GLU cc_start: 0.8355 (tp30) cc_final: 0.7874 (tp30) REVERT: K 84 LEU cc_start: 0.8164 (mt) cc_final: 0.7797 (mt) REVERT: L 219 PHE cc_start: 0.9017 (m-80) cc_final: 0.8567 (m-80) REVERT: M 194 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8291 (tm-30) REVERT: M 267 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7732 (mpt) REVERT: N 13 LYS cc_start: 0.9126 (ttmm) cc_final: 0.8870 (ttpp) REVERT: N 64 ILE cc_start: 0.9087 (mp) cc_final: 0.8723 (mt) REVERT: N 76 GLU cc_start: 0.8237 (tp30) cc_final: 0.7639 (tp30) REVERT: N 77 LYS cc_start: 0.8729 (tttm) cc_final: 0.8431 (tptp) REVERT: O 195 PHE cc_start: 0.8608 (p90) cc_final: 0.8365 (p90) REVERT: O 447 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: P 214 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: P 242 LYS cc_start: 0.8900 (mptt) cc_final: 0.8672 (mptt) REVERT: P 267 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7513 (mpt) REVERT: P 289 LEU cc_start: 0.9593 (OUTLIER) cc_final: 0.9361 (mm) REVERT: Q 13 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8711 (ttmm) REVERT: Q 51 ASN cc_start: 0.8982 (p0) cc_final: 0.8555 (p0) REVERT: Q 76 GLU cc_start: 0.8261 (tp30) cc_final: 0.7378 (tp30) REVERT: R 215 LEU cc_start: 0.8742 (mp) cc_final: 0.8292 (mt) REVERT: R 295 LEU cc_start: 0.9403 (mt) cc_final: 0.9122 (tp) REVERT: S 267 MET cc_start: 0.7956 (mpt) cc_final: 0.7577 (mpt) REVERT: S 309 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7873 (mt) REVERT: T 13 LYS cc_start: 0.9103 (tttp) cc_final: 0.8890 (ttmt) REVERT: T 76 GLU cc_start: 0.8026 (tp30) cc_final: 0.7588 (tp30) REVERT: T 79 ASP cc_start: 0.8801 (p0) cc_final: 0.8530 (p0) outliers start: 138 outliers final: 89 residues processed: 694 average time/residue: 0.5490 time to fit residues: 652.4787 Evaluate side-chains 667 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 563 time to evaluate : 5.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 435 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 433 ASN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 214 GLU Chi-restraints excluded: chain P residue 267 MET Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 13 LYS Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 0.6980 chunk 688 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 448 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 401 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 2 ASN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 505 GLN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 59780 Z= 0.181 Angle : 0.482 9.121 80822 Z= 0.256 Chirality : 0.042 0.194 9814 Planarity : 0.003 0.032 10507 Dihedral : 8.242 89.674 8911 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.23 % Allowed : 17.15 % Favored : 80.62 % 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: 1.33 (0.09), residues: 7966 helix: 1.91 (0.08), residues: 4235 sheet: 0.34 (0.16), residues: 1092 loop : -0.53 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 7 PHE 0.011 0.001 PHE C 219 TYR 0.014 0.001 TYR O 199 ARG 0.008 0.000 ARG N 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 591 time to evaluate : 5.271 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: I 309 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7957 (mt) REVERT: W 76 GLU cc_start: 0.8146 (tp30) cc_final: 0.7397 (tp30) REVERT: W 77 LYS cc_start: 0.8715 (tttm) cc_final: 0.8372 (tptp) REVERT: A 121 ASP cc_start: 0.6845 (t0) cc_final: 0.6515 (t0) REVERT: A 219 PHE cc_start: 0.9092 (m-80) cc_final: 0.8673 (m-80) REVERT: B 309 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8019 (mt) REVERT: B 483 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: D 15 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7451 (mtmt) REVERT: D 50 GLU cc_start: 0.7502 (pm20) cc_final: 0.7046 (pm20) REVERT: D 51 ASN cc_start: 0.8546 (p0) cc_final: 0.8247 (p0) REVERT: D 76 GLU cc_start: 0.8414 (tp30) cc_final: 0.8084 (tp30) REVERT: E 121 ASP cc_start: 0.6457 (t0) cc_final: 0.6166 (t0) REVERT: F 194 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8524 (tm-30) REVERT: F 267 MET cc_start: 0.8079 (mpp) cc_final: 0.7609 (mpp) REVERT: F 309 