Starting phenix.real_space_refine on Sat Feb 24 05:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfe_25871/02_2024/7tfe_25871.pdb" } resolution = 2.85 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= 0.044 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: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 216 5.16 5 C 26592 2.51 5 N 6948 2.21 5 O 7608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41388 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "G" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "H" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "I" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "K" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "L" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3447 Classifications: {'peptide': 443} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 25, 'TRANS': 417} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU A 350 " occ=0.92 residue: pdb=" N LEU G 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU G 350 " occ=0.92 residue: pdb=" N LEU H 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU H 350 " occ=0.92 residue: pdb=" N LEU I 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU I 350 " occ=0.92 residue: pdb=" N LEU B 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU B 350 " occ=0.92 residue: pdb=" N LEU C 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU C 350 " occ=0.92 residue: pdb=" N LEU J 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU J 350 " occ=0.92 residue: pdb=" N LEU D 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU D 350 " occ=0.92 residue: pdb=" N LEU E 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU E 350 " occ=0.92 residue: pdb=" N LEU F 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU F 350 " occ=0.92 residue: pdb=" N LEU K 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU K 350 " occ=0.92 residue: pdb=" N LEU L 350 " occ=0.92 ... (6 atoms not shown) pdb=" CD2 LEU L 350 " occ=0.92 Time building chain proxies: 21.85, per 1000 atoms: 0.53 Number of scatterers: 41388 At special positions: 0 Unit cell: (159.28, 152.24, 122.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 Mg 24 11.99 O 7608 8.00 N 6948 7.00 C 26592 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: 16.63 Conformation dependent library (CDL) restraints added in 8.0 seconds 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9912 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 72 sheets defined 46.4% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.14 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 41 through 47 Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 62 " --> pdb=" O GLY A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 62' Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR A 76 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 Processing helix chain 'A' and resid 167 through 180 Processing helix chain 'A' and resid 203 through 225 Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 294 through 299' Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER A 329 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 361 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 41 through 47 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL G 61 " --> pdb=" O GLU G 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 62 " --> pdb=" O GLY G 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 62' Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR G 76 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 123 Processing helix chain 'G' and resid 167 through 180 Processing helix chain 'G' and resid 203 through 225 Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 268 through 281 Processing helix chain 'G' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL G 288 " --> pdb=" O GLY G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG G 298 " --> pdb=" O ASN G 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 299 " --> pdb=" O SER G 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 299' Processing helix chain 'G' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER G 329 " --> pdb=" O ARG G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 361 Processing helix chain 'G' and resid 376 through 383 Processing helix chain 'G' and resid 391 through 402 Processing helix chain 'G' and resid 403 through 410 Processing helix chain 'G' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE G 414 " --> pdb=" O GLY G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG G 437 " --> pdb=" O HIS G 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 16 Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL H 61 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG H 62 " --> pdb=" O GLY H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR H 76 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 123 Processing helix chain 'H' and resid 167 through 180 Processing helix chain 'H' and resid 203 through 225 Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA H 287 " --> pdb=" O ARG H 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL H 288 " --> pdb=" O GLY H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 removed outlier: 4.036A pdb=" N PHE H 296 " --> pdb=" O THR H 292 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS H 297 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG H 298 " --> pdb=" O ASN H 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU H 299 " --> pdb=" O SER H 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 299' Processing helix chain 'H' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER H 329 " --> pdb=" O ARG H 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 361 Processing helix chain 'H' and resid 376 through 383 Processing helix chain 'H' and resid 391 through 402 Processing helix chain 'H' and resid 403 through 410 Processing helix chain 'H' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE H 414 " --> pdb=" O GLY H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG H 437 " --> pdb=" O HIS H 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 41 through 47 Processing helix chain 'I' and resid 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL I 61 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG I 62 " --> pdb=" O GLY I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 62' Processing helix chain 'I' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR I 76 " --> pdb=" O ASP I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 123 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'I' and resid 203 through 225 Processing helix chain 'I' and resid 263 through 267 Processing helix chain 'I' and resid 268 through 281 Processing helix chain 'I' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA I 287 " --> pdb=" O ARG I 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL I 288 " --> pdb=" O GLY I 284 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG I 298 " --> pdb=" O ASN I 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 299 " --> pdb=" O SER I 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 294 through 299' Processing helix chain 'I' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER I 329 " --> pdb=" O ARG I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 361 Processing helix chain 'I' and resid 376 through 383 Processing helix chain 'I' and resid 391 through 402 Processing helix chain 'I' and resid 403 through 410 Processing helix chain 'I' and resid 410 through 431 removed outlier: 3.550A pdb=" N PHE I 414 " --> pdb=" O GLY I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG I 437 " --> pdb=" O HIS I 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 16 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL B 61 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 62 " --> pdb=" O GLY B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR B 76 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 203 through 225 Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 268 through 281 Processing helix chain 'B' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 299' Processing helix chain 'B' and resid 326 through 330 removed outlier: 3.628A pdb=" N SER B 329 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.620A pdb=" N ARG B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL C 61 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 62' Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR C 76 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 167 through 180 Processing helix chain 'C' and resid 203 through 225 Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 268 through 281 Processing helix chain 'C' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG C 298 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 294 through 299' Processing helix chain 'C' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER C 329 " --> pdb=" O ARG C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 361 Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 391 through 402 Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.646A pdb=" N ARG C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 16 Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG J 62 " --> pdb=" O GLY J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR J 76 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 123 Processing helix chain 'J' and resid 167 through 180 Processing helix chain 'J' and resid 203 through 225 Processing helix chain 'J' and resid 263 through 267 Processing helix chain 'J' and resid 268 through 281 Processing helix chain 'J' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA J 287 " --> pdb=" O ARG J 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL J 288 " --> pdb=" O GLY J 284 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG J 298 " --> pdb=" O ASN J 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 299 " --> pdb=" O SER J 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 294 through 299' Processing helix chain 'J' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER J 329 " --> pdb=" O ARG J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 360 Processing helix chain 'J' and resid 376 through 383 Processing helix chain 'J' and resid 391 through 402 Processing helix chain 'J' and resid 403 through 410 Processing helix chain 'J' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE J 414 " --> pdb=" O GLY J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG J 437 " --> pdb=" O HIS J 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL D 61 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 62 " --> pdb=" O GLY D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 62' Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR D 76 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 123 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 203 through 225 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 268 through 281 Processing helix chain 'D' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA D 287 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 4.043A pdb=" N PHE D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS D 297 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 299 " --> pdb=" O SER D 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 299' Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER D 329 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 361 Processing helix chain 'D' and resid 376 through 383 Processing helix chain 'D' and resid 391 through 402 Processing helix chain 'D' and resid 403 through 410 Processing helix chain 'D' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE D 414 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 41 through 47 Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL E 61 " --> pdb=" O GLU E 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 62 " --> pdb=" O GLY E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 62' Processing helix chain 'E' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR E 76 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 167 through 180 Processing helix chain 'E' and resid 203 through 225 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 299 removed outlier: 4.035A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 299' Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER E 329 " --> pdb=" O ARG E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 361 Processing helix chain 'E' and resid 376 through 383 Processing helix chain 'E' and resid 391 through 402 Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE E 414 " --> pdb=" O GLY E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG E 437 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 16 Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL F 61 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG F 62 " --> pdb=" O GLY F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 58 through 62' Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.616A pdb=" N THR F 76 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 Processing helix chain 'F' and resid 167 through 180 Processing helix chain 'F' and resid 203 through 225 Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA F 287 " --> pdb=" O ARG F 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL F 288 " --> pdb=" O GLY F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG F 298 " --> pdb=" O ASN F 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 294 through 299' Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER F 329 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 361 Processing helix chain 'F' and resid 376 through 383 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 403 through 410 Processing helix chain 'F' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE F 414 " --> pdb=" O GLY F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG F 437 " --> pdb=" O HIS F 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 16 Processing helix chain 'K' and resid 41 through 47 Processing helix chain 'K' and resid 55 through 57 No H-bonds generated for 'chain 'K' and resid 55 through 57' Processing helix chain 'K' and resid 58 through 62 removed outlier: 4.165A pdb=" N VAL K 61 " --> pdb=" O GLU K 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG K 62 " --> pdb=" O GLY K 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 62' Processing helix chain 'K' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR K 76 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 123 Processing helix chain 'K' and resid 167 through 180 Processing helix chain 'K' and resid 203 through 225 Processing helix chain 'K' and resid 263 through 267 Processing helix chain 'K' and resid 268 through 281 Processing helix chain 'K' and resid 281 through 290 removed outlier: 4.960A pdb=" N ALA K 287 " --> pdb=" O ARG K 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL K 288 " --> pdb=" O GLY K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG K 298 " --> pdb=" O ASN K 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU K 299 " --> pdb=" O SER K 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 294 through 299' Processing helix chain 'K' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER K 329 " --> pdb=" O ARG K 326 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 361 Processing helix chain 'K' and resid 376 through 383 Processing helix chain 'K' and resid 391 through 402 Processing helix chain 'K' and resid 403 through 410 Processing helix chain 'K' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE K 414 " --> pdb=" O GLY K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 441 removed outlier: 3.628A pdb=" N ARG K 437 " --> pdb=" O HIS K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 16 Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 55 through 57 No H-bonds generated for 'chain 'L' and resid 55 through 57' Processing helix chain 'L' and resid 58 through 62 removed outlier: 4.164A pdb=" N VAL L 61 " --> pdb=" O GLU L 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG L 62 " --> pdb=" O GLY L 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 58 through 62' Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.615A pdb=" N THR L 76 " --> pdb=" O ASP L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 123 Processing helix chain 'L' and resid 167 through 180 Processing helix chain 'L' and resid 203 through 225 Processing helix chain 'L' and resid 263 through 267 Processing helix chain 'L' and resid 268 through 281 Processing helix chain 'L' and resid 281 through 290 removed outlier: 4.961A pdb=" N ALA L 287 " --> pdb=" O ARG L 283 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL L 288 " --> pdb=" O GLY L 284 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.746A pdb=" N ARG L 298 " --> pdb=" O ASN L 294 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 299 " --> pdb=" O SER L 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 294 through 299' Processing helix chain 'L' and resid 326 through 330 removed outlier: 3.629A pdb=" N SER L 329 " --> pdb=" O ARG L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 361 Processing helix chain 'L' and resid 376 through 383 Processing helix chain 'L' and resid 391 through 402 Processing helix chain 'L' and resid 403 through 410 Processing helix chain 'L' and resid 410 through 431 removed outlier: 3.551A pdb=" N PHE L 414 " --> pdb=" O GLY L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 433 through 441 removed outlier: 3.557A pdb=" N ARG L 437 " --> pdb=" O HIS L 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS A 88 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A 89 " --> pdb=" O PHE A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU A 126 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS A 245 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 185 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU A 149 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS G 88 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL G 89 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'G' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU G 126 " --> pdb=" O PHE G 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS G 245 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA G 185 " --> pdb=" O ASP G 198 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU G 149 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS H 88 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 89 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB6, first strand: chain 'H' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR H 102 " --> pdb=" O ASN H 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU H 126 " --> pdb=" O PHE H 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS H 245 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA H 185 " --> pdb=" O ASP H 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU H 149 " --> pdb=" O LYS H 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS I 88 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL I 89 " --> pdb=" O PHE I 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AC3, first strand: chain 'I' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU I 126 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS I 245 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA I 185 " --> pdb=" O ASP I 198 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU I 149 " --> pdb=" O LYS I 139 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS B 88 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AC9, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 126 through 132 removed outlier: 3.675A pdb=" N GLU B 126 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS B 245 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 185 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU B 149 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS C 88 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL C 89 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD6, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU C 126 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS C 245 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA C 185 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU C 149 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS J 88 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL J 89 " --> pdb=" O PHE J 80 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 53 Processing sheet with id=AE3, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU J 126 " --> pdb=" O PHE J 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS J 245 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU J 149 " --> pdb=" O LYS J 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA J 185 " --> pdb=" O ASP J 198 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU J 149 " --> pdb=" O LYS J 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS D 88 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL D 89 " --> pdb=" O PHE D 80 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE9, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU D 126 " --> pdb=" O PHE D 251 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS D 245 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU D 149 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 185 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 146 through 150 removed outlier: 5.556A pdb=" N GLU D 149 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS E 88 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL E 89 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 51 through 53 Processing sheet with id=AF6, first strand: chain 'E' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU E 126 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS E 245 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU E 149 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA E 185 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU E 149 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS F 88 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL F 89 " --> pdb=" O PHE F 80 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AG3, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU F 126 " --> pdb=" O PHE F 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS F 245 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA F 185 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU F 149 " --> pdb=" O LYS F 139 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 32 through 38 removed outlier: 5.526A pdb=" N LYS K 88 " --> pdb=" O VAL K 18 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL K 89 " --> pdb=" O PHE K 80 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 51 through 53 Processing sheet with id=AG9, first strand: chain 'K' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR K 102 " --> pdb=" O ASN K 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU K 126 " --> pdb=" O PHE K 251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS K 245 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU K 149 " --> pdb=" O LYS K 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA K 185 " --> pdb=" O ASP K 198 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU K 149 " --> pdb=" O LYS K 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 32 through 38 removed outlier: 5.527A pdb=" N LYS L 88 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL L 89 " --> pdb=" O PHE L 80 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 51 through 53 Processing sheet with id=AH6, first strand: chain 'L' and resid 97 through 98 removed outlier: 3.867A pdb=" N THR L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 126 through 132 removed outlier: 3.674A pdb=" N GLU L 126 " --> pdb=" O PHE L 251 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS L 245 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU L 149 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA L 185 " --> pdb=" O ASP L 198 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 146 through 150 removed outlier: 5.557A pdb=" N GLU L 149 " --> pdb=" O LYS L 139 " (cutoff:3.500A) 1979 hydrogen bonds defined for protein. 5721 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: 17.17 Time building geometry restraints manager: 17.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10940 1.33 - 1.45: 7687 1.45 - 1.57: 23397 1.57 - 1.69: 0 1.69 - 1.81: 372 Bond restraints: 42396 Sorted by residual: bond pdb=" N THR H 292 " pdb=" CA THR H 292 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.18e-02 7.18e+03 1.01e+01 bond pdb=" N THR D 292 " pdb=" CA THR D 292 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 1.00e+01 bond pdb=" N THR E 292 " pdb=" CA THR E 292 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.18e-02 7.18e+03 9.80e+00 bond pdb=" N ILE I 358 " pdb=" CA ILE I 358 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 8.95e+00 bond pdb=" N ILE B 221 " pdb=" CA ILE B 221 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.92e+00 ... (remaining 42391 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.15: 1541 107.15 - 113.97: 23535 113.97 - 120.78: 18433 120.78 - 127.60: 13551 127.60 - 134.41: 444 Bond angle restraints: 57504 Sorted by residual: angle pdb=" CA ILE E 418 " pdb=" C ILE E 418 " pdb=" O ILE E 418 " ideal model delta sigma weight residual 121.27 117.64 3.63 1.04e+00 9.25e-01 1.22e+01 angle pdb=" CA ILE A 418 " pdb=" C ILE A 418 " pdb=" O ILE A 418 " ideal model delta sigma weight residual 121.27 117.70 3.57 1.04e+00 9.25e-01 1.18e+01 angle pdb=" CA ILE C 418 " pdb=" C ILE C 418 " pdb=" O ILE C 418 " ideal model delta sigma weight residual 121.27 117.71 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" CA ILE I 418 " pdb=" C ILE I 418 " pdb=" O ILE I 418 " ideal model delta sigma weight residual 121.27 117.71 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" N TYR J 373 " pdb=" CA TYR J 373 " pdb=" C TYR J 373 " ideal model delta sigma weight residual 114.75 110.64 4.11 1.26e+00 6.30e-01 1.06e+01 ... (remaining 57499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 23089 17.97 - 35.95: 1643 35.95 - 53.92: 461 53.92 - 71.89: 90 71.89 - 89.87: 49 Dihedral angle restraints: 25332 sinusoidal: 9948 harmonic: 15384 Sorted by residual: dihedral pdb=" CA GLU L 15 " pdb=" C GLU L 15 " pdb=" N GLN L 16 " pdb=" CA GLN L 16 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA GLU F 15 " pdb=" C GLU F 15 " pdb=" N GLN F 16 " pdb=" CA GLN F 16 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.84e+00 dihedral pdb=" CA GLU K 15 " pdb=" C GLU K 15 " pdb=" N GLN K 16 " pdb=" CA GLN K 16 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.84e+00 ... (remaining 25329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4593 0.045 - 0.089: 1082 0.089 - 0.134: 540 0.134 - 0.179: 75 0.179 - 0.223: 10 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CA ILE E 293 " pdb=" N ILE E 293 " pdb=" C ILE E 293 " pdb=" CB ILE E 293 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE H 293 " pdb=" N ILE H 293 " pdb=" C ILE H 293 " pdb=" CB ILE H 293 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE D 293 " pdb=" N ILE D 293 " pdb=" C ILE D 293 " pdb=" CB ILE D 293 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 6297 not shown) Planarity restraints: 7512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 244 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C MET A 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET A 244 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS A 245 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 244 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C MET I 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET I 244 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS I 245 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 244 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C MET C 244 " -0.025 2.00e-02 2.50e+03 pdb=" O MET C 244 " 0.009 2.00e-02 2.50e+03 pdb=" N HIS C 245 " 0.008 2.00e-02 2.50e+03 ... (remaining 7509 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 592 2.65 - 3.21: 38398 3.21 - 3.77: 65063 3.77 - 4.34: 92844 4.34 - 4.90: 154434 Nonbonded interactions: 351331 Sorted by model distance: nonbonded pdb=" OE2 GLU I 333 " pdb="MG MG I 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU J 333 " pdb="MG MG J 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU A 333 " pdb="MG MG A 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU C 333 " pdb="MG MG C 502 " model vdw 2.083 2.170 nonbonded pdb=" OE2 GLU G 333 " pdb="MG MG G 502 " model vdw 2.084 2.170 ... (remaining 351326 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.92 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.630 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 109.060 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 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 0.038 42396 Z= 0.277 Angle : 0.675 6.218 57504 Z= 0.448 Chirality : 0.048 0.223 6300 Planarity : 0.004 0.034 7512 Dihedral : 14.579 89.866 15420 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.18 % Allowed : 1.87 % Favored : 95.95 % 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: 0.27 (0.12), residues: 5292 helix: 1.41 (0.11), residues: 2052 sheet: -0.30 (0.18), residues: 900 loop : -0.69 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 435 HIS 0.003 0.000 HIS A 416 PHE 0.010 0.001 PHE G 124 TYR 0.011 0.001 TYR E 285 ARG 0.002 0.000 ARG F 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 938 time to evaluate : 4.582 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7389 (mmt) cc_final: 0.6992 (tpt) REVERT: A 69 TYR cc_start: 0.6868 (m-80) cc_final: 0.6577 (m-80) REVERT: A 73 ASP cc_start: 0.6510 (t0) cc_final: 0.5227 (m-30) REVERT: A 181 PHE cc_start: 0.4973 (m-10) cc_final: 0.4531 (m-80) REVERT: A 182 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6613 (mt-10) REVERT: A 224 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6997 (pttm) REVERT: A 361 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6023 (mm-30) REVERT: A 386 TYR cc_start: 0.5478 (m-80) cc_final: 0.4852 (m-80) REVERT: A 390 GLU cc_start: 0.6803 (pm20) cc_final: 0.6344 (pm20) REVERT: A 398 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5405 (mm-30) REVERT: G 43 LYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5681 (mptt) REVERT: G 51 MET cc_start: 0.7459 (mmt) cc_final: 0.7257 (tpt) REVERT: G 67 ASP cc_start: 0.5943 (m-30) cc_final: 0.5574 (p0) REVERT: G 69 TYR cc_start: 0.6877 (m-80) cc_final: 0.6565 (m-80) REVERT: G 73 ASP cc_start: 0.6407 (t0) cc_final: 0.5440 (m-30) REVERT: G 182 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6520 (mt-10) REVERT: G 223 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6032 (tpt90) REVERT: G 361 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6082 (mm-30) REVERT: G 386 TYR cc_start: 0.5238 (m-80) cc_final: 0.4684 (m-80) REVERT: G 390 GLU cc_start: 0.6713 (pm20) cc_final: 0.6209 (pm20) REVERT: H 24 GLN cc_start: 0.5429 (pt0) cc_final: 0.5224 (pt0) REVERT: H 51 MET cc_start: 0.7391 (mmt) cc_final: 0.7044 (tpt) REVERT: H 69 TYR cc_start: 0.7100 (m-80) cc_final: 0.6856 (m-80) REVERT: H 73 ASP cc_start: 0.6576 (t0) cc_final: 0.5409 (m-30) REVERT: H 118 GLU cc_start: 0.5036 (mt-10) cc_final: 0.4715 (tt0) REVERT: H 119 MET cc_start: 0.6552 (ttp) cc_final: 0.6318 (ttp) REVERT: H 181 PHE cc_start: 0.4790 (m-10) cc_final: 0.4342 (m-80) REVERT: H 182 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6629 (mt-10) REVERT: H 223 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6256 (tpt90) REVERT: H 360 ASP cc_start: 0.6494 (m-30) cc_final: 0.6276 (m-30) REVERT: H 361 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6228 (mm-30) REVERT: H 386 TYR cc_start: 0.5524 (m-80) cc_final: 0.4886 (m-80) REVERT: I 7 GLU cc_start: 0.5553 (mp0) cc_final: 0.5057 (mm-30) REVERT: I 51 MET cc_start: 0.7667 (mmt) cc_final: 0.7284 (tpt) REVERT: I 67 ASP cc_start: 0.6267 (m-30) cc_final: 0.5521 (p0) REVERT: I 69 TYR cc_start: 0.6548 (m-80) cc_final: 0.6118 (m-80) REVERT: I 73 ASP cc_start: 0.6306 (t0) cc_final: 0.5387 (m-30) REVERT: I 93 ILE cc_start: 0.6138 (mm) cc_final: 0.5778 (mm) REVERT: I 128 ASN cc_start: 0.7476 (m-40) cc_final: 0.7202 (m110) REVERT: I 181 PHE cc_start: 0.4831 (m-10) cc_final: 0.4405 (m-80) REVERT: I 182 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6486 (mt-10) REVERT: I 223 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6295 (tpt90) REVERT: I 361 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6134 (mm-30) REVERT: I 386 TYR cc_start: 0.5443 (m-80) cc_final: 0.4775 (m-80) REVERT: I 390 GLU cc_start: 0.6829 (pm20) cc_final: 0.6330 (pm20) REVERT: I 398 GLU cc_start: 0.5783 (mm-30) cc_final: 0.5301 (mm-30) REVERT: B 7 GLU cc_start: 0.5946 (mp0) cc_final: 0.5293 (mm-30) REVERT: B 67 ASP cc_start: 0.6128 (m-30) cc_final: 0.5638 (p0) REVERT: B 69 TYR cc_start: 0.6735 (m-80) cc_final: 0.6418 (m-80) REVERT: B 73 ASP cc_start: 0.6448 (t0) cc_final: 0.5518 (m-30) REVERT: B 181 PHE cc_start: 0.4735 (m-10) cc_final: 0.4345 (m-80) REVERT: B 182 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6502 (mt-10) REVERT: B 223 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6156 (tpt170) REVERT: B 361 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6132 (mm-30) REVERT: B 390 GLU cc_start: 0.6597 (pm20) cc_final: 0.6239 (pt0) REVERT: C 7 GLU cc_start: 0.5889 (mp0) cc_final: 0.5390 (mm-30) REVERT: C 43 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5645 (mptt) REVERT: C 49 LYS cc_start: 0.6953 (mmmm) cc_final: 0.6572 (mmmt) REVERT: C 67 ASP cc_start: 0.6194 (m-30) cc_final: 0.5683 (p0) REVERT: C 73 ASP cc_start: 0.6449 (t0) cc_final: 0.5447 (m-30) REVERT: C 93 ILE cc_start: 0.6339 (mm) cc_final: 0.6019 (mm) REVERT: C 181 PHE cc_start: 0.4807 (m-10) cc_final: 0.4362 (m-80) REVERT: C 182 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6634 (mt-10) REVERT: C 223 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6175 (tpt90) REVERT: C 240 ASN cc_start: 0.5652 (t0) cc_final: 0.5424 (p0) REVERT: C 386 TYR cc_start: 0.5550 (m-80) cc_final: 0.4812 (m-80) REVERT: C 390 GLU cc_start: 0.6772 (pm20) cc_final: 0.6244 (pm20) REVERT: J 43 LYS cc_start: 0.6441 (ttmm) cc_final: 0.5829 (mptt) REVERT: J 47 ASP cc_start: 0.5817 (m-30) cc_final: 0.5616 (t0) REVERT: J 51 MET cc_start: 0.7573 (mmt) cc_final: 0.7159 (tpt) REVERT: J 73 ASP cc_start: 0.6555 (t0) cc_final: 0.5263 (m-30) REVERT: J 181 PHE cc_start: 0.4681 (m-10) cc_final: 0.4216 (m-80) REVERT: J 182 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6595 (mt-10) REVERT: J 223 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6215 (tpt90) REVERT: J 360 ASP cc_start: 0.6529 (m-30) cc_final: 0.6312 (m-30) REVERT: J 361 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6140 (mm-30) REVERT: J 386 TYR cc_start: 0.5563 (m-80) cc_final: 0.4883 (m-80) REVERT: J 390 GLU cc_start: 0.6819 (pm20) cc_final: 0.6361 (pm20) REVERT: J 398 GLU cc_start: 0.5853 (mm-30) cc_final: 0.5454 (mm-30) REVERT: D 51 MET cc_start: 0.7567 (mmt) cc_final: 0.7359 (tpt) REVERT: D 67 ASP cc_start: 0.6078 (m-30) cc_final: 0.5640 (p0) REVERT: D 69 TYR cc_start: 0.6790 (m-80) cc_final: 0.6517 (m-80) REVERT: D 73 ASP cc_start: 0.6440 (t0) cc_final: 0.5535 (m-30) REVERT: D 93 ILE cc_start: 0.6130 (mm) cc_final: 0.5928 (mm) REVERT: D 181 PHE cc_start: 0.4644 (m-10) cc_final: 0.4248 (m-80) REVERT: D 182 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6417 (mt-10) REVERT: D 223 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6008 (tpt90) REVERT: D 361 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6073 (mm-30) REVERT: D 386 TYR cc_start: 0.5414 (m-80) cc_final: 0.4730 (m-80) REVERT: D 390 GLU cc_start: 0.6723 (pm20) cc_final: 0.6232 (pm20) REVERT: E 51 MET cc_start: 0.7430 (mmt) cc_final: 0.7135 (tpt) REVERT: E 69 TYR cc_start: 0.7008 (m-80) cc_final: 0.6664 (m-80) REVERT: E 73 ASP cc_start: 0.6566 (t0) cc_final: 0.5402 (m-30) REVERT: E 118 GLU cc_start: 0.5150 (mt-10) cc_final: 0.4797 (tt0) REVERT: E 167 ASN cc_start: 0.6341 (t0) cc_final: 0.6134 (t0) REVERT: E 181 PHE cc_start: 0.4735 (m-10) cc_final: 0.4259 (m-80) REVERT: E 182 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6642 (mt-10) REVERT: E 240 ASN cc_start: 