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7744 (mt) REVERT: G 51 ASN cc_start: 0.8586 (p0) cc_final: 0.8243 (p0) REVERT: G 58 ASP cc_start: 0.8567 (t70) cc_final: 0.8285 (t0) REVERT: G 76 GLU cc_start: 0.8200 (tp30) cc_final: 0.7570 (tp30) REVERT: G 77 LYS cc_start: 0.8907 (tttp) cc_final: 0.8659 (tttp) REVERT: G 79 ASP cc_start: 0.8815 (p0) cc_final: 0.8564 (p0) REVERT: H 219 PHE cc_start: 0.8994 (m-80) cc_final: 0.8454 (m-80) REVERT: H 233 MET cc_start: 0.8944 (pmm) cc_final: 0.8466 (pmm) REVERT: H 447 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8360 (mtp) REVERT: J 309 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7816 (mp) REVERT: K 13 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8930 (ttmm) REVERT: K 27 LEU cc_start: 0.9116 (tp) cc_final: 0.8832 (tp) REVERT: K 51 ASN cc_start: 0.8679 (p0) cc_final: 0.8304 (p0) REVERT: K 76 GLU cc_start: 0.8369 (tp30) cc_final: 0.7894 (tp30) REVERT: L 219 PHE cc_start: 0.9010 (m-80) cc_final: 0.8563 (m-80) REVERT: M 194 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: M 483 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7325 (mt-10) REVERT: N 13 LYS cc_start: 0.9114 (ttmm) cc_final: 0.8850 (ttpp) REVERT: N 20 LYS cc_start: 0.9031 (mtmt) cc_final: 0.8819 (mtpp) REVERT: N 64 ILE cc_start: 0.9076 (mp) cc_final: 0.8719 (mt) REVERT: N 76 GLU cc_start: 0.8196 (tp30) cc_final: 0.7598 (tp30) REVERT: N 77 LYS cc_start: 0.8706 (tttm) cc_final: 0.8304 (tptp) REVERT: O 267 MET cc_start: 0.5464 (mpp) cc_final: 0.4005 (ttm) REVERT: O 447 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: P 214 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7737 (mm-30) REVERT: P 309 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7817 (mt) REVERT: P 514 MET cc_start: 0.8448 (mtm) cc_final: 0.8239 (mtp) REVERT: Q 51 ASN cc_start: 0.8944 (p0) cc_final: 0.8522 (p0) REVERT: Q 76 GLU cc_start: 0.7990 (tp30) cc_final: 0.7610 (tp30) REVERT: R 215 LEU cc_start: 0.8747 (mp) cc_final: 0.8296 (mt) REVERT: R 295 LEU cc_start: 0.9383 (mt) cc_final: 0.9102 (tp) REVERT: S 267 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7591 (mpt) REVERT: S 309 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7866 (mt) REVERT: T 76 GLU cc_start: 0.8032 (tp30) cc_final: 0.7156 (tp30) REVERT: T 88 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8248 (tm-30) outliers start: 138 outliers final: 83 residues processed: 692 average time/residue: 0.5657 time to fit residues: 673.2487 Evaluate side-chains 663 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 566 time to evaluate : 5.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain W residue 81 GLU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 214 GLU Chi-restraints excluded: chain P residue 309 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 153 ASN Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Chi-restraints excluded: chain T residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 436 optimal weight: 1.9990 chunk 558 optimal weight: 5.9990 chunk 433 optimal weight: 6.9990 chunk 644 optimal weight: 0.8980 chunk 427 optimal weight: 2.9990 chunk 762 optimal weight: 6.9990 chunk 477 optimal weight: 10.0000 chunk 464 optimal weight: 0.9980 chunk 351 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** M 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 2 ASN P 82 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 59780 Z= 0.186 Angle : 0.493 9.629 80822 Z= 0.260 Chirality : 0.042 0.192 9814 Planarity : 0.003 0.029 10507 Dihedral : 8.120 89.968 8911 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.36 % Allowed : 17.47 % Favored : 80.17 % 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: 1.40 (0.09), residues: 7966 helix: 1.93 (0.08), residues: 4235 sheet: 0.62 (0.16), residues: 1050 loop : -0.54 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 7 PHE 0.011 0.001 PHE C 219 TYR 0.014 0.001 TYR R 199 ARG 0.006 0.000 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 583 time to evaluate : 5.312 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: I 309 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7941 (mt) REVERT: W 20 LYS cc_start: 0.8935 (mmmm) cc_final: 0.8574 (mmmm) REVERT: W 87 SER cc_start: 0.8746 (m) cc_final: 0.8343 (t) REVERT: A 121 ASP cc_start: 0.6860 (t0) cc_final: 0.6519 (t0) REVERT: A 219 PHE cc_start: 0.9084 (m-80) cc_final: 0.8740 (m-80) REVERT: B 193 MET cc_start: 0.7817 (mmm) cc_final: 0.7579 (mmt) REVERT: B 309 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8031 (mt) REVERT: B 483 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: D 50 GLU cc_start: 0.7500 (pm20) cc_final: 0.7029 (pm20) REVERT: D 51 ASN cc_start: 0.8528 (p0) cc_final: 0.8238 (p0) REVERT: D 76 GLU cc_start: 0.8676 (tp30) cc_final: 0.7812 (tp30) REVERT: E 121 ASP cc_start: 0.6464 (t0) cc_final: 0.6166 (t0) REVERT: F 194 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8534 (tm-30) REVERT: F 309 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7729 (mt) REVERT: G 51 ASN cc_start: 0.8543 (p0) cc_final: 0.8215 (p0) REVERT: G 58 ASP cc_start: 0.8557 (t70) cc_final: 0.8294 (t0) REVERT: G 76 GLU cc_start: 0.8196 (tp30) cc_final: 0.7567 (tp30) REVERT: G 77 LYS cc_start: 0.8903 (tttp) cc_final: 0.8653 (tttp) REVERT: G 79 ASP cc_start: 0.8790 (p0) cc_final: 0.8556 (p0) REVERT: G 88 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8054 (tm-30) REVERT: H 219 PHE cc_start: 0.9028 (m-80) cc_final: 0.8494 (m-80) REVERT: H 447 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: J 309 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7834 (mp) REVERT: K 27 LEU cc_start: 0.9124 (tp) cc_final: 0.8827 (tp) REVERT: K 51 ASN cc_start: 0.8668 (p0) cc_final: 0.8303 (p0) REVERT: K 76 GLU cc_start: 0.8375 (tp30) cc_final: 0.7968 (tp30) REVERT: K 77 LYS cc_start: 0.8492 (tptt) cc_final: 0.8275 (tptp) REVERT: L 219 PHE cc_start: 0.9008 (m-80) cc_final: 0.8575 (m-80) REVERT: L 233 MET cc_start: 0.9075 (pmm) cc_final: 0.8513 (pmm) REVERT: M 194 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: M 483 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: N 13 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8862 (ttpp) REVERT: N 76 GLU cc_start: 0.8118 (tp30) cc_final: 0.7532 (tp30) REVERT: N 77 LYS cc_start: 0.8715 (tttm) cc_final: 0.8296 (tptp) REVERT: N 88 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8394 (tm-30) REVERT: O 121 ASP cc_start: 0.6284 (t0) cc_final: 0.6052 (t0) REVERT: O 195 PHE cc_start: 0.8648 (p90) cc_final: 0.8444 (p90) REVERT: O 267 MET cc_start: 0.5503 (mpp) cc_final: 0.4047 (ttm) REVERT: O 447 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8080 (mpp) REVERT: P 36 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8372 (mtt180) REVERT: Q 16 GLU cc_start: 0.8926 (pm20) cc_final: 0.8656 (pp20) REVERT: Q 51 ASN cc_start: 0.8931 (p0) cc_final: 0.8497 (p0) REVERT: Q 55 LYS cc_start: 0.8799 (tppt) cc_final: 0.8376 (ttpp) REVERT: Q 76 GLU cc_start: 0.8228 (tp30) cc_final: 0.7368 (tp30) REVERT: R 215 LEU cc_start: 0.8718 (mp) cc_final: 0.8253 (mt) REVERT: R 295 LEU cc_start: 0.9372 (mt) cc_final: 0.9097 (tp) REVERT: R 491 MET cc_start: 0.8779 (mtm) cc_final: 0.8371 (mtm) REVERT: S 267 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7618 (mpt) REVERT: S 309 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7881 (mt) REVERT: S 483 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: T 76 GLU cc_start: 0.7834 (tp30) cc_final: 0.7259 (tp30) outliers start: 146 outliers final: 103 residues processed: 694 average time/residue: 0.5448 time to fit residues: 648.6674 Evaluate side-chains 683 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 566 time to evaluate : 5.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 351 GLN Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 64 ILE Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 351 GLN Chi-restraints excluded: chain H residue 433 ASN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 11 ASP Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 483 GLU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 30.0000 chunk 304 optimal weight: 0.9980 chunk 455 optimal weight: 0.4980 chunk 229 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 519 optimal weight: 8.9990 chunk 376 optimal weight: 5.9990 chunk 71 optimal weight: 0.0370 chunk 599 optimal weight: 5.9990 overall best weight: 2.