0.5602 (t0) cc_final: 0.5270 (p0) REVERT: E 361 GLU cc_start: 0.6758 (mt-10) cc_final: 0.6179 (mm-30) REVERT: E 386 TYR cc_start: 0.5570 (m-80) cc_final: 0.4928 (m-80) REVERT: E 390 GLU cc_start: 0.6781 (pm20) cc_final: 0.6234 (pm20) REVERT: F 7 GLU cc_start: 0.5783 (mp0) cc_final: 0.5213 (mm-30) REVERT: F 51 MET cc_start: 0.7495 (mmt) cc_final: 0.7082 (tpt) REVERT: F 69 TYR cc_start: 0.6611 (m-80) cc_final: 0.6265 (m-80) REVERT: F 73 ASP cc_start: 0.6281 (t0) cc_final: 0.5238 (m-30) REVERT: F 144 ARG cc_start: 0.6621 (mmm160) cc_final: 0.6361 (mmm160) REVERT: F 181 PHE cc_start: 0.4799 (m-10) cc_final: 0.4443 (m-80) REVERT: F 182 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6579 (mt-10) REVERT: F 223 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6139 (tpt90) REVERT: F 361 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6038 (mm-30) REVERT: F 386 TYR cc_start: 0.5327 (m-80) cc_final: 0.4783 (m-80) REVERT: F 390 GLU cc_start: 0.6701 (pm20) cc_final: 0.6336 (pt0) REVERT: F 398 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5301 (mm-30) REVERT: K 49 LYS cc_start: 0.6736 (mmmm) cc_final: 0.6498 (mmmt) REVERT: K 51 MET cc_start: 0.7451 (mmt) cc_final: 0.7242 (tpt) REVERT: K 67 ASP cc_start: 0.5992 (m-30) cc_final: 0.5619 (p0) REVERT: K 73 ASP cc_start: 0.6442 (t0) cc_final: 0.5538 (m-30) REVERT: K 182 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6541 (mt-10) REVERT: K 223 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6030 (tpt90) REVERT: K 240 ASN cc_start: 0.5827 (t0) cc_final: 0.5595 (p0) REVERT: K 361 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6130 (mm-30) REVERT: K 390 GLU cc_start: 0.6748 (pm20) cc_final: 0.6240 (pm20) REVERT: L 7 GLU cc_start: 0.5897 (mp0) cc_final: 0.5375 (mm-30) REVERT: L 43 LYS cc_start: 0.6622 (ttmm) cc_final: 0.5852 (mptt) REVERT: L 47 ASP cc_start: 0.5627 (m-30) cc_final: 0.5331 (t0) REVERT: L 51 MET cc_start: 0.7475 (mmt) cc_final: 0.7184 (tpt) REVERT: L 69 TYR cc_start: 0.6708 (m-80) cc_final: 0.6452 (m-80) REVERT: L 73 ASP cc_start: 0.6558 (t0) cc_final: 0.5445 (m-30) REVERT: L 93 ILE cc_start: 0.6045 (mm) cc_final: 0.5811 (mm) REVERT: L 181 PHE cc_start: 0.4806 (m-10) cc_final: 0.4376 (m-80) REVERT: L 182 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6630 (mt-10) REVERT: L 223 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6278 (tpt90) REVERT: L 240 ASN cc_start: 0.5559 (t0) cc_final: 0.5329 (p0) REVERT: L 360 ASP cc_start: 0.6530 (m-30) cc_final: 0.6313 (m-30) REVERT: L 361 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6299 (mm-30) REVERT: L 386 TYR cc_start: 0.5644 (m-80) cc_final: 0.4932 (m-80) outliers start: 93 outliers final: 1 residues processed: 999 average time/residue: 1.6636 time to fit residues: 1999.6057 Evaluate side-chains 706 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 692 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 223 ARG Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain I residue 223 ARG Chi-restraints excluded: chain I residue 421 LYS Chi-restraints excluded: chain B residue 223 ARG Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain J residue 223 ARG Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain K residue 223 ARG Chi-restraints excluded: chain L residue 223 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 413 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 479 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 34 ASN A 128 ASN A 194 GLN A 281 HIS G 17 ASN G 24 GLN G 34 ASN G 128 ASN G 281 HIS H 17 ASN H 34 ASN H 194 GLN H 281 HIS I 17 ASN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN I 281 HIS B 17 ASN B 24 GLN B 34 ASN B 128 ASN B 281 HIS C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS J 17 ASN J 34 ASN J 128 ASN J 194 GLN J 281 HIS D 17 ASN D 24 GLN D 34 ASN D 128 ASN D 194 GLN D 281 HIS E 17 ASN E 34 ASN E 128 ASN E 281 HIS F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN F 194 GLN F 281 HIS K 17 ASN K 24 GLN K 34 ASN K 128 ASN K 281 HIS L 17 ASN L 34 ASN L 281 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6404 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 42396 Z= 0.241 Angle : 0.591 7.952 57504 Z= 0.300 Chirality : 0.043 0.199 6300 Planarity : 0.004 0.041 7512 Dihedral : 4.915 59.722 5780 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.02 % Allowed : 10.30 % Favored : 86.68 % 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: 0.35 (0.12), residues: 5292 helix: 1.85 (0.11), residues: 2052 sheet: -0.54 (0.18), residues: 900 loop : -0.90 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 435 HIS 0.005 0.001 HIS L 416 PHE 0.017 0.002 PHE A 20 TYR 0.018 0.002 TYR I 285 ARG 0.003 0.000 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 708 time to evaluate : 4.925 Fit side-chains revert: symmetry clash REVERT: A 51 MET cc_start: 0.7732 (mmt) cc_final: 0.7311 (tpt) REVERT: A 67 ASP cc_start: 0.6328 (m-30) cc_final: 0.5627 (p0) REVERT: A 73 ASP cc_start: 0.6347 (t0) cc_final: 0.5316 (m-30) REVERT: A 181 PHE cc_start: 0.4655 (m-10) cc_final: 0.4154 (m-80) REVERT: A 182 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6516 (mt-10) REVERT: A 224 LYS cc_start: 0.6848 (tmmt) cc_final: 0.6640 (ttpt) REVERT: A 360 ASP cc_start: 0.6014 (m-30) cc_final: 0.5733 (m-30) REVERT: A 361 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6070 (mm-30) REVERT: A 390 GLU cc_start: 0.6868 (pm20) cc_final: 0.6328 (pm20) REVERT: A 398 GLU cc_start: 0.5937 (mm-30) cc_final: 0.5559 (mm-30) REVERT: G 7 GLU cc_start: 0.5755 (mp0) cc_final: 0.5227 (mm-30) REVERT: G 16 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.5962 (mm-40) REVERT: G 17 ASN cc_start: 0.7164 (t0) cc_final: 0.6914 (t0) REVERT: G 43 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5920 (mptt) REVERT: G 51 MET cc_start: 0.7692 (mmt) cc_final: 0.7446 (tpt) REVERT: G 67 ASP cc_start: 0.5905 (m-30) cc_final: 0.5652 (p0) REVERT: G 73 ASP cc_start: 0.6402 (t0) cc_final: 0.5460 (m-30) REVERT: G 181 PHE cc_start: 0.4665 (m-10) cc_final: 0.4230 (m-80) REVERT: G 182 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6390 (mt-10) REVERT: G 223 ARG cc_start: 0.6660 (ttm-80) cc_final: 0.6161 (tpt170) REVERT: G 224 LYS cc_start: 0.6481 (pttt) cc_final: 0.6235 (pttm) REVERT: G 278 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6382 (mtm) REVERT: G 361 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6127 (mm-30) REVERT: G 390 GLU cc_start: 0.6705 (pm20) cc_final: 0.6400 (pt0) REVERT: G 414 PHE cc_start: 0.6905 (t80) cc_final: 0.6644 (t80) REVERT: H 7 GLU cc_start: 0.5778 (mp0) cc_final: 0.5449 (mm-30) REVERT: H 16 GLN cc_start: 0.6655 (OUTLIER) cc_final: 0.6111 (mm-40) REVERT: H 36 GLU cc_start: 0.6040 (mt-10) cc_final: 0.5747 (mp0) REVERT: H 51 MET cc_start: 0.7645 (mmt) cc_final: 0.7377 (mmp) REVERT: H 67 ASP cc_start: 0.6264 (m-30) cc_final: 0.5547 (p0) REVERT: H 73 ASP cc_start: 0.6231 (t0) cc_final: 0.5281 (m-30) REVERT: H 144 ARG cc_start: 0.6416 (mmm160) cc_final: 0.6135 (mmm160) REVERT: H 181 PHE cc_start: 0.4600 (m-10) cc_final: 0.4121 (m-80) REVERT: H 182 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6554 (mt-10) REVERT: H 223 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.6122 (tpt90) REVERT: H 224 LYS cc_start: 0.6594 (pttt) cc_final: 0.6356 (pttm) REVERT: H 361 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6389 (mm-30) REVERT: I 7 GLU cc_start: 0.5606 (mp0) cc_final: 0.5200 (mm-30) REVERT: I 33 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6243 (mmmt) REVERT: I 51 MET cc_start: 0.7668 (mmt) cc_final: 0.7336 (tpt) REVERT: I 67 ASP cc_start: 0.5935 (m-30) cc_final: 0.5728 (p0) REVERT: I 69 TYR cc_start: 0.7305 (m-80) cc_final: 0.7102 (m-80) REVERT: I 73 ASP cc_start: 0.6333 (t0) cc_final: 0.5309 (m-30) REVERT: I 145 ARG cc_start: 0.5650 (mmm160) cc_final: 0.5373 (mmp-170) REVERT: I 181 PHE cc_start: 0.4797 (m-10) cc_final: 0.4399 (m-80) REVERT: I 182 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6401 (mt-10) REVERT: I 361 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6188 (mm-30) REVERT: I 390 GLU cc_start: 0.6805 (pm20) cc_final: 0.6594 (pt0) REVERT: I 398 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5589 (mm-30) REVERT: I 419 GLU cc_start: 0.4991 (tt0) cc_final: 0.4600 (mt-10) REVERT: B 7 GLU cc_start: 0.5839 (mp0) cc_final: 0.5371 (mm-30) REVERT: B 51 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7447 (tpt) REVERT: B 67 ASP cc_start: 0.5870 (m-30) cc_final: 0.5642 (p0) REVERT: B 73 ASP cc_start: 0.6434 (t0) cc_final: 0.5521 (m-30) REVERT: B 139 LYS cc_start: 0.6870 (mttt) cc_final: 0.6655 (mtpp) REVERT: B 181 PHE cc_start: 0.4839 (m-10) cc_final: 0.4459 (m-80) REVERT: B 182 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6301 (mt-10) REVERT: B 223 ARG cc_start: 0.6753 (ttm-80) cc_final: 0.6148 (tpt170) REVERT: B 224 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6139 (pttm) REVERT: B 338 ASP cc_start: 0.7297 (p0) cc_final: 0.6843 (p0) REVERT: B 361 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6283 (mm-30) REVERT: B 390 GLU cc_start: 0.6508 (pm20) cc_final: 0.6276 (pt0) REVERT: C 7 GLU cc_start: 0.5968 (mp0) cc_final: 0.5646 (mm-30) REVERT: C 43 LYS cc_start: 0.6834 (ttmm) cc_final: 0.6132 (mptt) REVERT: C 49 LYS cc_start: 0.7015 (mmmm) cc_final: 0.6781 (mmmt) REVERT: C 67 ASP cc_start: 0.6032 (m-30) cc_final: 0.5818 (p0) REVERT: C 69 TYR cc_start: 0.7128 (m-80) cc_final: 0.6717 (m-80) REVERT: C 73 ASP cc_start: 0.6404 (t0) cc_final: 0.5392 (m-30) REVERT: C 181 PHE cc_start: 0.4599 (m-10) cc_final: 0.4119 (m-80) REVERT: C 182 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6602 (mt-10) REVERT: C 223 ARG cc_start: 0.6637 (ttm-80) cc_final: 0.6125 (tpt90) REVERT: C 224 LYS cc_start: 0.6559 (pttt) cc_final: 0.6321 (pttm) REVERT: C 390 GLU cc_start: 0.6747 (pm20) cc_final: 0.6467 (pt0) REVERT: J 7 GLU cc_start: 0.5945 (mp0) cc_final: 0.5371 (mm-30) REVERT: J 16 GLN cc_start: 0.6848 (mt0) cc_final: 0.6271 (mm-40) REVERT: J 17 ASN cc_start: 0.7037 (OUTLIER) cc_final: 0.6828 (t0) REVERT: J 43 LYS cc_start: 0.6501 (ttmm) cc_final: 0.5864 (mptt) REVERT: J 51 MET cc_start: 0.7783 (mmt) cc_final: 0.7351 (tpt) REVERT: J 67 ASP cc_start: 0.6394 (m-30) cc_final: 0.5648 (p0) REVERT: J 73 ASP cc_start: 0.6372 (t0) cc_final: 0.5334 (m-30) REVERT: J 181 PHE cc_start: 0.4765 (m-10) cc_final: 0.4269 (m-80) REVERT: J 182 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6524 (mt-10) REVERT: J 361 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6193 (mm-30) REVERT: J 390 GLU cc_start: 0.6837 (pm20) cc_final: 0.6322 (pm20) REVERT: J 398 GLU cc_start: 0.5971 (mm-30) cc_final: 0.5608 (mm-30) REVERT: D 17 ASN cc_start: 0.7138 (t0) cc_final: 0.6858 (t0) REVERT: D 51 MET cc_start: 0.7520 (mmt) cc_final: 0.7250 (tpt) REVERT: D 73 ASP cc_start: 0.6396 (t0) cc_final: 0.5501 (m-30) REVERT: D 181 PHE cc_start: 0.4755 (m-10) cc_final: 0.4324 (m-80) REVERT: D 182 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6308 (mt-10) REVERT: D 223 ARG cc_start: 0.6652 (ttm-80) cc_final: 0.6173 (tpt170) REVERT: D 224 LYS cc_start: 0.6463 (pttt) cc_final: 0.6218 (pttm) REVERT: D 338 ASP cc_start: 0.7362 (p0) cc_final: 0.6844 (p0) REVERT: D 361 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6150 (mm-30) REVERT: D 390 GLU cc_start: 0.6747 (pm20) cc_final: 0.6436 (pt0) REVERT: E 7 GLU cc_start: 0.5777 (mp0) cc_final: 0.5452 (mm-30) REVERT: E 16 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.6116 (mm-40) REVERT: E 51 MET cc_start: 0.7640 (mmt) cc_final: 0.7380 (mmp) REVERT: E 67 ASP cc_start: 0.6174 (m-30) cc_final: 0.5540 (p0) REVERT: E 73 ASP cc_start: 0.6326 (t0) cc_final: 0.5276 (m-30) REVERT: E 144 ARG cc_start: 0.6447 (mmm160) cc_final: 0.6160 (mmm160) REVERT: E 181 PHE cc_start: 0.4570 (m-10) cc_final: 0.4074 (m-80) REVERT: E 182 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6539 (mt-10) REVERT: E 223 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6548 (tpp-160) REVERT: E 248 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6535 (ptp) REVERT: E 361 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6326 (mm-30) REVERT: E 390 GLU cc_start: 0.6735 (pm20) cc_final: 0.6427 (pt0) REVERT: F 7 GLU cc_start: 0.5777 (mp0) cc_final: 0.5363 (mm-30) REVERT: F 16 GLN cc_start: 0.7132 (mt0) cc_final: 0.6552 (mm-40) REVERT: F 51 MET cc_start: 0.7670 (mmt) cc_final: 0.7226 (tpt) REVERT: F 67 ASP cc_start: 0.6265 (m-30) cc_final: 0.5530 (p0) REVERT: F 68 MET cc_start: 0.6988 (ptm) cc_final: 0.6760 (ptm) REVERT: F 73 ASP cc_start: 0.6195 (t0) cc_final: 0.5213 (m-30) REVERT: F 145 ARG cc_start: 0.5674 (mmm160) cc_final: 0.3639 (ptm-80) REVERT: F 181 PHE cc_start: 0.4770 (m-10) cc_final: 0.4290 (m-80) REVERT: F 182 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6525 (mt-10) REVERT: F 361 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6159 (mm-30) REVERT: F 390 GLU cc_start: 0.6674 (pm20) cc_final: 0.6434 (pt0) REVERT: F 398 GLU cc_start: 0.5997 (mm-30) cc_final: 0.5631 (mm-30) REVERT: K 16 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.5895 (mm-40) REVERT: K 17 ASN cc_start: 0.7122 (t0) cc_final: 0.6898 (t0) REVERT: K 51 MET cc_start: 0.7662 (mmt) cc_final: 0.7425 (tpt) REVERT: K 73 ASP cc_start: 0.6379 (t0) cc_final: 0.5438 (m-30) REVERT: K 175 GLU cc_start: 0.4843 (tp30) cc_final: 0.4509 (tp30) REVERT: K 178 GLU cc_start: 0.6417 (tt0) cc_final: 0.6028 (pt0) REVERT: K 181 PHE cc_start: 0.4617 (m-10) cc_final: 0.4175 (m-80) REVERT: K 182 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6345 (mt-10) REVERT: K 223 ARG cc_start: 0.6625 (ttm-80) cc_final: 0.6092 (tpt170) REVERT: K 224 LYS cc_start: 0.6521 (pttt) cc_final: 0.6269 (pttm) REVERT: K 240 ASN cc_start: 0.5833 (t0) cc_final: 0.5377 (p0) REVERT: K 278 MET cc_start: 0.6722 (mtp) cc_final: 0.6431 (mtm) REVERT: K 361 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6074 (mm-30) REVERT: K 390 GLU cc_start: 0.6719 (pm20) cc_final: 0.6395 (pt0) REVERT: K 414 PHE cc_start: 0.6884 (t80) cc_final: 0.6610 (t80) REVERT: L 7 GLU cc_start: 0.5819 (mp0) cc_final: 0.5488 (mm-30) REVERT: L 16 GLN cc_start: 0.6614 (OUTLIER) cc_final: 0.6182 (mm-40) REVERT: L 43 LYS cc_start: 0.6735 (ttmm) cc_final: 0.5968 (mptt) REVERT: L 51 MET cc_start: 0.7619 (mmt) cc_final: 0.7388 (mmp) REVERT: L 67 ASP cc_start: 0.6232 (m-30) cc_final: 0.5521 (p0) REVERT: L 73 ASP cc_start: 0.6365 (t0) cc_final: 0.5347 (m-30) REVERT: L 145 ARG cc_start: 0.5644 (mmm160) cc_final: 0.5367 (mmp-170) REVERT: L 181 PHE cc_start: 0.4568 (m-10) cc_final: 0.4116 (m-80) REVERT: L 182 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6505 (mt-10) REVERT: L 223 ARG cc_start: 0.6607 (ttm-80) cc_final: 0.6070 (tpt90) REVERT: L 361 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6396 (mm-30) REVERT: L 398 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5742 (mm-30) outliers start: 129 outliers final: 54 residues processed: 775 average time/residue: 1.5677 time to fit residues: 1475.4545 Evaluate side-chains 702 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 635 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 179 MET Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 16 GLN Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 16 GLN Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 328 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.2980 chunk 148 optimal weight: 0.0020 chunk 399 optimal weight: 3.9990 chunk 326 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 480 optimal weight: 3.9990 chunk 518 optimal weight: 4.9990 chunk 427 optimal weight: 8.9990 chunk 476 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 385 optimal weight: 2.