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 ASN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN J 82 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 59780 Z= 0.318 Angle : 0.540 10.384 80822 Z= 0.285 Chirality : 0.044 0.199 9814 Planarity : 0.003 0.041 10507 Dihedral : 8.511 89.700 8911 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.25 % Allowed : 17.65 % Favored : 80.10 % 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: 7966 helix: 1.70 (0.08), residues: 4242 sheet: 0.75 (0.17), residues: 903 loop : -0.58 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS N 7 PHE 0.010 0.001 PHE S 195 TYR 0.014 0.001 TYR R 199 ARG 0.007 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 588 time to evaluate : 5.282 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: C 233 MET cc_start: 0.7663 (pmm) cc_final: 0.7398 (pmm) REVERT: C 389 MET cc_start: 0.2908 (mmm) cc_final: 0.2565 (mmm) REVERT: I 309 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7885 (mt) REVERT: W 76 GLU cc_start: 0.8416 (tp30) cc_final: 0.7621 (tp30) REVERT: W 77 LYS cc_start: 0.8712 (tttp) cc_final: 0.8423 (tptp) REVERT: W 87 SER cc_start: 0.8817 (m) cc_final: 0.8412 (t) REVERT: A 121 ASP cc_start: 0.6939 (t0) cc_final: 0.6628 (t0) REVERT: A 219 PHE cc_start: 0.9113 (m-80) cc_final: 0.8743 (m-80) REVERT: B 193 MET cc_start: 0.7889 (mmm) cc_final: 0.7609 (mmp) REVERT: B 309 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (mt) REVERT: B 483 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7567 (mt-10) REVERT: D 50 GLU cc_start: 0.7534 (pm20) cc_final: 0.7045 (pm20) REVERT: D 51 ASN cc_start: 0.8519 (p0) cc_final: 0.8211 (p0) REVERT: D 76 GLU cc_start: 0.8521 (tp30) cc_final: 0.8249 (tp30) REVERT: D 81 GLU cc_start: 0.6011 (tm-30) cc_final: 0.5153 (tm-30) REVERT: E 121 ASP cc_start: 0.6515 (t0) cc_final: 0.6241 (t0) REVERT: E 193 MET cc_start: 0.7616 (ppp) cc_final: 0.7319 (ppp) REVERT: E 233 MET cc_start: 0.8502 (pmm) cc_final: 0.7952 (pmm) REVERT: F 194 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: F 309 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7735 (mt) REVERT: G 51 ASN cc_start: 0.8515 (p0) cc_final: 0.8185 (p0) REVERT: G 58 ASP cc_start: 0.8577 (t70) cc_final: 0.8007 (t0) REVERT: G 76 GLU cc_start: 0.8179 (tp30) cc_final: 0.7561 (tp30) REVERT: G 79 ASP cc_start: 0.8847 (p0) cc_final: 0.8531 (p0) REVERT: H 219 PHE cc_start: 0.9037 (m-80) cc_final: 0.8476 (m-80) REVERT: H 447 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8429 (mtp) REVERT: J 309 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7884 (mp) REVERT: K 27 LEU cc_start: 0.9135 (tp) cc_final: 0.8850 (tp) REVERT: K 51 ASN cc_start: 0.8630 (p0) cc_final: 0.8309 (p0) REVERT: K 76 GLU cc_start: 0.8441 (tp30) cc_final: 0.8035 (tp30) REVERT: L 166 MET cc_start: 0.8932 (tpp) cc_final: 0.8628 (tpp) REVERT: L 219 PHE cc_start: 0.9015 (m-80) cc_final: 0.8589 (m-80) REVERT: M 194 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8353 (tm-30) REVERT: M 288 MET cc_start: 0.8970 (ptt) cc_final: 0.8743 (ptp) REVERT: M 483 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: N 13 LYS cc_start: 0.9101 (ttmm) cc_final: 0.8825 (ttpp) REVERT: N 58 ASP cc_start: 0.8340 (t0) cc_final: 0.7997 (t0) REVERT: N 60 LYS cc_start: 0.8368 (mptt) cc_final: 0.8093 (mptt) REVERT: N 76 GLU cc_start: 0.8190 (tp30) cc_final: 0.7661 (tp30) REVERT: N 77 LYS cc_start: 0.8731 (tttm) cc_final: 0.8448 (tptp) REVERT: N 88 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8499 (tm-30) REVERT: O 121 ASP cc_start: 0.6413 (t0) cc_final: 0.6140 (t0) REVERT: O 195 PHE cc_start: 0.8662 (p90) cc_final: 0.8432 (p90) REVERT: O 267 MET cc_start: 0.5491 (mpp) cc_final: 0.4118 (ttm) REVERT: O 447 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8095 (mpp) REVERT: P 36 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8333 (mtt90) REVERT: P 309 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7864 (mt) REVERT: Q 51 ASN cc_start: 0.8914 (p0) cc_final: 0.8455 (p0) REVERT: Q 55 LYS cc_start: 0.8895 (tppt) cc_final: 0.8478 (ttpp) REVERT: Q 76 GLU cc_start: 0.8073 (tp30) cc_final: 0.7639 (tp30) REVERT: Q 81 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: R 215 LEU cc_start: 0.8745 (mp) cc_final: 0.8297 (mt) REVERT: R 295 LEU cc_start: 0.9411 (mt) cc_final: 0.9105 (tp) REVERT: S 267 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7708 (mpt) REVERT: S 309 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7895 (mt) REVERT: S 483 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: T 20 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8616 (mtpp) REVERT: T 53 GLU cc_start: 0.8326 (mp0) cc_final: 0.8058 (mp0) REVERT: T 76 GLU cc_start: 0.8080 (tp30) cc_final: 0.7456 (tp30) REVERT: T 79 ASP cc_start: 0.8891 (p0) cc_final: 0.8680 (p0) outliers start: 139 outliers final: 102 residues processed: 701 average time/residue: 0.5501 time to fit residues: 663.3413 Evaluate side-chains 685 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 567 time to evaluate : 5.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 435 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 433 ASN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 309 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 483 GLU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.4980 chunk 730 optimal weight: 0.9980 chunk 666 optimal weight: 5.9990 chunk 710 optimal weight: 9.9990 chunk 427 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 chunk 557 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 641 optimal weight: 4.9990 chunk 671 optimal weight: 2.9990 chunk 707 optimal weight: 30.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN B 351 GLN ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** M 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 59780 Z= 0.261 Angle : 0.526 9.773 80822 Z= 0.277 Chirality : 0.043 0.202 9814 Planarity : 0.003 0.028 10507 Dihedral : 8.388 89.439 8911 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.22 % Allowed : 17.89 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 7966 helix: 1.72 (0.08), residues: 4228 sheet: 0.72 (0.17), residues: 952 loop : -0.63 (0.11), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS N 7 PHE 0.011 0.001 PHE C 219 TYR 0.014 0.001 TYR O 199 ARG 0.006 0.000 ARG W 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 579 time to evaluate : 5.177 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: C 389 MET cc_start: 0.2856 (mmm) cc_final: 0.2461 (mmm) REVERT: I 309 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7890 (mt) REVERT: W 20 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8335 (mmmt) REVERT: W 76 GLU cc_start: 0.8009 (tp30) cc_final: 0.7512 (tp30) REVERT: W 77 LYS cc_start: 0.8661 (tttp) cc_final: 0.8318 (tptp) REVERT: W 87 SER cc_start: 0.8824 (m) cc_final: 0.8420 (t) REVERT: A 121 ASP cc_start: 0.6941 (t0) cc_final: 0.6610 (t0) REVERT: A 219 PHE cc_start: 0.9104 (m-80) cc_final: 0.8737 (m-80) REVERT: B 193 MET cc_start: 0.7881 (mmm) cc_final: 0.7562 (mmt) REVERT: B 309 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8017 (mt) REVERT: B 483 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: D 50 GLU cc_start: 0.7489 (pm20) cc_final: 0.6995 (pm20) REVERT: D 51 ASN cc_start: 0.8527 (p0) cc_final: 0.8172 (p0) REVERT: D 76 GLU cc_start: 0.8712 (tp30) cc_final: 0.7986 (tp30) REVERT: E 121 ASP cc_start: 0.6497 (t0) cc_final: 0.6203 (t0) REVERT: F 194 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8511 (tm-30) REVERT: F 309 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7693 (mt) REVERT: G 51 ASN cc_start: 0.8499 (p0) cc_final: 0.8154 (p0) REVERT: G 58 ASP cc_start: 0.8452 (t70) cc_final: 0.8153 (t0) REVERT: G 76 GLU cc_start: 0.8179 (tp30) cc_final: 0.7536 (tp30) REVERT: G 77 LYS cc_start: 0.8905 (tttp) cc_final: 0.8450 (tptp) REVERT: G 79 ASP cc_start: 0.8829 (p0) cc_final: 0.8516 (p0) REVERT: G 88 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8091 (tm-30) REVERT: H 121 ASP cc_start: 0.6758 (t0) cc_final: 0.6458 (t0) REVERT: H 219 PHE cc_start: 0.9032 (m-80) cc_final: 0.8475 (m-80) REVERT: H 233 MET cc_start: 0.8979 (pmm) cc_final: 0.8320 (pmm) REVERT: H 447 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8421 (mtp) REVERT: J 309 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7845 (mp) REVERT: K 27 LEU cc_start: 0.9163 (tp) cc_final: 0.8879 (tp) REVERT: K 51 ASN cc_start: 0.8633 (p0) cc_final: 0.8350 (p0) REVERT: K 76 GLU cc_start: 0.8459 (tp30) cc_final: 0.8102 (tp30) REVERT: K 77 LYS cc_start: 0.8494 (tptt) cc_final: 0.8034 (tptp) REVERT: L 166 MET cc_start: 0.8928 (tpp) cc_final: 0.8591 (tpp) REVERT: L 219 PHE cc_start: 0.9006 (m-80) cc_final: 0.8592 (m-80) REVERT: L 233 MET cc_start: 0.8956 (pmm) cc_final: 0.8406 (pmm) REVERT: M 194 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: M 483 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: N 13 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8818 (ttpp) REVERT: N 58 ASP cc_start: 0.8357 (t0) cc_final: 0.7954 (t0) REVERT: N 60 LYS cc_start: 0.8439 (mptt) cc_final: 0.8181 (mptt) REVERT: N 76 GLU cc_start: 0.8146 (tp30) cc_final: 0.7504 (tp30) REVERT: N 77 LYS cc_start: 0.8704 (tttm) cc_final: 0.8429 (tptp) REVERT: N 88 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8100 (tm-30) REVERT: O 121 ASP cc_start: 0.6397 (t0) cc_final: 0.6099 (t0) REVERT: O 267 MET cc_start: 0.5432 (mpp) cc_final: 0.4162 (ttm) REVERT: O 447 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8085 (mpp) REVERT: P 36 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8347 (mtt90) REVERT: P 309 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7864 (mt) REVERT: Q 51 ASN cc_start: 0.8887 (p0) cc_final: 0.8466 (p0) REVERT: Q 55 LYS cc_start: 0.8896 (tppt) cc_final: 0.8544 (ttpp) REVERT: Q 76 GLU cc_start: 0.8265 (tp30) cc_final: 0.7310 (tp30) REVERT: R 215 LEU cc_start: 0.8748 (mp) cc_final: 0.8288 (mt) REVERT: R 295 LEU cc_start: 0.9412 (mt) cc_final: 0.9121 (tp) REVERT: R 389 MET cc_start: 0.2670 (mmm) cc_final: 0.2190 (mmm) REVERT: S 267 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7689 (mpt) REVERT: S 309 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7904 (mt) REVERT: S 483 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: T 20 LYS cc_start: 0.8869 (mtmt) cc_final: 0.8654 (mtpp) REVERT: T 47 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8343 (tpp80) REVERT: T 53 GLU cc_start: 0.8288 (mp0) cc_final: 0.8035 (mp0) REVERT: T 76 GLU cc_start: 0.8056 (tp30) cc_final: 0.7406 (tp30) outliers start: 137 outliers final: 100 residues processed: 687 average time/residue: 0.5496 time to fit residues: 649.3773 Evaluate side-chains 681 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 566 time to evaluate : 5.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain I residue 435 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 433 ASN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 307 MET Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 309 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 422 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 307 MET Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 483 GLU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 64 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 10.0000 chunk 751 optimal weight: 0.9990 chunk 458 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 522 optimal weight: 0.5980 chunk 788 optimal weight: 7.9990 chunk 725 optimal weight: 0.7980 chunk 627 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 484 optimal weight: 20.0000 chunk 384 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 82 ASN ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 59780 Z= 0.185 Angle : 0.514 10.069 80822 Z= 0.270 Chirality : 0.043 0.197 9814 Planarity : 0.003 0.027 10507 Dihedral : 8.121 89.878 8911 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 18.57 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 7966 helix: 1.82 (0.08), residues: 4235 sheet: 0.77 (0.17), residues: 952 loop : -0.59 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 7 PHE 0.013 0.001 PHE K 67 TYR 0.014 0.001 TYR O 199 ARG 0.006 0.000 ARG K 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15932 Ramachandran restraints generated. 