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 24 GLN A 34 ASN G 24 GLN G 34 ASN G 128 ASN H 17 ASN H 34 ASN H 194 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 ASN B 24 GLN B 34 ASN C 17 ASN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN J 24 GLN J 34 ASN D 24 GLN D 34 ASN D 128 ASN D 194 GLN E 17 ASN E 34 ASN F 17 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN K 24 GLN K 34 ASN K 128 ASN L 17 ASN L 34 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42396 Z= 0.260 Angle : 0.581 6.952 57504 Z= 0.297 Chirality : 0.043 0.199 6300 Planarity : 0.004 0.041 7512 Dihedral : 4.540 46.465 5728 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.82 % Allowed : 12.31 % Favored : 83.87 % 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: 0.16 (0.11), residues: 5292 helix: 1.71 (0.11), residues: 2064 sheet: -0.87 (0.17), residues: 900 loop : -0.93 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 435 HIS 0.004 0.001 HIS H 416 PHE 0.015 0.002 PHE J 20 TYR 0.015 0.002 TYR I 285 ARG 0.005 0.001 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 673 time to evaluate : 5.009 Fit side-chains REVERT: A 7 GLU cc_start: 0.5704 (mp0) cc_final: 0.5307 (mm-30) REVERT: A 16 GLN cc_start: 0.7096 (mt0) cc_final: 0.6475 (mm-40) REVERT: A 51 MET cc_start: 0.7767 (mmt) cc_final: 0.7417 (tpt) REVERT: A 67 ASP cc_start: 0.6032 (m-30) cc_final: 0.5557 (p0) REVERT: A 73 ASP cc_start: 0.6268 (t0) cc_final: 0.5327 (m-30) REVERT: A 139 LYS cc_start: 0.7318 (mttt) cc_final: 0.7086 (mttm) REVERT: A 145 ARG cc_start: 0.5723 (mmm160) cc_final: 0.3657 (ptm-80) REVERT: A 181 PHE cc_start: 0.4837 (m-10) cc_final: 0.4292 (m-80) REVERT: A 182 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6435 (mt-10) REVERT: A 223 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6367 (tpt90) REVERT: A 224 LYS cc_start: 0.6831 (ttmt) cc_final: 0.6584 (tttt) REVERT: A 360 ASP cc_start: 0.5949 (m-30) cc_final: 0.5624 (m-30) REVERT: A 361 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6111 (mm-30) REVERT: A 390 GLU cc_start: 0.6910 (pm20) cc_final: 0.6649 (pt0) REVERT: A 415 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5631 (mp0) REVERT: A 419 GLU cc_start: 0.4940 (tt0) cc_final: 0.4622 (mt-10) REVERT: A 444 TYR cc_start: 0.6130 (m-80) cc_final: 0.5889 (m-80) REVERT: G 7 GLU cc_start: 0.5732 (mp0) cc_final: 0.5343 (mm-30) REVERT: G 16 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6250 (mm-40) REVERT: G 43 LYS cc_start: 0.6599 (ttmm) cc_final: 0.5746 (mptt) REVERT: G 51 MET cc_start: 0.7639 (mmt) cc_final: 0.7352 (tpt) REVERT: G 67 ASP cc_start: 0.6009 (m-30) cc_final: 0.5794 (p0) REVERT: G 73 ASP cc_start: 0.6301 (t0) cc_final: 0.5412 (m-30) REVERT: G 181 PHE cc_start: 0.4779 (m-10) cc_final: 0.4294 (m-80) REVERT: G 182 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6346 (mt-10) REVERT: G 223 ARG cc_start: 0.6800 (ttm-80) cc_final: 0.6148 (tpt170) REVERT: G 224 LYS cc_start: 0.6527 (pttt) cc_final: 0.6287 (pttm) REVERT: G 361 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6155 (mm-30) REVERT: G 390 GLU cc_start: 0.6699 (pm20) cc_final: 0.6386 (pt0) REVERT: G 414 PHE cc_start: 0.6919 (t80) cc_final: 0.6683 (t80) REVERT: H 7 GLU cc_start: 0.5848 (mp0) cc_final: 0.5503 (mm-30) REVERT: H 16 GLN cc_start: 0.6657 (mt0) cc_final: 0.6282 (mm-40) REVERT: H 51 MET cc_start: 0.7690 (mmt) cc_final: 0.7060 (mmt) REVERT: H 73 ASP cc_start: 0.6284 (t0) cc_final: 0.5231 (m-30) REVERT: H 144 ARG cc_start: 0.6468 (mmm160) cc_final: 0.6206 (mmm160) REVERT: H 181 PHE cc_start: 0.4680 (m-10) cc_final: 0.4209 (m-80) REVERT: H 182 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6500 (mt-10) REVERT: H 223 ARG cc_start: 0.6761 (ttm-80) cc_final: 0.6134 (tpt90) REVERT: H 224 LYS cc_start: 0.6434 (pttt) cc_final: 0.6226 (pttm) REVERT: H 361 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6355 (mm-30) REVERT: I 7 GLU cc_start: 0.5782 (mp0) cc_final: 0.5419 (mm-30) REVERT: I 51 MET cc_start: 0.7761 (mmt) cc_final: 0.7515 (tpt) REVERT: I 67 ASP cc_start: 0.6084 (m-30) cc_final: 0.5844 (p0) REVERT: I 73 ASP cc_start: 0.6369 (t0) cc_final: 0.5387 (m-30) REVERT: I 145 ARG cc_start: 0.5705 (mmm160) cc_final: 0.3680 (ptm-80) REVERT: I 181 PHE cc_start: 0.4799 (m-10) cc_final: 0.4343 (m-80) REVERT: I 182 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6460 (mt-10) REVERT: I 361 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6134 (mm-30) REVERT: I 390 GLU cc_start: 0.6778 (pm20) cc_final: 0.6399 (pt0) REVERT: I 398 GLU cc_start: 0.6055 (mm-30) cc_final: 0.5691 (mm-30) REVERT: I 415 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5575 (mp0) REVERT: I 419 GLU cc_start: 0.4899 (tt0) cc_final: 0.4556 (mt-10) REVERT: B 7 GLU cc_start: 0.5769 (mp0) cc_final: 0.5368 (mm-30) REVERT: B 17 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6639 (t0) REVERT: B 73 ASP cc_start: 0.6352 (t0) cc_final: 0.5450 (m-30) REVERT: B 139 LYS cc_start: 0.6987 (mttt) cc_final: 0.6762 (mtpp) REVERT: B 149 GLU cc_start: 0.7156 (pt0) cc_final: 0.6881 (pt0) REVERT: B 181 PHE cc_start: 0.4832 (m-10) cc_final: 0.4376 (m-80) REVERT: B 182 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6313 (mt-10) REVERT: B 223 ARG cc_start: 0.6737 (ttm-80) cc_final: 0.6234 (tpt170) REVERT: B 224 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6130 (pttm) REVERT: B 361 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6246 (mm-30) REVERT: B 387 ASP cc_start: 0.7706 (m-30) cc_final: 0.7446 (m-30) REVERT: B 390 GLU cc_start: 0.6682 (pm20) cc_final: 0.6430 (pt0) REVERT: B 414 PHE cc_start: 0.6957 (t80) cc_final: 0.6736 (t80) REVERT: C 7 GLU cc_start: 0.5947 (mp0) cc_final: 0.5550 (mm-30) REVERT: C 17 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.6782 (t0) REVERT: C 43 LYS cc_start: 0.6867 (ttmm) cc_final: 0.6004 (mptt) REVERT: C 49 LYS cc_start: 0.7103 (mmmm) cc_final: 0.6871 (mmpt) REVERT: C 67 ASP cc_start: 0.6178 (m-30) cc_final: 0.5886 (p0) REVERT: C 73 ASP cc_start: 0.6275 (t0) cc_final: 0.5307 (m-30) REVERT: C 120 GLU cc_start: 0.6048 (OUTLIER) cc_final: 0.5828 (mm-30) REVERT: C 181 PHE cc_start: 0.4796 (m-10) cc_final: 0.4326 (m-80) REVERT: C 182 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6517 (mt-10) REVERT: C 224 LYS cc_start: 0.6415 (pttt) cc_final: 0.6195 (pttm) REVERT: C 361 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6337 (mm-30) REVERT: C 390 GLU cc_start: 0.6715 (pm20) cc_final: 0.6361 (pt0) REVERT: C 419 GLU cc_start: 0.5146 (tt0) cc_final: 0.4754 (mt-10) REVERT: J 7 GLU cc_start: 0.5748 (mp0) cc_final: 0.5423 (mm-30) REVERT: J 43 LYS cc_start: 0.6591 (ttmm) cc_final: 0.5783 (mptt) REVERT: J 51 MET cc_start: 0.7866 (mmt) cc_final: 0.7493 (tpt) REVERT: J 67 ASP cc_start: 0.6042 (m-30) cc_final: 0.5540 (p0) REVERT: J 73 ASP cc_start: 0.6290 (t0) cc_final: 0.5211 (m-30) REVERT: J 181 PHE cc_start: 0.4893 (m-10) cc_final: 0.4352 (m-80) REVERT: J 182 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6433 (mt-10) REVERT: J 361 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6129 (mm-30) REVERT: J 375 MET cc_start: 0.5452 (ptp) cc_final: 0.5138 (ptt) REVERT: J 390 GLU cc_start: 0.6958 (pm20) cc_final: 0.6685 (pt0) REVERT: J 415 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.5558 (mp0) REVERT: D 7 GLU cc_start: 0.5596 (mp0) cc_final: 0.5255 (mm-30) REVERT: D 17 ASN cc_start: 0.7265 (t0) cc_final: 0.7039 (t0) REVERT: D 51 MET cc_start: 0.7647 (mmt) cc_final: 0.7422 (tpt) REVERT: D 73 ASP cc_start: 0.6300 (t0) cc_final: 0.5455 (m-30) REVERT: D 145 ARG cc_start: 0.5562 (mmm160) cc_final: 0.5229 (mmt180) REVERT: D 181 PHE cc_start: 0.4740 (m-10) cc_final: 0.4224 (m-80) REVERT: D 182 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6292 (mt-10) REVERT: D 223 ARG cc_start: 0.6793 (ttm-80) cc_final: 0.6262 (tpt170) REVERT: D 224 LYS cc_start: 0.6491 (pttt) cc_final: 0.6245 (pttm) REVERT: D 361 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6210 (mm-30) REVERT: D 390 GLU cc_start: 0.6689 (pm20) cc_final: 0.6392 (pt0) REVERT: D 414 PHE cc_start: 0.7177 (t80) cc_final: 0.6833 (t80) REVERT: D 419 GLU cc_start: 0.5339 (tt0) cc_final: 0.5116 (mt-10) REVERT: E 7 GLU cc_start: 0.5800 (mp0) cc_final: 0.5456 (mm-30) REVERT: E 16 GLN cc_start: 0.6700 (mt0) cc_final: 0.6282 (mm-40) REVERT: E 51 MET cc_start: 0.7664 (mmt) cc_final: 0.7043 (mmt) REVERT: E 73 ASP cc_start: 0.6324 (t0) cc_final: 0.5271 (m-30) REVERT: E 144 ARG cc_start: 0.6491 (mmm160) cc_final: 0.6211 (mmm160) REVERT: E 181 PHE cc_start: 0.4749 (m-10) cc_final: 0.4313 (m-80) REVERT: E 182 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6446 (mt-10) REVERT: E 223 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6585 (tpp-160) REVERT: E 361 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6372 (mm-30) REVERT: E 390 GLU cc_start: 0.6695 (pm20) cc_final: 0.6434 (pt0) REVERT: E 419 GLU cc_start: 0.5089 (tt0) cc_final: 0.4765 (mt-10) REVERT: F 7 GLU cc_start: 0.5739 (mp0) cc_final: 0.5374 (mm-30) REVERT: F 16 GLN cc_start: 0.6878 (mt0) cc_final: 0.6522 (mm110) REVERT: F 17 ASN cc_start: 0.7126 (t0) cc_final: 0.6917 (t0) REVERT: F 51 MET cc_start: 0.7799 (mmt) cc_final: 0.7490 (tpt) REVERT: F 67 ASP cc_start: 0.6208 (m-30) cc_final: 0.5583 (p0) REVERT: F 73 ASP cc_start: 0.6320 (t0) cc_final: 0.5355 (m-30) REVERT: F 145 ARG cc_start: 0.5746 (mmm160) cc_final: 0.3676 (ptm-80) REVERT: F 181 PHE cc_start: 0.4810 (m-10) cc_final: 0.4323 (m-80) REVERT: F 182 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6413 (mt-10) REVERT: F 361 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6136 (mm-30) REVERT: F 390 GLU cc_start: 0.6789 (pm20) cc_final: 0.6464 (pt0) REVERT: F 398 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5674 (mm-30) REVERT: K 7 GLU cc_start: 0.5703 (mp0) cc_final: 0.5325 (mm-30) REVERT: K 16 GLN cc_start: 0.6652 (OUTLIER) cc_final: 0.6220 (mm-40) REVERT: K 51 MET cc_start: 0.7656 (mmt) cc_final: 0.7425 (tpt) REVERT: K 73 ASP cc_start: 0.6286 (t0) cc_final: 0.5399 (m-30) REVERT: K 181 PHE cc_start: 0.4733 (m-10) cc_final: 0.4244 (m-80) REVERT: K 182 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6275 (mt-10) REVERT: K 223 ARG cc_start: 0.6775 (ttm-80) cc_final: 0.6197 (tpt170) REVERT: K 224 LYS cc_start: 0.6518 (pttt) cc_final: 0.6269 (pttm) REVERT: K 361 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6226 (mm-30) REVERT: K 390 GLU cc_start: 0.6692 (pm20) cc_final: 0.6400 (pt0) REVERT: K 414 PHE cc_start: 0.6906 (t80) cc_final: 0.6676 (t80) REVERT: L 7 GLU cc_start: 0.5816 (mp0) cc_final: 0.5460 (mm-30) REVERT: L 16 GLN cc_start: 0.6707 (mt0) cc_final: 0.6339 (mm-40) REVERT: L 43 LYS cc_start: 0.6913 (ttmm) cc_final: 0.5945 (mptt) REVERT: L 73 ASP cc_start: 0.6303 (t0) cc_final: 0.5214 (m-30) REVERT: L 181 PHE cc_start: 0.4746 (m-10) cc_final: 0.4316 (m-80) REVERT: L 182 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6435 (mt-10) REVERT: L 223 ARG cc_start: 0.6661 (ttm-80) cc_final: 0.6105 (tpt90) REVERT: L 361 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6386 (mm-30) outliers start: 163 outliers final: 61 residues processed: 760 average time/residue: 1.5520 time to fit residues: 1435.3908 Evaluate side-chains 708 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 636 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain G residue 16 GLN Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 179 MET Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 265 LEU Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain J residue 415 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 363 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 3.9990 chunk 361 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 chunk 482 optimal weight: 4.9990 chunk 510 optimal weight: 7.9990 chunk 251 optimal weight: 6.9990 chunk 456 optimal weight: 0.0570 chunk 137 optimal weight: 4.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 34 ASN G 24 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN H 34 ASN I 24 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN C 34 ASN J 17 ASN J 24 GLN J 34 ASN D 24 GLN D 34 ASN E 34 ASN E 128 ASN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN L 17 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 42396 Z= 0.332 Angle : 0.613 6.203 57504 Z= 0.315 Chirality : 0.045 0.176 6300 Planarity : 0.005 0.041 7512 Dihedral : 4.828 43.494 5724 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.12 % Allowed : 13.83 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.11), residues: 5292 helix: 1.48 (0.11), residues: 2064 sheet: -0.95 (0.17), residues: 900 loop : -1.07 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP F 77 HIS 0.005 0.001 HIS C 416 PHE 0.016 0.002 PHE B 71 TYR 0.016 0.002 TYR B 285 ARG 0.006 0.001 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 671 time to evaluate : 4.591 Fit side-chains REVERT: A 7 GLU cc_start: 0.5674 (mp0) cc_final: 0.5267 (mm-30) REVERT: A 16 GLN cc_start: 0.7088 (mt0) cc_final: 0.6638 (mm110) REVERT: A 51 MET cc_start: 0.7523 (mmt) cc_final: 0.7314 (tpt) REVERT: A 67 ASP cc_start: 0.5980 (m-30) cc_final: 0.5552 (p0) REVERT: A 73 ASP cc_start: 0.6242 (t0) cc_final: 0.5229 (m-30) REVERT: A 145 ARG cc_start: 0.5773 (mmm160) cc_final: 0.3659 (ptm-80) REVERT: A 181 PHE cc_start: 0.4917 (m-10) cc_final: 0.4335 (m-80) REVERT: A 182 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6320 (mt-10) REVERT: A 361 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6107 (mm-30) REVERT: A 390 GLU cc_start: 0.6861 (pm20) cc_final: 0.6626 (pt0) REVERT: A 398 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5641 (mm-30) REVERT: A 419 GLU cc_start: 0.4961 (tt0) cc_final: 0.4608 (mt-10) REVERT: A 427 MET cc_start: 0.6279 (ttm) cc_final: 0.6000 (mtp) REVERT: A 439 GLN cc_start: 0.5922 (tt0) cc_final: 0.5597 (mm-40) REVERT: G 7 GLU cc_start: 0.5651 (mp0) cc_final: 0.5391 (mm-30) REVERT: G 16 GLN cc_start: 0.6758 (mt0) cc_final: 0.6270 (mm-40) REVERT: G 43 LYS cc_start: 0.6620 (ttmm) cc_final: 0.5779 (mptt) REVERT: G 73 ASP cc_start: 0.6189 (t0) cc_final: 0.5398 (m-30) REVERT: G 181 PHE cc_start: 0.4853 (m-10) cc_final: 0.4302 (m-10) REVERT: G 182 GLU cc_start: 0.6832 (mm-30) cc_final: 0.6401 (mt-10) REVERT: G 200 LYS cc_start: 0.7619 (mmmm) cc_final: 0.6753 (mttp) REVERT: G 223 ARG cc_start: 0.6713 (ttm-80) cc_final: 0.6174 (tpt170) REVERT: G 224 LYS cc_start: 0.6421 (pttt) cc_final: 0.6189 (pttm) REVERT: G 361 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6138 (mm-30) REVERT: G 390 GLU cc_start: 0.6726 (pm20) cc_final: 0.6473 (pt0) REVERT: H 7 GLU cc_start: 0.5820 (mp0) cc_final: 0.5322 (mm-30) REVERT: H 16 GLN cc_start: 0.6713 (mt0) cc_final: 0.6380 (mm110) REVERT: H 17 ASN cc_start: 0.6945 (t0) cc_final: 0.6420 (t0) REVERT: H 67 ASP cc_start: 0.6074 (m-30) cc_final: 0.5614 (p0) REVERT: H 73 ASP cc_start: 0.6228 (t0) cc_final: 0.5237 (m-30) REVERT: H 144 ARG cc_start: 0.6556 (mmm160) cc_final: 0.6191 (mmm160) REVERT: H 145 ARG cc_start: 0.5857 (mmm160) cc_final: 0.3874 (ptm-80) REVERT: H 181 PHE cc_start: 0.4910 (m-10) cc_final: 0.4452 (m-10) REVERT: H 182 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6417 (mt-10) REVERT: H 361 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6438 (mm-30) REVERT: H 387 ASP cc_start: 0.8027 (m-30) cc_final: 0.7763 (m-30) REVERT: H 390 GLU cc_start: 0.6701 (pm20) cc_final: 0.6472 (pt0) REVERT: H 415 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.5623 (mm-30) REVERT: I 7 GLU cc_start: 0.5749 (mp0) cc_final: 0.5312 (mm-30) REVERT: I 67 ASP cc_start: 0.6057 (m-30) cc_final: 0.5848 (p0) REVERT: I 73 ASP cc_start: 0.6204 (t0) cc_final: 0.5312 (m-30) REVERT: I 145 ARG cc_start: 0.5778 (mmm160) cc_final: 0.3663 (ptm-80) REVERT: I 181 PHE cc_start: 0.4792 (m-10) cc_final: 0.4239 (m-80) REVERT: I 182 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6405 (mt-10) REVERT: I 360 ASP cc_start: 0.6078 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: I 361 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6075 (mm-30) REVERT: I 390 GLU cc_start: 0.6861 (pm20) cc_final: 0.6625 (pt0) REVERT: I 398 GLU cc_start: 0.6053 (mm-30) cc_final: 0.5645 (mm-30) REVERT: I 419 GLU cc_start: 0.4978 (tt0) cc_final: 0.4605 (mt-10) REVERT: I 439 GLN cc_start: 0.5915 (tt0) cc_final: 0.5528 (mm-40) REVERT: B 7 GLU cc_start: 0.5648 (mp0) cc_final: 0.5402 (mm-30) REVERT: B 17 ASN cc_start: 0.7158 (t0) cc_final: 0.6759 (t0) REVERT: B 73 ASP cc_start: 0.6221 (t0) cc_final: 0.5454 (m-30) REVERT: B 139 LYS cc_start: 0.7247 (mttt) cc_final: 0.7016 (mttm) REVERT: B 145 ARG cc_start: 0.5618 (mmm160) cc_final: 0.3638 (ptm-80) REVERT: B 181 PHE cc_start: 0.4901 (m-10) cc_final: 0.4383 (m-10) REVERT: B 182 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6448 (mt-10) REVERT: B 200 LYS cc_start: 0.7601 (mmmm) cc_final: 0.6800 (mttp) REVERT: B 223 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.6256 (tpt170) REVERT: B 224 LYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6092 (pttm) REVERT: B 361 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6183 (mm-30) REVERT: B 390 GLU cc_start: 0.6717 (pm20) cc_final: 0.6390 (pt0) REVERT: C 7 GLU cc_start: 0.5895 (mp0) cc_final: 0.5571 (mm-30) REVERT: C 43 LYS cc_start: 0.6999 (ttmm) cc_final: 0.6123 (mptt) REVERT: C 49 LYS cc_start: 0.7159 (mmmm) cc_final: 0.6907 (mmpt) REVERT: C 73 ASP cc_start: 0.6267 (t0) cc_final: 0.5186 (m-30) REVERT: C 121 GLU cc_start: 0.5857 (pp20) cc_final: 0.5648 (pt0) REVERT: C 181 PHE cc_start: 0.4908 (m-10) cc_final: 0.4438 (m-10) REVERT: C 182 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6499 (mt-10) REVERT: C 200 LYS cc_start: 0.7443 (mmmm) cc_final: 0.6936 (mmmm) REVERT: C 224 LYS cc_start: 0.6422 (pttt) cc_final: 0.6196 (pttm) REVERT: C 361 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6330 (mm-30) REVERT: C 390 GLU cc_start: 0.6700 (pm20) cc_final: 0.6454 (pt0) REVERT: C 398 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5760 (mm-30) REVERT: C 415 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5734 (mm-30) REVERT: C 427 MET cc_start: 0.6479 (ttm) cc_final: 0.6177 (mtp) REVERT: J 7 GLU cc_start: 0.5792 (mp0) cc_final: 0.5389 (mm-30) REVERT: J 17 ASN cc_start: 0.7006 (OUTLIER) cc_final: 0.6592 (t0) REVERT: J 43 LYS cc_start: 0.6495 (ttmm) cc_final: 0.5664 (mptt) REVERT: J 67 ASP cc_start: 0.5943 (m-30) cc_final: 0.5551 (p0) REVERT: J 73 ASP cc_start: 0.6179 (t0) cc_final: 0.5148 (m-30) REVERT: J 145 ARG cc_start: 0.5737 (mmm160) cc_final: 0.3670 (ptm-80) REVERT: J 181 PHE cc_start: 0.4888 (m-10) cc_final: 0.4298 (m-80) REVERT: J 182 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6363 (mt-10) REVERT: J 361 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6089 (mm-30) REVERT: J 390 GLU cc_start: 0.6867 (pm20) cc_final: 0.6392 (pm20) REVERT: J 398 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5664 (mm-30) REVERT: J 439 GLN cc_start: 0.5915 (tt0) cc_final: 0.5585 (mm-40) REVERT: D 7 GLU cc_start: 0.5595 (mp0) cc_final: 0.5315 (mm-30) REVERT: D 73 ASP cc_start: 0.6224 (t0) cc_final: 0.5420 (m-30) REVERT: D 145 ARG cc_start: 0.5643 (mmm160) cc_final: 0.3601 (ptm-80) REVERT: D 181 PHE cc_start: 0.4915 (m-10) cc_final: 0.4355 (m-10) REVERT: D 182 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6445 (mt-10) REVERT: D 200 LYS cc_start: 0.7625 (mmmm) cc_final: 0.6764 (mttp) REVERT: D 223 ARG cc_start: 0.6709 (ttm-80) cc_final: 0.6187 (tpt170) REVERT: D 224 LYS cc_start: 0.6398 (pttt) cc_final: 0.6163 (pttm) REVERT: D 361 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6228 (mm-30) REVERT: D 387 ASP cc_start: 0.7735 (m-30) cc_final: 0.7424 (m-30) REVERT: D 390 GLU cc_start: 0.6751 (pm20) cc_final: 0.6460 (pt0) REVERT: D 419 GLU cc_start: 0.5395 (tt0) cc_final: 0.5031 (mt-10) REVERT: E 7 GLU cc_start: 0.5843 (mp0) cc_final: 0.5557 (mm-30) REVERT: E 16 GLN cc_start: 0.6643 (mt0) cc_final: 0.6394 (mm110) REVERT: E 67 ASP cc_start: 0.6231 (m-30) cc_final: 0.5769 (p0) REVERT: E 73 ASP cc_start: 0.6236 (t0) cc_final: 0.5242 (m-30) REVERT: E 91 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6571 (ppt-90) REVERT: E 144 ARG cc_start: 0.6555 (mmm160) cc_final: 0.6197 (mmm160) REVERT: E 145 ARG cc_start: 0.5876 (mmm160) cc_final: 0.3896 (ptm-80) REVERT: E 181 PHE cc_start: 0.4806 (m-10) cc_final: 0.4350 (m-10) REVERT: E 182 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6417 (mt-10) REVERT: E 223 ARG cc_start: 0.6806 (OUTLIER) cc_final: 0.6572 (tpp-160) REVERT: E 361 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6386 (mm-30) REVERT: E 390 GLU cc_start: 0.6680 (pm20) cc_final: 0.6468 (pt0) REVERT: E 398 GLU cc_start: 0.6017 (mm-30) cc_final: 0.5741 (mm-30) REVERT: E 415 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5662 (mm-30) REVERT: F 7 GLU cc_start: 0.5774 (mp0) cc_final: 0.5383 (mm-30) REVERT: F 16 GLN cc_start: 0.6856 (mt0) cc_final: 0.6549 (mm110) REVERT: F 51 MET cc_start: 0.7494 (mmt) cc_final: 0.7269 (tpt) REVERT: F 67 ASP cc_start: 0.6019 (m-30) cc_final: 0.5565 (p0) REVERT: F 73 ASP cc_start: 0.6250 (t0) cc_final: 0.5253 (m-30) REVERT: F 145 ARG cc_start: 0.5828 (mmm160) cc_final: 0.3694 (ptm-80) REVERT: F 181 PHE cc_start: 0.4828 (m-10) cc_final: 0.4293 (m-80) REVERT: F 182 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6385 (mt-10) REVERT: F 361 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6204 (mm-30) REVERT: F 398 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5628 (mm-30) REVERT: F 439 GLN cc_start: 0.5934 (tt0) cc_final: 0.5653 (mm-40) REVERT: K 7 GLU cc_start: 0.5653 (mp0) cc_final: 0.5371 (mm-30) REVERT: K 16 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6279 (mm-40) REVERT: K 73 ASP cc_start: 0.6165 (t0) cc_final: 0.5385 (m-30) REVERT: K 181 PHE cc_start: 0.4848 (m-10) cc_final: 0.4304 (m-10) REVERT: K 182 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6392 (mt-10) REVERT: K 200 LYS cc_start: 0.7654 (mmmm) cc_final: 0.6782 (mttp) REVERT: K 223 ARG cc_start: 0.6695 (ttm-80) cc_final: 0.6234 (tpt170) REVERT: K 224 LYS cc_start: 0.6411 (pttt) cc_final: 0.6173 (pttm) REVERT: K 361 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6140 (mm-30) REVERT: K 390 GLU cc_start: 0.6739 (pm20) cc_final: 0.6466 (pt0) REVERT: L 7 GLU cc_start: 0.5921 (mp0) cc_final: 0.5573 (mm-30) REVERT: L 43 LYS cc_start: 0.6895 (ttmm) cc_final: 0.5952 (mptt) REVERT: L 67 ASP cc_start: 0.6173 (m-30) cc_final: 0.5715 (p0) REVERT: L 73 ASP cc_start: 0.6229 (t0) cc_final: 0.5232 (m-30) REVERT: L 145 ARG cc_start: 0.6005 (mmp-170) cc_final: 0.3988 (ptm-80) REVERT: L 181 PHE cc_start: 0.4852 (m-10) cc_final: 0.4371 (m-10) REVERT: L 182 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6388 (mt-10) REVERT: L 361 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6386 (mm-30) REVERT: L 387 ASP cc_start: 0.8015 (m-30) cc_final: 0.7763 (m-30) REVERT: L 390 GLU cc_start: 0.6714 (pm20) cc_final: 0.6468 (pt0) REVERT: L 398 GLU cc_start: 0.6005 (mm-30) cc_final: 0.5669 (mm-30) REVERT: L 415 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5540 (mm-30) outliers start: 176 outliers final: 79 residues processed: 770 average time/residue: 1.5810 time to fit residues: 1479.2283 Evaluate side-chains 711 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 622 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 268 SER Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 328 LEU Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 328 LEU Chi-restraints excluded: chain I residue 360 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 125 THR Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 SER Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 179 MET Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 268 SER Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 159 LEU Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 328 LEU Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 380 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 435 optimal weight: 0.9980 chunk 352 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 458 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 34 ASN H 34 ASN I 34 ASN B 34 ASN C 17 ASN C 34 ASN J 34 ASN D 34 ASN D 128 ASN E 34 ASN F 34 ASN K 24 GLN K 34 ASN L 34 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 42396 Z= 0.189 Angle : 0.531 6.321 57504 Z= 0.274 Chirality : 0.042 0.147 6300 Planarity : 0.004 0.035 7512 Dihedral : 4.544 39.775 5724 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.44 % Allowed : 15.54 % Favored : 81.02 % 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: 0.18 (0.11), residues: 5292 helix: 1.72 (0.11), residues: 2064 sheet: -1.07 (0.17), residues: 960 loop : -0.81 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 77 HIS 0.002 0.001 HIS H 416 PHE 0.023 0.001 PHE D 414 TYR 0.015 0.001 TYR J 285 ARG 0.003 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 645 time to evaluate : 4.649 Fit side-chains REVERT: A 7 GLU cc_start: 0.5727 (mp0) cc_final: 0.5310 (mm-30) REVERT: A 16 GLN cc_start: 0.7124 (mt0) cc_final: 0.6679 (mm110) REVERT: A 73 ASP cc_start: 0.6160 (t0) cc_final: 0.5213 (m-30) REVERT: A 145 ARG cc_start: 0.5785 (mmm160) cc_final: 0.3662 (ptm-80) REVERT: A 181 PHE cc_start: 0.4805 (m-10) cc_final: 0.4259 (m-80) REVERT: A 182 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6306 (mt-10) REVERT: A 361 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6149 (mm-30) REVERT: A 375 MET cc_start: 0.5447 (ptp) cc_final: 0.5189 (ptt) REVERT: A 387 ASP cc_start: 0.7759 (m-30) cc_final: 0.7477 (m-30) REVERT: A 390 GLU cc_start: 0.6858 (pm20) cc_final: 0.6617 (pt0) REVERT: A 398 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5610 (mm-30) REVERT: A 439 GLN cc_start: 0.5911 (tp40) cc_final: 0.5639 (mm-40) REVERT: G 7 GLU cc_start: 0.5754 (mp0) cc_final: 0.5408 (mm-30) REVERT: G 16 GLN cc_start: 0.6719 (mt0) cc_final: 0.6332 (mm-40) REVERT: G 73 ASP cc_start: 0.6222 (t0) cc_final: 0.5371 (m-30) REVERT: G 181 PHE cc_start: 0.4841 (m-10) cc_final: 0.4322 (m-10) REVERT: G 182 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6340 (mt-10) REVERT: G 200 LYS cc_start: 0.7632 (mmmm) cc_final: 0.6759 (mttp) REVERT: G 223 ARG cc_start: 0.6688 (ttm-80) cc_final: 0.6125 (tpt170) REVERT: G 361 GLU cc_start: 0.6948 (mt-10) cc_final: 0.6164 (mm-30) REVERT: G 387 ASP cc_start: 0.7672 (m-30) cc_final: 0.7258 (m-30) REVERT: G 390 GLU cc_start: 0.6746 (pm20) cc_final: 0.6472 (pt0) REVERT: G 398 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5643 (mm-30) REVERT: H 7 GLU cc_start: 0.5810 (mp0) cc_final: 0.5487 (mm-30) REVERT: H 67 ASP cc_start: 0.6003 (m-30) cc_final: 0.5614 (p0) REVERT: H 73 ASP cc_start: 0.6243 (t0) cc_final: 0.5202 (m-30) REVERT: H 181 PHE cc_start: 0.4882 (m-10) cc_final: 0.4433 (m-10) REVERT: H 182 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6435 (mt-10) REVERT: H 223 ARG cc_start: 0.6699 (tpp-160) cc_final: 0.6467 (tpp80) REVERT: H 361 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6437 (mm-30) REVERT: H 387 ASP cc_start: 0.7995 (m-30) cc_final: 0.7721 (m-30) REVERT: H 390 GLU cc_start: 0.6679 (pm20) cc_final: 0.6454 (pt0) REVERT: H 415 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5568 (mm-30) REVERT: I 7 GLU cc_start: 0.5804 (mp0) cc_final: 0.5315 (mm-30) REVERT: I 73 ASP cc_start: 0.6242 (t0) cc_final: 0.5208 (m-30) REVERT: I 145 ARG cc_start: 0.5798 (mmm160) cc_final: 0.3720 (ptm-80) REVERT: I 181 PHE cc_start: 0.4775 (m-10) cc_final: 0.4273 (m-80) REVERT: I 182 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6389 (mt-10) REVERT: I 361 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6103 (mm-30) REVERT: I 390 GLU cc_start: 0.6871 (pm20) cc_final: 0.6624 (pt0) REVERT: I 398 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5613 (mm-30) REVERT: I 415 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5507 (mp0) REVERT: I 419 GLU cc_start: 0.5011 (tt0) cc_final: 0.4634 (mt-10) REVERT: I 439 GLN cc_start: 0.5926 (tp40) cc_final: 0.5680 (mm-40) REVERT: B 7 GLU cc_start: 0.5706 (mp0) cc_final: 0.5375 (mm-30) REVERT: B 17 ASN cc_start: 0.6999 (t0) cc_final: 0.6759 (t0) REVERT: B 73 ASP cc_start: 0.6303 (t0) cc_final: 0.5408 (m-30) REVERT: B 139 LYS cc_start: 0.7185 (mttt) cc_final: 0.6961 (mttm) REVERT: B 181 PHE cc_start: 0.4906 (m-10) cc_final: 0.4439 (m-10) REVERT: B 182 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6415 (mt-10) REVERT: B 200 LYS cc_start: 0.7634 (mmmm) cc_final: 0.6799 (mttp) REVERT: B 223 ARG cc_start: 0.6687 (ttm-80) cc_final: 0.6263 (tpt170) REVERT: B 224 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5999 (pttm) REVERT: B 361 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6141 (mm-30) REVERT: B 390 GLU cc_start: 0.6712 (pm20) cc_final: 0.6398 (pt0) REVERT: B 398 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5648 (mm-30) REVERT: C 7 GLU cc_start: 0.5942 (mp0) cc_final: 0.5599 (mm-30) REVERT: C 17 ASN cc_start: 0.7083 (t0) cc_final: 0.6795 (t0) REVERT: C 43 LYS cc_start: 0.6767 (ttmm) cc_final: 0.5835 (mptt) REVERT: C 49 LYS cc_start: 0.7054 (mmmm) cc_final: 0.6820 (mmpt) REVERT: C 73 ASP cc_start: 0.6260 (t0) cc_final: 0.5150 (m-30) REVERT: C 145 ARG cc_start: 0.5926 (mmp-170) cc_final: 0.3900 (ptm-80) REVERT: C 181 PHE cc_start: 0.4989 (m-10) cc_final: 0.4498 (m-10) REVERT: C 182 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6586 (mt-10) REVERT: C 200 LYS cc_start: 0.7450 (mmmm) cc_final: 0.6752 (mttp) REVERT: C 224 LYS cc_start: 0.6314 (pttt) cc_final: 0.6091 (pttm) REVERT: C 361 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6285 (mm-30) REVERT: C 390 GLU cc_start: 0.6698 (pm20) cc_final: 0.6348 (pt0) REVERT: C 398 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5729 (mm-30) REVERT: C 415 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5525 (mm-30) REVERT: C 427 MET cc_start: 0.6388 (ttm) cc_final: 0.6100 (mtp) REVERT: J 7 GLU cc_start: 0.5747 (mp0) cc_final: 0.5351 (mm-30) REVERT: J 17 ASN cc_start: 0.6971 (t0) cc_final: 0.6517 (t0) REVERT: J 43 LYS cc_start: 0.6464 (ttmm) cc_final: 0.5651 (mptt) REVERT: J 73 ASP cc_start: 0.6347 (t0) cc_final: 0.5248 (m-30) REVERT: J 139 LYS cc_start: 0.7249 (mttt) cc_final: 0.6985 (mttm) REVERT: J 181 PHE cc_start: 0.4794 (m-10) cc_final: 0.4249 (m-80) REVERT: J 182 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6350 (mt-10) REVERT: J 361 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6080 (mm-30) REVERT: J 390 GLU cc_start: 0.6872 (pm20) cc_final: 0.6607 (pt0) REVERT: J 398 GLU cc_start: 0.6072 (mm-30) cc_final: 0.5595 (mm-30) REVERT: J 439 GLN cc_start: 0.5898 (tt0) cc_final: 0.5602 (mm-40) REVERT: D 7 GLU cc_start: 0.5719 (mp0) cc_final: 0.5346 (mm-30) REVERT: D 73 ASP cc_start: 0.6263 (t0) cc_final: 0.5385 (m-30) REVERT: D 145 ARG cc_start: 0.5771 (mmm160) cc_final: 0.3772 (ptm-80) REVERT: D 181 PHE cc_start: 0.4835 (m-10) cc_final: 0.4313 (m-10) REVERT: D 182 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6378 (mt-10) REVERT: D 200 LYS cc_start: 0.7625 (mmmm) cc_final: 0.6764 (mttp) REVERT: D 223 ARG cc_start: 0.6690 (ttm-80) cc_final: 0.6150 (tpt170) REVERT: D 361 GLU cc_start: 0.6958 (mt-10) cc_final: 0.6196 (mm-30) REVERT: D 387 ASP cc_start: 0.7706 (m-30) cc_final: 0.7420 (m-30) REVERT: D 390 GLU cc_start: 0.6730 (pm20) cc_final: 0.6460 (pt0) REVERT: D 398 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5659 (mm-30) REVERT: D 419 GLU cc_start: 0.5390 (tt0) cc_final: 0.5121 (mt-10) REVERT: E 7 GLU cc_start: 0.5816 (mp0) cc_final: 0.5492 (mm-30) REVERT: E 16 GLN cc_start: 0.6738 (mt0) cc_final: 0.6535 (mm110) REVERT: E 67 ASP cc_start: 0.6121 (m-30) cc_final: 0.5716 (p0) REVERT: E 73 ASP cc_start: 0.6247 (t0) cc_final: 0.5206 (m-30) REVERT: E 91 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6510 (ppt-90) REVERT: E 144 ARG cc_start: 0.6566 (mmm160) cc_final: 0.6248 (mmm160) REVERT: E 145 ARG cc_start: 0.5849 (mmm160) cc_final: 0.3858 (ptm-80) REVERT: E 181 PHE cc_start: 0.4859 (m-10) cc_final: 0.4372 (m-10) REVERT: E 182 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6505 (mt-10) REVERT: E 200 LYS cc_start: 0.7458 (mmmm) cc_final: 0.6905 (mmmm) REVERT: E 223 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6560 (tpp-160) REVERT: E 361 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6041 (mm-30) REVERT: E 390 GLU cc_start: 0.6675 (pm20) cc_final: 0.6358 (pt0) REVERT: E 398 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5721 (mm-30) REVERT: E 415 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.5487 (mm-30) REVERT: F 7 GLU cc_start: 0.5834 (mp0) cc_final: 0.5358 (mm-30) REVERT: F 16 GLN cc_start: 0.6773 (mt0) cc_final: 0.6549 (mm110) REVERT: F 73 ASP cc_start: 0.6304 (t0) cc_final: 0.5273 (m-30) REVERT: F 145 ARG cc_start: 0.5827 (mmm160) cc_final: 0.3696 (ptm-80) REVERT: F 181 PHE cc_start: 0.4802 (m-10) cc_final: 0.4291 (m-80) REVERT: F 182 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6326 (mt-10) REVERT: F 361 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6116 (mm-30) REVERT: F 387 ASP cc_start: 0.7754 (m-30) cc_final: 0.7482 (m-30) REVERT: F 398 GLU cc_start: 0.6041 (mm-30) cc_final: 0.5607 (mm-30) REVERT: F 439 GLN cc_start: 0.5890 (tp40) cc_final: 0.5646 (mm-40) REVERT: K 7 GLU cc_start: 0.5764 (mp0) cc_final: 0.5416 (mm-30) REVERT: K 16 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6259 (mm-40) REVERT: K 73 ASP cc_start: 0.6206 (t0) cc_final: 0.5359 (m-30) REVERT: K 181 PHE cc_start: 0.4840 (m-10) cc_final: 0.4320 (m-10) REVERT: K 182 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6336 (mt-10) REVERT: K 200 LYS cc_start: 0.7674 (mmmm) cc_final: 0.6845 (mttp) REVERT: K 223 ARG cc_start: 0.6695 (ttm-80) cc_final: 0.6241 (tpt170) REVERT: K 361 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6145 (mm-30) REVERT: K 390 GLU cc_start: 0.6732 (pm20) cc_final: 0.6450 (pt0) REVERT: K 398 GLU cc_start: 0.6063 (mm-30) cc_final: 0.5638 (mm-30) REVERT: L 7 GLU cc_start: 0.5918 (mp0) cc_final: 0.5560 (mm-30) REVERT: L 43 LYS cc_start: 0.6867 (ttmm) cc_final: 0.5923 (mptt) REVERT: L 67 ASP cc_start: 0.5953 (m-30) cc_final: 0.5655 (p0) REVERT: L 73 ASP cc_start: 0.6246 (t0) cc_final: 0.5179 (m-30) REVERT: L 145 ARG cc_start: 0.6015 (mmp-170) cc_final: 0.4000 (ptm-80) REVERT: L 181 PHE cc_start: 0.4943 (m-10) cc_final: 0.4515 (m-10) REVERT: L 182 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6397 (mt-10) REVERT: L 361 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6425 (mm-30) REVERT: L 387 ASP cc_start: 0.7975 (m-30) cc_final: 0.7673 (m-30) REVERT: L 390 GLU cc_start: 0.6689 (pm20) cc_final: 0.6461 (pt0) REVERT: L 398 GLU cc_start: 0.6038 (mm-30) cc_final: 0.5685 (mm-30) REVERT: L 415 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.5553 (mm-30) outliers start: 147 outliers final: 60 residues processed: 734 average time/residue: 1.6181 time to fit residues: 1448.5307 Evaluate side-chains 679 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 610 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 328 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.9980 chunk 459 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 125 optimal weight: 0.0980 chunk 510 optimal weight: 8.9990 chunk 424 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 268 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 24 GLN G 34 ASN G 128 ASN H 34 ASN I 34 ASN B 24 GLN B 34 ASN B 128 ASN C 34 ASN J 34 ASN D 24 GLN D 34 ASN E 34 ASN F 34 ASN K 24 GLN K 34 ASN K 128 ASN L 34 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42396 Z= 0.195 Angle : 0.524 6.191 57504 Z= 0.270 Chirality : 0.041 0.169 6300 Planarity : 0.004 0.033 7512 Dihedral : 4.444 37.934 5724 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.35 % Allowed : 16.25 % Favored : 80.41 % 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: 0.22 (0.11), residues: 5292 helix: 1.77 (0.11), residues: 2064 sheet: -1.05 (0.17), residues: 960 loop : -0.78 (0.12), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 77 HIS 0.002 0.001 HIS H 416 PHE 0.010 0.001 PHE B 71 TYR 0.015 0.001 TYR F 285 ARG 0.003 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 625 time to evaluate : 5.143 Fit side-chains REVERT: A 7 GLU cc_start: 0.5716 (mp0) cc_final: 0.5331 (mm-30) REVERT: A 16 GLN cc_start: 0.7052 (mt0) cc_final: 0.6647 (mm110) REVERT: A 73 ASP cc_start: 0.6268 (t0) cc_final: 0.5319 (m-30) REVERT: A 145 ARG cc_start: 0.5817 (mmm160) cc_final: 0.3706 (ptm-80) REVERT: A 181 PHE cc_start: 0.4802 (m-10) cc_final: 0.4256 (m-80) REVERT: A 182 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6304 (mt-10) REVERT: A 361 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6161 (mm-30) REVERT: A 375 MET cc_start: 0.5435 (ptp) cc_final: 0.5056 (ptt) REVERT: A 387 ASP cc_start: 0.7666 (m-30) cc_final: 0.7404 (m-30) REVERT: A 390 GLU cc_start: 0.6863 (pm20) cc_final: 0.6618 (pt0) REVERT: A 398 GLU cc_start: 0.6090 (mm-30) cc_final: 0.5622 (mm-30) REVERT: A 439 GLN cc_start: 0.5920 (tp40) cc_final: 0.5675 (mm-40) REVERT: G 7 GLU cc_start: 0.5723 (mp0) cc_final: 0.5373 (mm-30) REVERT: G 16 GLN cc_start: 0.6589 (mt0) cc_final: 0.6270 (mm110) REVERT: G 51 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6983 (mmm) REVERT: G 73 ASP cc_start: 0.6221 (t0) cc_final: 0.5331 (m-30) REVERT: G 181 PHE cc_start: 0.4865 (m-10) cc_final: 0.4355 (m-10) REVERT: G 182 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6333 (mt-10) REVERT: G 200 LYS cc_start: 0.7666 (mmmm) cc_final: 0.6771 (mttp) REVERT: G 223 ARG cc_start: 0.6700 (ttm-80) cc_final: 0.6121 (tpt170) REVERT: G 361 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6155 (mm-30) REVERT: G 390 GLU cc_start: 0.6741 (pm20) cc_final: 0.6397 (pt0) REVERT: G 398 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5660 (mm-30) REVERT: H 7 GLU cc_start: 0.5811 (mp0) cc_final: 0.5487 (mm-30) REVERT: H 67 ASP cc_start: 0.5941 (m-30) cc_final: 0.5614 (p0) REVERT: H 73 ASP cc_start: 0.6230 (t0) cc_final: 0.5183 (m-30) REVERT: H 181 PHE cc_start: 0.4901 (m-10) cc_final: 0.4454 (m-10) REVERT: H 182 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6501 (mt-10) REVERT: H 200 LYS cc_start: 0.7431 (mmmm) cc_final: 0.6908 (mmmm) REVERT: H 361 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6417 (mm-30) REVERT: H 387 ASP cc_start: 0.8015 (m-30) cc_final: 0.7715 (m-30) REVERT: H 390 GLU cc_start: 0.6662 (pm20) cc_final: 0.6345 (pt0) REVERT: H 415 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5611 (mm-30) REVERT: I 7 GLU cc_start: 0.5805 (mp0) cc_final: 0.5313 (mm-30) REVERT: I 73 ASP cc_start: 0.6152 (t0) cc_final: 0.5208 (m-30) REVERT: I 145 ARG cc_start: 0.5793 (mmm160) cc_final: 0.3682 (ptm-80) REVERT: I 181 PHE cc_start: 0.4715 (m-10) cc_final: 0.4223 (m-80) REVERT: I 182 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6350 (mt-10) REVERT: I 361 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6126 (mm-30) REVERT: I 390 GLU cc_start: 0.6886 (pm20) cc_final: 0.6624 (pt0) REVERT: I 398 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5629 (mm-30) REVERT: I 415 GLU cc_start: 0.5769 (OUTLIER) cc_final: 0.5514 (mp0) REVERT: I 419 GLU