7966 Oldfield, 0 Emsley, 7966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 574 time to evaluate : 5.263 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: C 389 MET cc_start: 0.2972 (mmm) cc_final: 0.2610 (mmm) REVERT: I 309 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7887 (mt) REVERT: W 20 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8285 (mmmt) REVERT: W 76 GLU cc_start: 0.7889 (tp30) cc_final: 0.7403 (tp30) REVERT: W 77 LYS cc_start: 0.8635 (tttp) cc_final: 0.8358 (tptp) REVERT: W 87 SER cc_start: 0.8810 (m) cc_final: 0.8394 (t) REVERT: A 121 ASP cc_start: 0.6904 (t0) cc_final: 0.6567 (t0) REVERT: A 219 PHE cc_start: 0.9097 (m-80) cc_final: 0.8745 (m-80) REVERT: B 193 MET cc_start: 0.7841 (mmm) cc_final: 0.7571 (mmt) REVERT: B 309 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 389 MET cc_start: 0.8466 (tpp) cc_final: 0.7506 (tpp) REVERT: B 483 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: D 50 GLU cc_start: 0.7482 (pm20) cc_final: 0.6994 (pm20) REVERT: D 51 ASN cc_start: 0.8452 (p0) cc_final: 0.8108 (p0) REVERT: D 76 GLU cc_start: 0.8494 (tp30) cc_final: 0.8131 (tp30) REVERT: D 81 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5168 (tm-30) REVERT: D 84 LEU cc_start: 0.8377 (mt) cc_final: 0.8091 (mt) REVERT: E 121 ASP cc_start: 0.6441 (t0) cc_final: 0.6142 (t0) REVERT: E 233 MET cc_start: 0.8453 (pmm) cc_final: 0.7762 (pmm) REVERT: F 194 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: F 309 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7671 (mt) REVERT: G 51 ASN cc_start: 0.8483 (p0) cc_final: 0.8189 (p0) REVERT: G 58 ASP cc_start: 0.8465 (t70) cc_final: 0.8168 (t0) REVERT: G 76 GLU cc_start: 0.8111 (tp30) cc_final: 0.7548 (tp30) REVERT: G 88 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8059 (tm-30) REVERT: H 121 ASP cc_start: 0.6710 (t0) cc_final: 0.6365 (t0) REVERT: H 219 PHE cc_start: 0.9029 (m-80) cc_final: 0.8490 (m-80) REVERT: H 233 MET cc_start: 0.8972 (pmm) cc_final: 0.8363 (pmm) REVERT: H 295 LEU cc_start: 0.9287 (mt) cc_final: 0.9087 (pp) REVERT: H 447 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: J 309 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7800 (mp) REVERT: K 27 LEU cc_start: 0.9169 (tp) cc_final: 0.8908 (tp) REVERT: K 50 GLU cc_start: 0.7268 (pm20) cc_final: 0.6931 (pm20) REVERT: K 76 GLU cc_start: 0.8425 (tp30) cc_final: 0.8006 (tp30) REVERT: K 77 LYS cc_start: 0.8418 (tptt) cc_final: 0.7845 (tptp) REVERT: L 166 MET cc_start: 0.8880 (tpp) cc_final: 0.8535 (tpp) REVERT: L 219 PHE cc_start: 0.9004 (m-80) cc_final: 0.8612 (m-80) REVERT: L 233 MET cc_start: 0.8973 (pmm) cc_final: 0.8703 (pmm) REVERT: M 194 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8321 (tm-30) REVERT: M 288 MET cc_start: 0.8892 (ptt) cc_final: 0.8630 (ptp) REVERT: M 483 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: N 13 LYS cc_start: 0.9153 (ttmm) cc_final: 0.8870 (ttpp) REVERT: N 58 ASP cc_start: 0.8348 (t0) cc_final: 0.7940 (t0) REVERT: N 60 LYS cc_start: 0.8471 (mptt) cc_final: 0.8208 (mptt) REVERT: N 76 GLU cc_start: 0.8036 (tp30) cc_final: 0.7418 (tp30) REVERT: N 77 LYS cc_start: 0.8715 (tttm) cc_final: 0.8399 (tptp) REVERT: O 121 ASP cc_start: 0.6367 (t0) cc_final: 0.6068 (t0) REVERT: O 267 MET cc_start: 0.5407 (mpp) cc_final: 0.4221 (ttm) REVERT: O 447 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: P 309 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7872 (mt) REVERT: Q 51 ASN cc_start: 0.8891 (p0) cc_final: 0.8495 (p0) REVERT: Q 55 LYS cc_start: 0.8889 (tppt) cc_final: 0.8573 (ttpp) REVERT: Q 76 GLU cc_start: 0.8002 (tp30) cc_final: 0.7646 (tp30) REVERT: R 215 LEU cc_start: 0.8743 (mp) cc_final: 0.8279 (mt) REVERT: R 233 MET cc_start: 0.8775 (pmm) cc_final: 0.8473 (pmm) REVERT: R 295 LEU cc_start: 0.9393 (mt) cc_final: 0.9119 (tp) REVERT: R 389 MET cc_start: 0.2706 (mmm) cc_final: 0.2229 (mmm) REVERT: S 267 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7773 (mpt) REVERT: S 309 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7883 (mt) REVERT: S 483 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: T 47 ARG cc_start: 0.8662 (tpp80) cc_final: 0.8320 (tpp80) REVERT: T 76 GLU cc_start: 0.7957 (tp30) cc_final: 0.7334 (tp30) outliers start: 116 outliers final: 89 residues processed: 667 average time/residue: 0.5498 time to fit residues: 629.0752 