cc_start: 0.5027 (tt0) cc_final: 0.4634 (mt-10) REVERT: B 7 GLU cc_start: 0.5776 (mp0) cc_final: 0.5415 (mm-30) REVERT: B 17 ASN cc_start: 0.7074 (t0) cc_final: 0.6776 (t0) REVERT: B 73 ASP cc_start: 0.6260 (t0) cc_final: 0.5378 (m-30) REVERT: B 139 LYS cc_start: 0.7185 (mttt) cc_final: 0.6952 (mttm) REVERT: B 181 PHE cc_start: 0.4878 (m-10) cc_final: 0.4402 (m-10) REVERT: B 182 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6413 (mt-10) REVERT: B 200 LYS cc_start: 0.7601 (mmmm) cc_final: 0.6768 (mttp) REVERT: B 223 ARG cc_start: 0.6688 (ttm-80) cc_final: 0.6237 (tpt170) REVERT: B 224 LYS cc_start: 0.6316 (OUTLIER) cc_final: 0.6017 (pttm) REVERT: B 361 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6174 (mm-30) REVERT: B 390 GLU cc_start: 0.6686 (pm20) cc_final: 0.6313 (pt0) REVERT: B 398 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5662 (mm-30) REVERT: C 7 GLU cc_start: 0.5950 (mp0) cc_final: 0.5597 (mm-30) REVERT: C 17 ASN cc_start: 0.7236 (t0) cc_final: 0.6980 (t0) REVERT: C 43 LYS cc_start: 0.6769 (ttmm) cc_final: 0.5836 (mptt) REVERT: C 49 LYS cc_start: 0.7033 (mmmm) cc_final: 0.6799 (mmpt) REVERT: C 73 ASP cc_start: 0.6198 (t0) cc_final: 0.5082 (m-30) REVERT: C 145 ARG cc_start: 0.5992 (mmp-170) cc_final: 0.3936 (ptm-80) REVERT: C 181 PHE cc_start: 0.4988 (m-10) cc_final: 0.4531 (m-10) REVERT: C 182 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6524 (mt-10) REVERT: C 200 LYS cc_start: 0.7475 (mmmm) cc_final: 0.6905 (mmmm) REVERT: C 224 LYS cc_start: 0.6317 (pttt) cc_final: 0.6092 (pttm) REVERT: C 361 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6288 (mm-30) REVERT: C 390 GLU cc_start: 0.6701 (pm20) cc_final: 0.6360 (pt0) REVERT: C 398 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5742 (mm-30) REVERT: C 415 GLU cc_start: 0.5762 (OUTLIER) cc_final: 0.5503 (mm-30) REVERT: C 427 MET cc_start: 0.6389 (ttm) cc_final: 0.6050 (mtp) REVERT: J 7 GLU cc_start: 0.5741 (mp0) cc_final: 0.5342 (mm-30) REVERT: J 17 ASN cc_start: 0.6975 (t0) cc_final: 0.6613 (t0) REVERT: J 43 LYS cc_start: 0.6468 (ttmm) cc_final: 0.5658 (mptt) REVERT: J 73 ASP cc_start: 0.6244 (t0) cc_final: 0.5241 (m-30) REVERT: J 139 LYS cc_start: 0.7262 (mttt) cc_final: 0.7007 (mttm) REVERT: J 145 ARG cc_start: 0.5771 (mmm160) cc_final: 0.3654 (ptm-80) REVERT: J 181 PHE cc_start: 0.4758 (m-10) cc_final: 0.4215 (m-80) REVERT: J 182 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6342 (mt-10) REVERT: J 361 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6077 (mm-30) REVERT: J 390 GLU cc_start: 0.6881 (pm20) cc_final: 0.6616 (pt0) REVERT: J 398 GLU cc_start: 0.6081 (mm-30) cc_final: 0.5610 (mm-30) REVERT: D 7 GLU cc_start: 0.5759 (mp0) cc_final: 0.5371 (mm-30) REVERT: D 51 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7081 (mmm) REVERT: D 73 ASP cc_start: 0.6219 (t0) cc_final: 0.5350 (m-30) REVERT: D 145 ARG cc_start: 0.5688 (mmm160) cc_final: 0.3711 (ptm-80) REVERT: D 181 PHE cc_start: 0.4801 (m-10) cc_final: 0.4272 (m-10) REVERT: D 182 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6375 (mt-10) REVERT: D 200 LYS cc_start: 0.7582 (mmmm) cc_final: 0.6682 (mttp) REVERT: D 361 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6156 (mm-30) REVERT: D 387 ASP cc_start: 0.7736 (m-30) cc_final: 0.7490 (m-30) REVERT: D 390 GLU cc_start: 0.6723 (pm20) cc_final: 0.6386 (pt0) REVERT: D 398 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5656 (mm-30) REVERT: D 419 GLU cc_start: 0.5382 (tt0) cc_final: 0.5139 (mt-10) REVERT: E 7 GLU cc_start: 0.5795 (mp0) cc_final: 0.5480 (mm-30) REVERT: E 67 ASP cc_start: 0.5994 (m-30) cc_final: 0.5699 (p0) REVERT: E 73 ASP cc_start: 0.6276 (t0) cc_final: 0.5191 (m-30) REVERT: E 91 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6554 (ppt-90) REVERT: E 144 ARG cc_start: 0.6550 (mmm160) cc_final: 0.6224 (mmm160) REVERT: E 145 ARG cc_start: 0.5858 (mmm160) cc_final: 0.3872 (ptm-80) REVERT: E 181 PHE cc_start: 0.4888 (m-10) cc_final: 0.4439 (m-10) REVERT: E 182 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6491 (mt-10) REVERT: E 200 LYS cc_start: 0.7448 (mmmm) cc_final: 0.6926 (mmmm) REVERT: E 223 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6585 (tpp-160) REVERT: E 361 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6421 (mm-30) REVERT: E 390 GLU cc_start: 0.6702 (pm20) cc_final: 0.6374 (pt0) REVERT: E 398 GLU cc_start: 0.6065 (mm-30) cc_final: 0.5766 (mm-30) REVERT: E 415 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5497 (mm-30) REVERT: F 7 GLU cc_start: 0.5829 (mp0) cc_final: 0.5327 (mm-30) REVERT: F 16 GLN cc_start: 0.6701 (mt0) cc_final: 0.6448 (mm110) REVERT: F 73 ASP cc_start: 0.6268 (t0) cc_final: 0.5265 (m-30) REVERT: F 139 LYS cc_start: 0.7310 (mttt) cc_final: 0.7075 (mttm) REVERT: F 145 ARG cc_start: 0.5865 (mmm160) cc_final: 0.3711 (ptm-80) REVERT: F 181 PHE cc_start: 0.4790 (m-10) cc_final: 0.4277 (m-80) REVERT: F 182 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6322 (mt-10) REVERT: F 361 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6099 (mm-30) REVERT: F 387 ASP cc_start: 0.7681 (m-30) cc_final: 0.7417 (m-30) REVERT: F 398 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5618 (mm-30) REVERT: F 439 GLN cc_start: 0.5922 (tp40) cc_final: 0.5703 (mm-40) REVERT: K 7 GLU cc_start: 0.5734 (mp0) cc_final: 0.5382 (mm-30) REVERT: K 16 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6289 (mm-40) REVERT: K 73 ASP cc_start: 0.6211 (t0) cc_final: 0.5340 (m-30) REVERT: K 181 PHE cc_start: 0.4819 (m-10) cc_final: 0.4314 (m-10) REVERT: K 182 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6362 (mt-10) REVERT: K 200 LYS cc_start: 0.7629 (mmmm) cc_final: 0.6719 (mttp) REVERT: K 361 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6155 (mm-30) REVERT: K 390 GLU cc_start: 0.6728 (pm20) cc_final: 0.6374 (pt0) REVERT: K 398 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5646 (mm-30) REVERT: L 7 GLU cc_start: 0.5886 (mp0) cc_final: 0.5509 (mm-30) REVERT: L 43 LYS cc_start: 0.6714 (ttmm) cc_final: 0.5773 (mptt) REVERT: L 73 ASP cc_start: 0.6248 (t0) cc_final: 0.5165 (m-30) REVERT: L 145 ARG cc_start: 0.5940 (mmp-170) cc_final: 0.3972 (ptm-80) REVERT: L 181 PHE cc_start: 0.4962 (m-10) cc_final: 0.4540 (m-10) REVERT: L 182 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6580 (mt-10) REVERT: L 200 LYS cc_start: 0.7441 (mmmm) cc_final: 0.6741 (mttp) REVERT: L 361 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6417 (mm-30) REVERT: L 387 ASP cc_start: 0.7982 (m-30) cc_final: 0.7666 (m-30) REVERT: L 390 GLU cc_start: 0.6705 (pm20) cc_final: 0.6358 (pt0) REVERT: L 398 GLU cc_start: 0.6063 (mm-30) cc_final: 0.5723 (mm-30) REVERT: L 415 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5596 (mm-30) outliers start: 143 outliers final: 68 residues processed: 709 average time/residue: 1.6178 time to fit residues: 1386.2249 Evaluate side-chains 699 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 620 time to evaluate : 4.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 202 GLU Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain K residue 16 GLN Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 373 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 430 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 508 optimal weight: 1.9990 chunk 318 optimal weight: 0.9980 chunk 310 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 194 GLN G 34 ASN H 34 ASN I 34 ASN I 128 ASN I 194 GLN I 439 GLN B 34 ASN C 34 ASN J 34 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 GLN D 34 ASN ** E 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN K 34 ASN L 34 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 42396 Z= 0.296 Angle : 0.585 7.878 57504 Z= 0.300 Chirality : 0.044 0.216 6300 Planarity : 0.004 0.033 7512 Dihedral : 4.704 39.847 5724 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.79 % Allowed : 15.87 % Favored : 80.34 % 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: -0.01 (0.11), residues: 5292 helix: 1.56 (0.11), residues: 2064 sheet: -1.16 (0.16), residues: 984 loop : -0.90 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 435 HIS 0.004 0.001 HIS H 416 PHE 0.027 0.002 PHE K 414 TYR 0.015 0.002 TYR B 285 ARG 0.005 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 637 time to evaluate : 4.640 Fit side-chains REVERT: A 7 GLU cc_start: 0.5749 (mp0) cc_final: 0.5380 (mm-30) REVERT: A 16 GLN cc_start: 0.6934 (mt0) cc_final: 0.6566 (mm110) REVERT: A 73 ASP cc_start: 0.6197 (t0) cc_final: 0.5287 (m-30) REVERT: A 145 ARG cc_start: 0.5858 (mmm160) cc_final: 0.3687 (ptm-80) REVERT: A 181 PHE cc_start: 0.4836 (m-10) cc_final: 0.4242 (m-80) REVERT: A 182 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6283 (mt-10) REVERT: A 361 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6176 (mm-30) REVERT: A 387 ASP cc_start: 0.7745 (m-30) cc_final: 0.7483 (m-30) REVERT: A 390 GLU cc_start: 0.6830 (pm20) cc_final: 0.6354 (pm20) REVERT: A 398 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5567 (mm-30) REVERT: A 419 GLU cc_start: 0.5122 (tt0) cc_final: 0.4833 (tt0) REVERT: G 7 GLU cc_start: 0.5692 (mp0) cc_final: 0.5393 (mm-30) REVERT: G 16 GLN cc_start: 0.6569 (mt0) cc_final: 0.6307 (mm110) REVERT: G 73 ASP cc_start: 0.6133 (t0) cc_final: 0.5345 (m-30) REVERT: G 145 ARG cc_start: 0.5717 (mmm160) cc_final: 0.3756 (ptm-80) REVERT: G 181 PHE cc_start: 0.4893 (m-10) cc_final: 0.4330 (m-10) REVERT: G 182 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6295 (mt-10) REVERT: G 200 LYS cc_start: 0.7625 (mmmm) cc_final: 0.6703 (mttp) REVERT: G 361 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6165 (mm-30) REVERT: G 387 ASP cc_start: 0.7675 (m-30) cc_final: 0.7314 (m-30) REVERT: G 390 GLU cc_start: 0.6789 (pm20) cc_final: 0.6388 (pt0) REVERT: G 398 GLU cc_start: 0.6081 (mm-30) cc_final: 0.5663 (mm-30) REVERT: H 7 GLU cc_start: 0.5819 (mp0) cc_final: 0.5360 (mm-30) REVERT: H 67 ASP cc_start: 0.5938 (m-30) cc_final: 0.5685 (p0) REVERT: H 73 ASP cc_start: 0.6222 (t0) cc_final: 0.5202 (m-30) REVERT: H 181 PHE cc_start: 0.4972 (m-10) cc_final: 0.4524 (m-10) REVERT: H 182 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6504 (mt-10) REVERT: H 200 LYS cc_start: 0.7441 (mmmm) cc_final: 0.6860 (mmmm) REVERT: H 223 ARG cc_start: 0.6661 (OUTLIER) cc_final: 0.5373 (tpp80) REVERT: H 361 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6464 (mm-30) REVERT: H 387 ASP cc_start: 0.8018 (m-30) cc_final: 0.7717 (m-30) REVERT: H 390 GLU cc_start: 0.6672 (pm20) cc_final: 0.6355 (pt0) REVERT: H 398 GLU cc_start: 0.5921 (mm-30) cc_final: 0.5638 (mm-30) REVERT: H 415 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5674 (mm-30) REVERT: H 427 MET cc_start: 0.6329 (ttm) cc_final: 0.6025 (mtp) REVERT: I 7 GLU cc_start: 0.5785 (mp0) cc_final: 0.5269 (mm-30) REVERT: I 73 ASP cc_start: 0.6169 (t0) cc_final: 0.5257 (m-30) REVERT: I 145 ARG cc_start: 0.5842 (mmm160) cc_final: 0.3700 (ptm-80) REVERT: I 181 PHE cc_start: 0.4799 (m-10) cc_final: 0.4230 (m-80) REVERT: I 182 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6333 (mt-10) REVERT: I 361 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6170 (mm-30) REVERT: I 390 GLU cc_start: 0.6830 (pm20) cc_final: 0.6589 (pt0) REVERT: I 398 GLU cc_start: 0.6096 (mm-30) cc_final: 0.5573 (mm-30) REVERT: I 415 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5569 (mm-30) REVERT: I 419 GLU cc_start: 0.5129 (tt0) cc_final: 0.4885 (tt0) REVERT: B 7 GLU cc_start: 0.5725 (mp0) cc_final: 0.5406 (mm-30) REVERT: B 17 ASN cc_start: 0.7109 (t0) cc_final: 0.6814 (t0) REVERT: B 73 ASP cc_start: 0.6152 (t0) cc_final: 0.5357 (m-30) REVERT: B 145 ARG cc_start: 0.5887 (mmp-170) cc_final: 0.3868 (ptm-80) REVERT: B 181 PHE cc_start: 0.4916 (m-10) cc_final: 0.4419 (m-10) REVERT: B 182 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6381 (mt-10) REVERT: B 200 LYS cc_start: 0.7586 (mmmm) cc_final: 0.6716 (mttp) REVERT: B 224 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.6150 (pttm) REVERT: B 361 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6196 (mm-30) REVERT: B 390 GLU cc_start: 0.6699 (pm20) cc_final: 0.6334 (pt0) REVERT: B 398 GLU cc_start: 0.6120 (mm-30) cc_final: 0.5688 (mm-30) REVERT: C 7 GLU cc_start: 0.5940 (mp0) cc_final: 0.5591 (mm-30) REVERT: C 43 LYS cc_start: 0.6788 (ttmm) cc_final: 0.5822 (mptt) REVERT: C 49 LYS cc_start: 0.7064 (mmmm) cc_final: 0.6840 (mmpt) REVERT: C 73 ASP cc_start: 0.6180 (t0) cc_final: 0.5135 (m-30) REVERT: C 145 ARG cc_start: 0.5951 (mmp-170) cc_final: 0.3987 (ptm-80) REVERT: C 181 PHE cc_start: 0.4999 (m-10) cc_final: 0.4515 (m-10) REVERT: C 182 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6516 (mt-10) REVERT: C 200 LYS cc_start: 0.7471 (mmmm) cc_final: 0.6894 (mmmm) REVERT: C 223 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.5597 (tpp-160) REVERT: C 224 LYS cc_start: 0.6368 (pttt) cc_final: 0.6131 (pttm) REVERT: C 361 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6357 (mm-30) REVERT: C 390 GLU cc_start: 0.6663 (pm20) cc_final: 0.6381 (pt0) REVERT: C 398 GLU cc_start: 0.6098 (mm-30) cc_final: 0.5791 (mm-30) REVERT: C 415 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5536 (mm-30) REVERT: C 427 MET cc_start: 0.6453 (ttm) cc_final: 0.6140 (mtp) REVERT: J 7 GLU cc_start: 0.5771 (mp0) cc_final: 0.5338 (mm-30) REVERT: J 17 ASN cc_start: 0.7007 (t0) cc_final: 0.6685 (t0) REVERT: J 43 LYS cc_start: 0.6493 (ttmm) cc_final: 0.5666 (mptt) REVERT: J 73 ASP cc_start: 0.6253 (t0) cc_final: 0.5232 (m-30) REVERT: J 139 LYS cc_start: 0.7307 (mttt) cc_final: 0.6822 (mttm) REVERT: J 145 ARG cc_start: 0.5819 (mmm160) cc_final: 0.3658 (ptm-80) REVERT: J 181 PHE cc_start: 0.4842 (m-10) cc_final: 0.4248 (m-80) REVERT: J 182 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6283 (mt-10) REVERT: J 361 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6140 (mm-30) REVERT: J 390 GLU cc_start: 0.6887 (pm20) cc_final: 0.6406 (pm20) REVERT: J 398 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5553 (mm-30) REVERT: D 7 GLU cc_start: 0.5690 (mp0) cc_final: 0.5344 (mm-30) REVERT: D 73 ASP cc_start: 0.6155 (t0) cc_final: 0.5366 (m-30) REVERT: D 145 ARG cc_start: 0.5731 (mmm160) cc_final: 0.3772 (ptm-80) REVERT: D 181 PHE cc_start: 0.4837 (m-10) cc_final: 0.4294 (m-10) REVERT: D 182 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6328 (mt-10) REVERT: D 200 LYS cc_start: 0.7610 (mmmm) cc_final: 0.6766 (mttt) REVERT: D 361 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6180 (mm-30) REVERT: D 387 ASP cc_start: 0.7767 (m-30) cc_final: 0.7527 (m-30) REVERT: D 390 GLU cc_start: 0.6727 (pm20) cc_final: 0.6373 (pt0) REVERT: D 398 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5699 (mm-30) REVERT: D 419 GLU cc_start: 0.5437 (tt0) cc_final: 0.5171 (mt-10) REVERT: E 7 GLU cc_start: 0.5826 (mp0) cc_final: 0.5368 (mm-30) REVERT: E 67 ASP cc_start: 0.5896 (m-30) cc_final: 0.5681 (p0) REVERT: E 73 ASP cc_start: 0.6240 (t0) cc_final: 0.5178 (m-30) REVERT: E 91 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6597 (ppt-90) REVERT: E 144 ARG cc_start: 0.6576 (mmm160) cc_final: 0.6282 (mmm160) REVERT: E 145 ARG cc_start: 0.5892 (mmm160) cc_final: 0.3909 (ptm-80) REVERT: E 181 PHE cc_start: 0.5009 (m-10) cc_final: 0.4524 (m-10) REVERT: E 182 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6507 (mt-10) REVERT: E 200 LYS cc_start: 0.7463 (mmmm) cc_final: 0.6878 (mmmm) REVERT: E 223 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6606 (tpp-160) REVERT: E 361 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6449 (mm-30) REVERT: E 390 GLU cc_start: 0.6658 (pm20) cc_final: 0.6368 (pt0) REVERT: E 398 GLU cc_start: 0.6082 (mm-30) cc_final: 0.5711 (mm-30) REVERT: E 415 GLU cc_start: 0.5722 (OUTLIER) cc_final: 0.5461 (mm-30) REVERT: F 7 GLU cc_start: 0.5843 (mp0) cc_final: 0.5379 (mm-30) REVERT: F 16 GLN cc_start: 0.6768 (mt0) cc_final: 0.6510 (mm110) REVERT: F 73 ASP cc_start: 0.6160 (t0) cc_final: 0.5341 (m-30) REVERT: F 139 LYS cc_start: 0.7334 (mttt) cc_final: 0.6860 (mttm) REVERT: F 145 ARG cc_start: 0.5932 (mmm160) cc_final: 0.3815 (ptm-80) REVERT: F 181 PHE cc_start: 0.4761 (m-10) cc_final: 0.4185 (m-80) REVERT: F 182 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6325 (mt-10) REVERT: F 361 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6115 (mm-30) REVERT: F 387 ASP cc_start: 0.7803 (m-30) cc_final: 0.7511 (m-30) REVERT: F 398 GLU cc_start: 0.6093 (mm-30) cc_final: 0.5635 (mm-30) REVERT: K 7 GLU cc_start: 0.5711 (mp0) cc_final: 0.5428 (mm-30) REVERT: K 16 GLN cc_start: 0.6657 (mt0) cc_final: 0.6324 (mm-40) REVERT: K 67 ASP cc_start: 0.6953 (p0) cc_final: 0.5888 (m-30) REVERT: K 73 ASP cc_start: 0.6118 (t0) cc_final: 0.5337 (m-30) REVERT: K 145 ARG cc_start: 0.5722 (mmm160) cc_final: 0.3768 (ptm-80) REVERT: K 181 PHE cc_start: 0.4891 (m-10) cc_final: 0.4324 (m-10) REVERT: K 182 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6356 (mt-10) REVERT: K 200 LYS cc_start: 0.7623 (mmmm) cc_final: 0.6770 (mttt) REVERT: K 361 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6168 (mm-30) REVERT: K 390 GLU cc_start: 0.6759 (pm20) cc_final: 0.6478 (pt0) REVERT: K 398 GLU cc_start: 0.6039 (mm-30) cc_final: 0.5650 (mm-30) REVERT: L 7 GLU cc_start: 0.5952 (mp0) cc_final: 0.5582 (mm-30) REVERT: L 43 LYS cc_start: 0.6756 (ttmm) cc_final: 0.5792 (mptt) REVERT: L 73 ASP cc_start: 0.6226 (t0) cc_final: 0.5176 (m-30) REVERT: L 145 ARG cc_start: 0.6020 (mmp-170) cc_final: 0.4036 (ptm-80) REVERT: L 181 PHE cc_start: 0.4986 (m-10) cc_final: 0.4534 (m-10) REVERT: L 182 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6455 (mt-10) REVERT: L 200 LYS cc_start: 0.7467 (mmmm) cc_final: 0.6898 (mmmm) REVERT: L 223 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.5387 (tpp80) REVERT: L 361 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6446 (mm-30) REVERT: L 387 ASP cc_start: 0.8005 (m-30) cc_final: 0.7686 (m-30) REVERT: L 390 GLU cc_start: 0.6685 (pm20) cc_final: 0.6348 (pt0) REVERT: L 398 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5765 (mm-30) REVERT: L 415 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.5653 (mm-30) outliers start: 162 outliers final: 82 residues processed: 729 average time/residue: 1.6408 time to fit residues: 1443.6820 Evaluate side-chains 701 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 608 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 275 LEU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 223 ARG Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 383 THR Chi-restraints excluded: chain I residue 415 GLU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 179 MET Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 275 LEU Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 223 ARG Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 323 optimal weight: 3.9990 chunk 346 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 400 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 439 GLN G 34 ASN H 34 ASN I 34 ASN B 34 ASN C 34 ASN J 34 ASN J 128 ASN D 34 ASN E 34 ASN F 34 ASN F 439 GLN K 34 ASN K 128 ASN L 34 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42396 Z= 0.184 Angle : 0.534 8.218 57504 Z= 0.275 Chirality : 0.042 0.202 6300 Planarity : 0.004 0.032 7512 Dihedral : 4.523 37.412 5724 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.67 % Allowed : 16.95 % Favored : 80.38 % 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: 0.14 (0.11), residues: 5292 helix: 1.76 (0.11), residues: 2064 sheet: -1.12 (0.18), residues: 828 loop : -0.93 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 435 HIS 0.002 0.001 HIS H 416 PHE 0.016 0.001 PHE F 251 TYR 0.015 0.001 TYR F 285 ARG 0.003 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 627 time to evaluate : 4.968 Fit side-chains REVERT: A 7 GLU cc_start: 0.5741 (mp0) cc_final: 0.5292 (mm-30) REVERT: A 16 GLN cc_start: 0.6966 (mt0) cc_final: 0.6594 (mm110) REVERT: A 73 ASP cc_start: 0.6215 (t0) cc_final: 0.5237 (m-30) REVERT: A 145 ARG cc_start: 0.5910 (mmm160) cc_final: 0.3768 (ptm-80) REVERT: A 181 PHE cc_start: 0.4762 (m-10) cc_final: 0.4196 (m-80) REVERT: A 182 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6264 (mt-10) REVERT: A 361 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6140 (mm-30) REVERT: A 375 MET cc_start: 0.5398 (ptp) cc_final: 0.5178 (ptt) REVERT: A 387 ASP cc_start: 0.7724 (m-30) cc_final: 0.7492 (m-30) REVERT: A 390 GLU cc_start: 0.6891 (pm20) cc_final: 0.6419 (pm20) REVERT: A 398 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5633 (mm-30) REVERT: A 415 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: G 7 GLU cc_start: 0.5685 (mp0) cc_final: 0.5354 (mm-30) REVERT: G 16 GLN cc_start: 0.6535 (mt0) cc_final: 0.6318 (mm110) REVERT: G 73 ASP cc_start: 0.6239 (t0) cc_final: 0.5348 (m-30) REVERT: G 145 ARG cc_start: 0.5723 (mmm160) cc_final: 0.3769 (ptm-80) REVERT: G 181 PHE cc_start: 0.4841 (m-10) cc_final: 0.4324 (m-10) REVERT: G 182 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6175 (mt-10) REVERT: G 361 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6108 (mm-30) REVERT: G 368 VAL cc_start: 0.6197 (m) cc_final: 0.5863 (t) REVERT: G 387 ASP cc_start: 0.7703 (m-30) cc_final: 0.7357 (m-30) REVERT: G 390 GLU cc_start: 0.6776 (pm20) cc_final: 0.6371 (pt0) REVERT: G 398 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5678 (mm-30) REVERT: H 7 GLU cc_start: 0.5824 (mp0) cc_final: 0.5316 (mm-30) REVERT: H 51 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7288 (mmt) REVERT: H 67 ASP cc_start: 0.5929 (m-30) cc_final: 0.5606 (p0) REVERT: H 73 ASP cc_start: 0.6254 (t0) cc_final: 0.5181 (m-30) REVERT: H 181 PHE cc_start: 0.5019 (m-10) cc_final: 0.4559 (m-10) REVERT: H 182 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6521 (mt-10) REVERT: H 200 LYS cc_start: 0.7475 (mmmm) cc_final: 0.6900 (mmmm) REVERT: H 361 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6440 (mm-30) REVERT: H 387 ASP cc_start: 0.8027 (m-30) cc_final: 0.7704 (m-30) REVERT: H 390 GLU cc_start: 0.6678 (pm20) cc_final: 0.6355 (pt0) REVERT: H 398 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5625 (mm-30) REVERT: H 415 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5625 (mm-30) REVERT: H 427 MET cc_start: 0.6263 (ttm) cc_final: 0.5958 (mtp) REVERT: I 7 GLU cc_start: 0.5765 (mp0) cc_final: 0.5296 (mm-30) REVERT: I 73 ASP cc_start: 0.6140 (t0) cc_final: 0.5209 (m-30) REVERT: I 145 ARG cc_start: 0.5889 (mmm160) cc_final: 0.3778 (ptm-80) REVERT: I 181 PHE cc_start: 0.4693 (m-10) cc_final: 0.4166 (m-80) REVERT: I 182 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6325 (mt-10) REVERT: I 361 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6166 (mm-30) REVERT: I 390 GLU cc_start: 0.6880 (pm20) cc_final: 0.6624 (pt0) REVERT: I 398 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5642 (mm-30) REVERT: B 7 GLU cc_start: 0.5766 (mp0) cc_final: 0.5431 (mm-30) REVERT: B 17 ASN cc_start: 0.7100 (t0) cc_final: 0.6801 (t0) REVERT: B 73 ASP cc_start: 0.6223 (t0) cc_final: 0.5353 (m-30) REVERT: B 145 ARG cc_start: 0.5894 (mmp-170) cc_final: 0.3874 (ptm-80) REVERT: B 181 PHE cc_start: 0.4933 (m-10) cc_final: 0.4453 (m-10) REVERT: B 182 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6415 (mt-10) REVERT: B 200 LYS cc_start: 0.7600 (mmmm) cc_final: 0.6727 (mttp) REVERT: B 224 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.6016 (pttm) REVERT: B 361 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6179 (mm-30) REVERT: B 390 GLU cc_start: 0.6706 (pm20) cc_final: 0.6330 (pt0) REVERT: B 398 GLU cc_start: 0.6118 (mm-30) cc_final: 0.5701 (mm-30) REVERT: C 7 GLU cc_start: 0.5942 (mp0) cc_final: 0.5590 (mm-30) REVERT: C 43 LYS cc_start: 0.6764 (ttmm) cc_final: 0.5813 (mptt) REVERT: C 73 ASP cc_start: 0.6177 (t0) cc_final: 0.5092 (m-30) REVERT: C 145 ARG cc_start: 0.5971 (mmp-170) cc_final: 0.3970 (ptm-80) REVERT: C 181 PHE cc_start: 0.4974 (m-10) cc_final: 0.4531 (m-10) REVERT: C 182 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6515 (mt-10) REVERT: C 200 LYS cc_start: 0.7499 (mmmm) cc_final: 0.6919 (mmmm) REVERT: C 224 LYS cc_start: 0.6322 (pttt) cc_final: 0.6104 (pttm) REVERT: C 361 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6339 (mm-30) REVERT: C 390 GLU cc_start: 0.6676 (pm20) cc_final: 0.6372 (pt0) REVERT: C 398 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5756 (mm-30) REVERT: C 415 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5493 (mm-30) REVERT: C 427 MET cc_start: 0.6386 (ttm) cc_final: 0.6085 (mtp) REVERT: J 7 GLU cc_start: 0.5740 (mp0) cc_final: 0.5340 (mm-30) REVERT: J 17 ASN cc_start: 0.6926 (t0) cc_final: 0.6652 (t0) REVERT: J 43 LYS cc_start: 0.6422 (ttmm) cc_final: 0.5616 (mptt) REVERT: J 73 ASP cc_start: 0.6276 (t0) cc_final: 0.5202 (m-30) REVERT: J 139 LYS cc_start: 0.7293 (mttt) cc_final: 0.6809 (mttm) REVERT: J 145 ARG cc_start: 0.5831 (mmm160) cc_final: 0.3671 (ptm-80) REVERT: J 181 PHE cc_start: 0.4763 (m-10) cc_final: 0.4222 (m-80) REVERT: J 182 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6277 (mt-10) REVERT: J 361 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6131 (mm-30) REVERT: J 390 GLU cc_start: 0.6886 (pm20) cc_final: 0.6410 (pm20) REVERT: J 398 GLU cc_start: 0.6160 (mm-30) cc_final: 0.5624 (mm-30) REVERT: D 7 GLU cc_start: 0.5727 (mp0) cc_final: 0.5367 (mm-30) REVERT: D 67 ASP cc_start: 0.6954 (p0) cc_final: 0.5908 (m-30) REVERT: D 73 ASP cc_start: 0.6224 (t0) cc_final: 0.5347 (m-30) REVERT: D 139 LYS cc_start: 0.7289 (mttt) cc_final: 0.6917 (mttm) REVERT: D 145 ARG cc_start: 0.5747 (mmm160) cc_final: 0.3800 (ptm-80) REVERT: D 181 PHE cc_start: 0.4808 (m-10) cc_final: 0.4289 (m-10) REVERT: D 182 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6314 (mt-10) REVERT: D 200 LYS cc_start: 0.7614 (mmmm) cc_final: 0.6745 (mttp) REVERT: D 361 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6127 (mm-30) REVERT: D 387 ASP cc_start: 0.7759 (m-30) cc_final: 0.7529 (m-30) REVERT: D 390 GLU cc_start: 0.6716 (pm20) cc_final: 0.6364 (pt0) REVERT: D 398 GLU cc_start: 0.6099 (mm-30) cc_final: 0.5690 (mm-30) REVERT: D 415 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: D 419 GLU cc_start: 0.5384 (tt0) cc_final: 0.5147 (mt-10) REVERT: E 7 GLU cc_start: 0.5898 (mp0) cc_final: 0.5546 (mm-30) REVERT: E 51 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7301 (mmt) REVERT: E 67 ASP cc_start: 0.5948 (m-30) cc_final: 0.5660 (p0) REVERT: E 73 ASP cc_start: 0.6224 (t0) cc_final: 0.5093 (m-30) REVERT: E 91 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6553 (ppt-90) REVERT: E 145 ARG cc_start: 0.5887 (mmm160) cc_final: 0.5632 (mmp-170) REVERT: E 181 PHE cc_start: 0.4981 (m-10) cc_final: 0.4513 (m-10) REVERT: E 182 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6502 (mt-10) REVERT: E 200 LYS cc_start: 0.7474 (mmmm) cc_final: 0.6896 (mmmm) REVERT: E 223 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6609 (tpp-160) REVERT: E 361 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6417 (mm-30) REVERT: E 390 GLU cc_start: 0.6645 (pm20) cc_final: 0.6356 (pt0) REVERT: E 398 GLU cc_start: 0.6067 (mm-30) cc_final: 0.5764 (mm-30) REVERT: E 415 GLU cc_start: 0.5693 (OUTLIER) cc_final: 0.5425 (mm-30) REVERT: F 7 GLU cc_start: 0.5816 (mp0) cc_final: 0.5327 (mm-30) REVERT: F 16 GLN cc_start: 0.6661 (mt0) cc_final: 0.6381 (mm110) REVERT: F 73 ASP cc_start: 0.6355 (t0) cc_final: 0.5311 (m-30) REVERT: F 139 LYS cc_start: 0.7315 (mttt) cc_final: 0.6849 (mttm) REVERT: F 145 ARG cc_start: 0.5907 (mmm160) cc_final: 0.3765 (ptm-80) REVERT: F 181 PHE cc_start: 0.4753 (m-10) cc_final: 0.4215 (m-80) REVERT: F 182 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6343 (mt-10) REVERT: F 361 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6081 (mm-30) REVERT: F 375 MET cc_start: 0.5469 (ptp) cc_final: 0.5176 (ptt) REVERT: F 387 ASP cc_start: 0.7705 (m-30) cc_final: 0.7434 (m-30) REVERT: F 398 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5593 (mm-30) REVERT: F 415 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5533 (mp0) REVERT: K 7 GLU cc_start: 0.5764 (mp0) cc_final: 0.5444 (mm-30) REVERT: K 16 GLN cc_start: 0.6704 (mt0) cc_final: 0.6337 (mm-40) REVERT: K 73 ASP cc_start: 0.6229 (t0) cc_final: 0.5336 (m-30) REVERT: K 120 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5795 (mm-30) REVERT: K 145 ARG cc_start: 0.5720 (mmm160) cc_final: 0.3769 (ptm-80) REVERT: K 181 PHE cc_start: 0.4861 (m-10) cc_final: 0.4348 (m-10) REVERT: K 182 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6331 (mt-10) REVERT: K 200 LYS cc_start: 0.7641 (mmmm) cc_final: 0.6702 (mttp) REVERT: K 361 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6136 (mm-30) REVERT: K 387 ASP cc_start: 0.7752 (m-30) cc_final: 0.7538 (m-30) REVERT: K 390 GLU cc_start: 0.6750 (pm20) cc_final: 0.6394 (pt0) REVERT: K 398 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5657 (mm-30) REVERT: L 7 GLU cc_start: 0.5906 (mp0) cc_final: 0.5525 (mm-30) REVERT: L 43 LYS cc_start: 0.6673 (ttmm) cc_final: 0.5722 (mptt) REVERT: L 73 ASP cc_start: 0.6224 (t0) cc_final: 0.5127 (m-30) REVERT: L 93 ILE cc_start: 0.6382 (OUTLIER) cc_final: 0.6017 (mm) REVERT: L 145 ARG cc_start: 0.5992 (mmp-170) cc_final: 0.4032 (ptm-80) REVERT: L 181 PHE cc_start: 0.4986 (m-10) cc_final: 0.4525 (m-10) REVERT: L 182 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6467 (mt-10) REVERT: L 200 LYS cc_start: 0.7470 (mmmm) cc_final: 0.6899 (mmmm) REVERT: L 361 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6426 (mm-30) REVERT: L 387 ASP cc_start: 0.7984 (m-30) cc_final: 0.7652 (m-30) REVERT: L 390 GLU cc_start: 0.6703 (pm20) cc_final: 0.6363 (pt0) REVERT: L 398 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5745 (mm-30) REVERT: L 415 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5590 (mm-30) outliers start: 114 outliers final: 66 residues processed: 702 average time/residue: 1.6887 time to fit residues: 1425.4681 Evaluate side-chains 690 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 610 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 414 PHE Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 SER Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 415 GLU Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain K residue 120 GLU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 7.9990 chunk 487 optimal weight: 3.9990 chunk 444 optimal weight: 0.7980 chunk 474 optimal weight: 0.6980 chunk 285 optimal weight: 5.9990 chunk 206 optimal weight: 0.0030 chunk 372 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 428 optimal weight: 0.0050 chunk 448 optimal weight: 0.9990 chunk 472 optimal weight: 0.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 34 ASN G 128 ASN H 34 ASN I 34 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN C 34 ASN J 34 ASN J 128 ASN ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 34 ASN F 34 ASN K 34 ASN L 34 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 42396 Z= 0.152 Angle : 0.514 7.691 57504 Z= 0.265 Chirality : 0.041 0.168 6300 Planarity : 0.004 0.032 7512 Dihedral : 4.312 34.087 5724 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.41 % Allowed : 17.67 % Favored : 79.92 % 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: 0.40 (0.11), residues: 5292 helix: 1.94 (0.11), residues: 2064 sheet: -0.91 (0.19), residues: 768 loop : -0.78 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 435 HIS 0.002 0.001 HIS B 416 PHE 0.039 0.001 PHE D 414 TYR 0.015 0.001 TYR F 285 ARG 0.002 0.000 ARG L 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 640 time to evaluate : 4.345 Fit side-chains REVERT: A 7 GLU cc_start: 0.5775 (mp0) cc_final: 0.5355 (mm-30) REVERT: A 16 GLN cc_start: 0.6886 (mt0) cc_final: 0.6519 (mm110) REVERT: A 73 ASP cc_start: 0.6247 (t0) cc_final: 0.5252 (m-30) REVERT: A 145 ARG cc_start: 0.5904 (mmm160) cc_final: 0.3772 (ptm-80) REVERT: A 181 PHE cc_start: 0.4766 (m-10) cc_final: 0.4240 (m-80) REVERT: A 182 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6265 (mt-10) REVERT: A 223 ARG cc_start: 0.6719 (ttm-80) cc_final: 0.6216 (tpt90) REVERT: A 361 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6189 (mm-30) REVERT: A 387 ASP cc_start: 0.7646 (m-30) cc_final: 0.7402 (m-30) REVERT: A 390 GLU cc_start: 0.6882 (pm20) cc_final: 0.6412 (pm20) REVERT: A 398 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5693 (mm-30) REVERT: A 415 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: G 7 GLU cc_start: 0.5757 (mp0) cc_final: 0.5379 (mm-30) REVERT: G 73 ASP cc_start: 0.6219 (t0) cc_final: 0.5318 (m-30) REVERT: G 145 ARG cc_start: 0.5723 (mmm160) cc_final: 0.3767 (ptm-80) REVERT: G 181 PHE cc_start: 0.4788 (m-10) cc_final: 0.4327 (m-10) REVERT: G 182 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6164 (mt-10) REVERT: G 223 ARG cc_start: 0.6698 (tpp-160) cc_final: 0.6209 (tpt170) REVERT: G 361 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6087 (mm-30) REVERT: G 368 VAL cc_start: 0.6100 (m) cc_final: 0.5789 (t) REVERT: G 387 ASP cc_start: 0.7698 (m-30) cc_final: 0.7328 (m-30) REVERT: G 390 GLU cc_start: 0.6726 (pm20) cc_final: 0.6396 (pt0) REVERT: G 398 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5694 (mm-30) REVERT: H 7 GLU cc_start: 0.5827 (mp0) cc_final: 0.5497 (mm-30) REVERT: H 67 ASP cc_start: 0.5979 (m-30) cc_final: 0.5763 (p0) REVERT: H 73 ASP cc_start: 0.6245 (t0) cc_final: 0.5129 (m-30) REVERT: H 181 PHE cc_start: 0.5001 (m-10) cc_final: 0.4579 (m-10) REVERT: H 182 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6535 (mt-10) REVERT: H 200 LYS cc_start: 0.7488 (mmmm) cc_final: 0.6908 (mmmm) REVERT: H 361 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6467 (mm-30) REVERT: H 387 ASP cc_start: 0.8021 (m-30) cc_final: 0.7710 (m-30) REVERT: H 398 GLU cc_start: 0.5886 (mm-30) cc_final: 0.5680 (mm-30) REVERT: H 415 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.5479 (mm-30) REVERT: I 7 GLU cc_start: 0.5847 (mp0) cc_final: 0.5357 (mm-30) REVERT: I 73 ASP cc_start: 0.6159 (t0) cc_final: 0.5214 (m-30) REVERT: I 145 ARG cc_start: 0.5920 (mmm160) cc_final: 0.3799 (ptm-80) REVERT: I 181 PHE cc_start: 0.4706 (m-10) cc_final: 0.4234 (m-80) REVERT: I 182 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6326 (mt-10) REVERT: I 361 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6133 (mm-30) REVERT: I 390 GLU cc_start: 0.6874 (pm20) cc_final: 0.6405 (pm20) REVERT: I 398 GLU cc_start: 0.6162 (mm-30) cc_final: 0.5626 (mm-30) REVERT: B 7 GLU cc_start: 0.5779 (mp0) cc_final: 0.5400 (mm-30) REVERT: B 17 ASN cc_start: 0.7093 (t0) cc_final: 0.6841 (t0) REVERT: B 73 ASP cc_start: 0.6221 (t0) cc_final: 0.5333 (m-30) REVERT: B 145 ARG cc_start: 0.5903 (mmp-170) cc_final: 0.3886 (ptm-80) REVERT: B 181 PHE cc_start: 0.4876 (m-10) cc_final: 0.4438 (m-10) REVERT: B 182 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6430 (mt-10) REVERT: B 200 LYS cc_start: 0.7602 (mmmm) cc_final: 0.6726 (mttp) REVERT: B 224 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5982 (pttm) REVERT: B 361 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6123 (mm-30) REVERT: B 390 GLU cc_start: 0.6605 (pm20) cc_final: 0.6229 (pt0) REVERT: B 398 GLU cc_start: 0.6117 (mm-30) cc_final: 0.5702 (mm-30) REVERT: C 7 GLU cc_start: 0.5969 (mp0) cc_final: 0.5576 (mm-30) REVERT: C 43 LYS cc_start: 0.6753 (ttmm) cc_final: 0.5818 (mptt) REVERT: C 73 ASP cc_start: 0.6101 (t0) cc_final: 0.5016 (m-30) REVERT: C 181 PHE cc_start: 0.4997 (m-10) cc_final: 0.4550 (m-10) REVERT: C 182 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6408 (mt-10) REVERT: C 200 LYS cc_start: 0.7501 (mmmm) cc_final: 0.6930 (mmmm) REVERT: C 224 LYS cc_start: 0.6371 (pttt) cc_final: 0.6154 (pttm) REVERT: C 361 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6306 (mm-30) REVERT: C 390 GLU cc_start: 0.6695 (pm20) cc_final: 0.6383 (pt0) REVERT: C 398 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5742 (mm-30) REVERT: C 415 GLU cc_start: 0.5729 (OUTLIER) cc_final: 0.5511 (mm-30) REVERT: C 427 MET cc_start: 0.6400 (ttm) cc_final: 0.6066 (mtp) REVERT: J 7 GLU cc_start: 0.5797 (mp0) cc_final: 0.5352 (mm-30) REVERT: J 17 ASN cc_start: 0.6959 (t0) cc_final: 0.6659 (t0) REVERT: J 43 LYS cc_start: 0.6408 (ttmm) cc_final: 0.5615 (mptt) REVERT: J 73 ASP cc_start: 0.6266 (t0) cc_final: 0.5180 (m-30) REVERT: J 139 LYS cc_start: 0.7294 (mttt) cc_final: 0.6806 (mttm) REVERT: J 145 ARG cc_start: 0.5853 (mmm160) cc_final: 0.3751 (ptm-80) REVERT: J 181 PHE cc_start: 