Evaluate side-chains 661 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 558 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 433 ASN Chi-restraints excluded: chain C residue 467 ASN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain I residue 176 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 309 LEU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 351 GLN Chi-restraints excluded: chain E residue 422 VAL Chi-restraints excluded: chain E residue 433 ASN Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain F residue 176 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 194 GLN Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 372 LEU Chi-restraints excluded: chain F residue 400 LEU Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 433 ASN Chi-restraints excluded: chain H residue 447 MET Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain J residue 276 VAL Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 372 LEU Chi-restraints excluded: chain J residue 435 ASP Chi-restraints excluded: chain J residue 491 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 150 ILE Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 422 VAL Chi-restraints excluded: chain L residue 433 ASN Chi-restraints excluded: chain L residue 521 VAL Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 194 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain M residue 330 THR Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 150 ILE Chi-restraints excluded: chain O residue 236 VAL Chi-restraints excluded: chain O residue 387 VAL Chi-restraints excluded: chain O residue 433 ASN Chi-restraints excluded: chain O residue 447 MET Chi-restraints excluded: chain O residue 521 VAL Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 193 MET Chi-restraints excluded: chain P residue 229 ASN Chi-restraints excluded: chain P residue 233 MET Chi-restraints excluded: chain P residue 309 LEU Chi-restraints excluded: chain P residue 328 ASP Chi-restraints excluded: chain P residue 435 ASP Chi-restraints excluded: chain Q residue 49 LEU Chi-restraints excluded: chain R residue 77 VAL Chi-restraints excluded: chain R residue 124 VAL Chi-restraints excluded: chain R residue 150 ILE Chi-restraints excluded: chain R residue 387 VAL Chi-restraints excluded: chain R residue 433 ASN Chi-restraints excluded: chain R residue 521 VAL Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 267 MET Chi-restraints excluded: chain S residue 270 ILE Chi-restraints excluded: chain S residue 289 LEU Chi-restraints excluded: chain S residue 300 VAL Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 483 GLU Chi-restraints excluded: chain T residue 6 LEU Chi-restraints excluded: chain T residue 25 ILE Chi-restraints excluded: chain T residue 51 ASN Chi-restraints excluded: chain T residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.7980 chunk 668 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 578 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 628 optimal weight: 0.5980 chunk 263 optimal weight: 20.0000 chunk 645 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 115 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 GLN ** F 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** M 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.115424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075109 restraints weight = 128690.493| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.47 r_work: 0.2937 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 59780 Z= 0.157 Angle : 0.506 10.239 80822 Z= 0.265 Chirality : 0.042 0.195 9814 Planarity : 0.003 0.041 10507 Dihedral : 7.814 89.097 8911 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.65 % Allowed : 18.78 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.09), residues: 7966 helix: 2.02 (0.08), residues: 4193 sheet: 0.81 (0.17), residues: 959 loop : -0.53 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 7 PHE 0.012 0.001 PHE K 67 TYR 0.017 0.001 TYR R 476 ARG 0.007 0.000 ARG W 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12451.34 seconds wall clock time: 220 minutes 46.96 seconds (13246.96 seconds total)