0.4703 (m-10) cc_final: 0.4188 (m-80) REVERT: J 182 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6276 (mt-10) REVERT: J 361 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6147 (mm-30) REVERT: J 390 GLU cc_start: 0.6879 (pm20) cc_final: 0.6406 (pm20) REVERT: J 398 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5685 (mm-30) REVERT: D 7 GLU cc_start: 0.5740 (mp0) cc_final: 0.5339 (mm-30) REVERT: D 67 ASP cc_start: 0.6851 (p0) cc_final: 0.5765 (m-30) REVERT: D 73 ASP cc_start: 0.6234 (t0) cc_final: 0.5327 (m-30) REVERT: D 145 ARG cc_start: 0.5726 (mmm160) cc_final: 0.3770 (ptm-80) REVERT: D 181 PHE cc_start: 0.4758 (m-10) cc_final: 0.4278 (m-10) REVERT: D 182 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6287 (mt-10) REVERT: D 200 LYS cc_start: 0.7627 (mmmm) cc_final: 0.6693 (mttp) REVERT: D 361 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6088 (mm-30) REVERT: D 387 ASP cc_start: 0.7809 (m-30) cc_final: 0.7602 (m-30) REVERT: D 390 GLU cc_start: 0.6663 (pm20) cc_final: 0.6309 (pt0) REVERT: D 398 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5706 (mm-30) REVERT: D 419 GLU cc_start: 0.5397 (tt0) cc_final: 0.5141 (tt0) REVERT: E 7 GLU cc_start: 0.5848 (mp0) cc_final: 0.5460 (mm-30) REVERT: E 73 ASP cc_start: 0.6179 (t0) cc_final: 0.5016 (m-30) REVERT: E 91 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6496 (ppt-90) REVERT: E 145 ARG cc_start: 0.5863 (mmm160) cc_final: 0.5605 (mmp-170) REVERT: E 181 PHE cc_start: 0.4925 (m-10) cc_final: 0.4509 (m-10) REVERT: E 182 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6503 (mt-10) REVERT: E 200 LYS cc_start: 0.7494 (mmmm) cc_final: 0.6910 (mmmm) REVERT: E 361 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6408 (mm-30) REVERT: E 390 GLU cc_start: 0.6687 (pm20) cc_final: 0.6368 (pt0) REVERT: E 398 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5768 (mm-30) REVERT: E 415 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5396 (mm-30) REVERT: F 7 GLU cc_start: 0.5866 (mp0) cc_final: 0.5405 (mm-30) REVERT: F 16 GLN cc_start: 0.6623 (mt0) cc_final: 0.6340 (mm110) REVERT: F 73 ASP cc_start: 0.6139 (t0) cc_final: 0.5069 (m-30) REVERT: F 139 LYS cc_start: 0.7275 (mttt) cc_final: 0.6807 (mttm) REVERT: F 145 ARG cc_start: 0.5945 (mmm160) cc_final: 0.3824 (ptm-80) REVERT: F 181 PHE cc_start: 0.4702 (m-10) cc_final: 0.4211 (m-80) REVERT: F 182 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6339 (mt-10) REVERT: F 361 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6086 (mm-30) REVERT: F 375 MET cc_start: 0.5400 (ptp) cc_final: 0.5149 (ptt) REVERT: F 387 ASP cc_start: 0.7650 (m-30) cc_final: 0.7412 (m-30) REVERT: F 398 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5703 (mm-30) REVERT: F 415 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5565 (mp0) REVERT: K 7 GLU cc_start: 0.5797 (mp0) cc_final: 0.5459 (mm-30) REVERT: K 16 GLN cc_start: 0.6634 (mt0) cc_final: 0.6369 (mm-40) REVERT: K 67 ASP cc_start: 0.6864 (p0) cc_final: 0.5753 (m-30) REVERT: K 73 ASP cc_start: 0.6205 (t0) cc_final: 0.5300 (m-30) REVERT: K 145 ARG cc_start: 0.5721 (mmm160) cc_final: 0.3771 (ptm-80) REVERT: K 181 PHE cc_start: 0.4793 (m-10) cc_final: 0.4323 (m-10) REVERT: K 182 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6322 (mt-10) REVERT: K 200 LYS cc_start: 0.7642 (mmmm) cc_final: 0.6708 (mttp) REVERT: K 361 GLU cc_start: 0.6879 (mt-10) cc_final: 0.6075 (mm-30) REVERT: K 387 ASP cc_start: 0.7750 (m-30) cc_final: 0.7542 (m-30) REVERT: K 390 GLU cc_start: 0.6674 (pm20) cc_final: 0.6308 (pt0) REVERT: K 398 GLU cc_start: 0.6031 (mm-30) cc_final: 0.5657 (mm-30) REVERT: L 7 GLU cc_start: 0.5806 (mp0) cc_final: 0.5466 (mm-30) REVERT: L 43 LYS cc_start: 0.6633 (ttmm) cc_final: 0.5698 (mptt) REVERT: L 73 ASP cc_start: 0.6261 (t0) cc_final: 0.5086 (m-30) REVERT: L 145 ARG cc_start: 0.5985 (mmp-170) cc_final: 0.4038 (ptm-80) REVERT: L 181 PHE cc_start: 0.4980 (m-10) cc_final: 0.4559 (m-10) REVERT: L 182 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6417 (mt-10) REVERT: L 200 LYS cc_start: 0.7489 (mmmm) cc_final: 0.6929 (mmmm) REVERT: L 361 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6412 (mm-30) REVERT: L 387 ASP cc_start: 0.7957 (m-30) cc_final: 0.7628 (m-30) REVERT: L 398 GLU cc_start: 0.6061 (mm-30) cc_final: 0.5723 (mm-30) REVERT: L 415 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5434 (mm-30) outliers start: 103 outliers final: 60 residues processed: 709 average time/residue: 1.6668 time to fit residues: 1436.7349 Evaluate side-chains 676 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 608 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 91 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain F residue 415 GLU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.6980 chunk 501 optimal weight: 0.9990 chunk 306 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 526 optimal weight: 0.6980 chunk 484 optimal weight: 6.9990 chunk 418 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 256 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN G 24 GLN G 34 ASN H 34 ASN I 34 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 34 ASN C 34 ASN C 128 ASN J 34 ASN J 128 ASN ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 34 ASN D 128 ASN E 34 ASN E 128 ASN F 34 ASN K 24 GLN K 34 ASN L 34 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 42396 Z= 0.166 Angle : 0.522 7.935 57504 Z= 0.268 Chirality : 0.041 0.177 6300 Planarity : 0.004 0.032 7512 Dihedral : 4.263 32.635 5724 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.22 % Allowed : 17.81 % Favored : 79.96 % 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: 0.43 (0.11), residues: 5292 helix: 1.97 (0.11), residues: 2064 sheet: -0.87 (0.19), residues: 768 loop : -0.78 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 77 HIS 0.002 0.001 HIS H 416 PHE 0.015 0.001 PHE C 414 TYR 0.015 0.001 TYR B 285 ARG 0.002 0.000 ARG L 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10584 Ramachandran restraints generated. 5292 Oldfield, 0 Emsley, 5292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 623 time to evaluate : 4.973 Fit side-chains REVERT: A 7 GLU cc_start: 0.5770 (mp0) cc_final: 0.5347 (mm-30) REVERT: A 16 GLN cc_start: 0.6879 (mt0) cc_final: 0.6512 (mm110) REVERT: A 73 ASP cc_start: 0.6231 (t0) cc_final: 0.5239 (m-30) REVERT: A 126 GLU cc_start: 0.6626 (pt0) cc_final: 0.6363 (pt0) REVERT: A 145 ARG cc_start: 0.5914 (mmm160) cc_final: 0.3774 (ptm-80) REVERT: A 181 PHE cc_start: 0.4771 (m-10) cc_final: 0.4248 (m-80) REVERT: A 182 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6265 (mt-10) REVERT: A 361 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6187 (mm-30) REVERT: A 387 ASP cc_start: 0.7655 (m-30) cc_final: 0.7430 (m-30) REVERT: A 390 GLU cc_start: 0.6886 (pm20) cc_final: 0.6414 (pm20) REVERT: A 398 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5704 (mm-30) REVERT: A 415 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5689 (mp0) REVERT: G 7 GLU cc_start: 0.5742 (mp0) cc_final: 0.5366 (mm-30) REVERT: G 73 ASP cc_start: 0.6205 (t0) cc_final: 0.5303 (m-30) REVERT: G 145 ARG cc_start: 0.5730 (mmm160) cc_final: 0.3771 (ptm-80) REVERT: G 181 PHE cc_start: 0.4788 (m-10) cc_final: 0.4305 (m-10) REVERT: G 182 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6343 (mt-10) REVERT: G 200 LYS cc_start: 0.7641 (mmmm) cc_final: 0.6705 (mttp) REVERT: G 361 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6079 (mm-30) REVERT: G 368 VAL cc_start: 0.6083 (m) cc_final: 0.5757 (t) REVERT: G 387 ASP cc_start: 0.7699 (m-30) cc_final: 0.7343 (m-30) REVERT: G 390 GLU cc_start: 0.6661 (pm20) cc_final: 0.6317 (pt0) REVERT: G 398 GLU cc_start: 0.6134 (mm-30) cc_final: 0.5715 (mm-30) REVERT: H 7 GLU cc_start: 0.5876 (mp0) cc_final: 0.5550 (mm-30) REVERT: H 16 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6563 (mm-40) REVERT: H 73 ASP cc_start: 0.6268 (t0) cc_final: 0.5104 (m-30) REVERT: H 181 PHE cc_start: 0.4967 (m-10) cc_final: 0.4506 (m-10) REVERT: H 182 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6538 (mt-10) REVERT: H 200 LYS cc_start: 0.7478 (mmmm) cc_final: 0.6893 (mmmm) REVERT: H 361 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6478 (mm-30) REVERT: H 387 ASP cc_start: 0.7961 (m-30) cc_final: 0.7671 (m-30) REVERT: H 415 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5515 (mm-30) REVERT: I 7 GLU cc_start: 0.5843 (mp0) cc_final: 0.5353 (mm-30) REVERT: I 73 ASP cc_start: 0.6020 (t0) cc_final: 0.5111 (m-30) REVERT: I 145 ARG cc_start: 0.5909 (mmm160) cc_final: 0.3796 (ptm-80) REVERT: I 181 PHE cc_start: 0.4709 (m-10) cc_final: 0.4244 (m-80) REVERT: I 182 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6339 (mt-10) REVERT: I 361 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6146 (mm-30) REVERT: I 390 GLU cc_start: 0.6880 (pm20) cc_final: 0.6408 (pm20) REVERT: I 398 GLU cc_start: 0.6173 (mm-30) cc_final: 0.5710 (mm-30) REVERT: B 7 GLU cc_start: 0.5818 (mp0) cc_final: 0.5430 (mm-30) REVERT: B 17 ASN cc_start: 0.7139 (t0) cc_final: 0.6860 (t0) REVERT: B 73 ASP cc_start: 0.6232 (t0) cc_final: 0.5325 (m-30) REVERT: B 145 ARG cc_start: 0.5904 (mmp-170) cc_final: 0.3871 (ptm-80) REVERT: B 181 PHE cc_start: 0.4891 (m-10) cc_final: 0.4436 (m-10) REVERT: B 182 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6457 (mt-10) REVERT: B 200 LYS cc_start: 0.7655 (mmmm) cc_final: 0.6780 (mttp) REVERT: B 224 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5968 (pttm) REVERT: B 361 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6117 (mm-30) REVERT: B 390 GLU cc_start: 0.6607 (pm20) cc_final: 0.6226 (pt0) REVERT: B 398 GLU cc_start: 0.6121 (mm-30) cc_final: 0.5704 (mm-30) REVERT: B 415 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5649 (mp0) REVERT: C 7 GLU cc_start: 0.5965 (mp0) cc_final: 0.5572 (mm-30) REVERT: C 43 LYS cc_start: 0.6760 (ttmm) cc_final: 0.5833 (mptt) REVERT: C 73 ASP cc_start: 0.6059 (t0) cc_final: 0.4996 (m-30) REVERT: C 145 ARG cc_start: 0.5956 (mmp-170) cc_final: 0.4014 (ptm-80) REVERT: C 181 PHE cc_start: 0.4954 (m-10) cc_final: 0.4532 (m-10) REVERT: C 182 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6537 (mt-10) REVERT: C 200 LYS cc_start: 0.7488 (mmmm) cc_final: 0.6915 (mmmm) REVERT: C 224 LYS cc_start: 0.6376 (pttt) cc_final: 0.6163 (pttm) REVERT: C 361 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6307 (mm-30) REVERT: C 390 GLU cc_start: 0.6698 (pm20) cc_final: 0.6383 (pt0) REVERT: C 398 GLU cc_start: 0.6077 (mm-30) cc_final: 0.5741 (mm-30) REVERT: C 415 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5426 (mm-30) REVERT: J 7 GLU cc_start: 0.5786 (mp0) cc_final: 0.5337 (mm-30) REVERT: J 17 ASN cc_start: 0.6900 (t0) cc_final: 0.6616 (t0) REVERT: J 43 LYS cc_start: 0.6410 (ttmm) cc_final: 0.5618 (mptt) REVERT: J 73 ASP cc_start: 0.6256 (t0) cc_final: 0.5168 (m-30) REVERT: J 139 LYS cc_start: 0.7296 (mttt) cc_final: 0.6805 (mttm) REVERT: J 145 ARG cc_start: 0.5863 (mmm160) cc_final: 0.3756 (ptm-80) REVERT: J 181 PHE cc_start: 0.4717 (m-10) cc_final: 0.4201 (m-80) REVERT: J 182 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6271 (mt-10) REVERT: J 321 ARG cc_start: 0.6646 (ttp80) cc_final: 0.6414 (ttp80) REVERT: J 361 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6165 (mm-30) REVERT: J 390 GLU cc_start: 0.6884 (pm20) cc_final: 0.6410 (pm20) REVERT: J 398 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5693 (mm-30) REVERT: D 7 GLU cc_start: 0.5776 (mp0) cc_final: 0.5368 (mm-30) REVERT: D 51 MET cc_start: 0.7762 (mmm) cc_final: 0.7427 (tpt) REVERT: D 67 ASP cc_start: 0.6797 (p0) cc_final: 0.5698 (m-30) REVERT: D 73 ASP cc_start: 0.6220 (t0) cc_final: 0.5309 (m-30) REVERT: D 145 ARG cc_start: 0.5733 (mmm160) cc_final: 0.3784 (ptm-80) REVERT: D 181 PHE cc_start: 0.4751 (m-10) cc_final: 0.4243 (m-10) REVERT: D 182 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6340 (mt-10) REVERT: D 200 LYS cc_start: 0.7637 (mmmm) cc_final: 0.6703 (mttp) REVERT: D 361 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6067 (mm-30) REVERT: D 390 GLU cc_start: 0.6664 (pm20) cc_final: 0.6310 (pt0) REVERT: D 398 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5707 (mm-30) REVERT: D 419 GLU cc_start: 0.5327 (tt0) cc_final: 0.5080 (tt0) REVERT: E 7 GLU cc_start: 0.5842 (mp0) cc_final: 0.5456 (mm-30) REVERT: E 73 ASP cc_start: 0.6165 (t0) cc_final: 0.4939 (m-30) REVERT: E 145 ARG cc_start: 0.5844 (mmm160) cc_final: 0.3814 (ptm-80) REVERT: E 181 PHE cc_start: 0.4934 (m-10) cc_final: 0.4459 (m-10) REVERT: E 182 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6529 (mt-10) REVERT: E 200 LYS cc_start: 0.7488 (mmmm) cc_final: 0.6908 (mmmm) REVERT: E 361 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6405 (mm-30) REVERT: E 390 GLU cc_start: 0.6691 (pm20) cc_final: 0.6370 (pt0) REVERT: E 398 GLU cc_start: 0.6068 (mm-30) cc_final: 0.5773 (mm-30) REVERT: E 415 GLU cc_start: 0.5669 (OUTLIER) cc_final: 0.5410 (mm-30) REVERT: F 7 GLU cc_start: 0.5898 (mp0) cc_final: 0.5427 (mm-30) REVERT: F 16 GLN cc_start: 0.6631 (mt0) cc_final: 0.6361 (mm110) REVERT: F 73 ASP cc_start: 0.6072 (t0) cc_final: 0.5054 (m-30) REVERT: F 126 GLU cc_start: 0.6558 (pt0) cc_final: 0.6310 (pt0) REVERT: F 139 LYS cc_start: 0.7308 (mttt) cc_final: 0.6843 (mttm) REVERT: F 145 ARG cc_start: 0.5954 (mmm160) cc_final: 0.3829 (ptm-80) REVERT: F 181 PHE cc_start: 0.4727 (m-10) cc_final: 0.4242 (m-80) REVERT: F 182 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6358 (mt-10) REVERT: F 361 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6029 (mm-30) REVERT: F 375 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.5145 (ptt) REVERT: F 387 ASP cc_start: 0.7688 (m-30) cc_final: 0.7446 (m-30) REVERT: F 398 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5710 (mm-30) REVERT: K 7 GLU cc_start: 0.5855 (mp0) cc_final: 0.5392 (mm-30) REVERT: K 16 GLN cc_start: 0.6628 (mt0) cc_final: 0.6372 (mm110) REVERT: K 67 ASP cc_start: 0.6740 (p0) cc_final: 0.5659 (m-30) REVERT: K 73 ASP cc_start: 0.6191 (t0) cc_final: 0.5281 (m-30) REVERT: K 145 ARG cc_start: 0.5732 (mmm160) cc_final: 0.3794 (ptm-80) REVERT: K 181 PHE cc_start: 0.4769 (m-10) cc_final: 0.4319 (m-10) REVERT: K 182 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6351 (mt-10) REVERT: K 200 LYS cc_start: 0.7647 (mmmm) cc_final: 0.6707 (mttp) REVERT: K 361 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6056 (mm-30) REVERT: K 387 ASP cc_start: 0.7782 (m-30) cc_final: 0.7576 (m-30) REVERT: K 390 GLU cc_start: 0.6674 (pm20) cc_final: 0.6308 (pt0) REVERT: K 398 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5665 (mm-30) REVERT: L 7 GLU cc_start: 0.5841 (mp0) cc_final: 0.5518 (mm-30) REVERT: L 43 LYS cc_start: 0.6635 (ttmm) cc_final: 0.5701 (mptt) REVERT: L 73 ASP cc_start: 0.6219 (t0) cc_final: 0.5044 (m-30) REVERT: L 139 LYS cc_start: 0.7412 (mttt) cc_final: 0.7069 (mttm) REVERT: L 145 ARG cc_start: 0.6007 (mmp-170) cc_final: 0.4065 (ptm-80) REVERT: L 181 PHE cc_start: 0.4950 (m-10) cc_final: 0.4547 (m-10) REVERT: L 182 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6501 (mt-10) REVERT: L 200 LYS cc_start: 0.7481 (mmmm) cc_final: 0.6948 (mmmm) REVERT: L 361 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6471 (mm-30) REVERT: L 387 ASP cc_start: 0.7941 (m-30) cc_final: 0.7634 (m-30) REVERT: L 398 GLU cc_start: 0.6069 (mm-30) cc_final: 0.5750 (mm-30) REVERT: L 415 GLU cc_start: 0.5700 (OUTLIER) cc_final: 0.5464 (mm-30) outliers start: 95 outliers final: 65 residues processed: 695 average time/residue: 1.6767 time to fit residues: 1401.8736 Evaluate side-chains 680 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 607 time to evaluate : 4.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 415 GLU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 363 THR Chi-restraints excluded: chain G residue 442 GLU Chi-restraints excluded: chain H residue 34 ASN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 415 GLU Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 202 GLU Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 383 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 442 GLU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 34 ASN Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 442 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 34 ASN Chi-restraints excluded: chain J residue 203 ASP Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 363 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 363 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 375 MET Chi-restraints excluded: chain F residue 390 GLU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 203 ASP Chi-restraints excluded: chain K residue 363 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 442 GLU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 34 ASN Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 248 MET Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain L residue 383 THR Chi-restraints excluded: chain L residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 8.9990 chunk 446 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 386 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 419 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 ASN C 128 ASN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN J 128 ASN ** J 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN E 34 ASN K 34 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.177293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158411 restraints weight = 43757.993| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.50 r_work: 0.3771 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.253 42396 Z= 0.313 Angle : 0.887 59.200 57504 Z= 0.528 Chirality : 0.050 1.063 6300 Planarity : 0.005 0.152 7512 Dihedral : 4.282 32.646 5724 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.29 % Allowed : 17.88 % Favored : 79.82 % Cbeta Deviations : 0.14 % 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: 0.43 (0.11), residues: 5292 helix: 1.97 (0.11), residues: 2064 sheet: -0.85 (0.19), residues: 768 loop : -0.78 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 77 HIS 0.002 0.000 HIS H 416 PHE 0.023 0.001 PHE I 251 TYR 0.026 0.001 TYR G 69 ARG 0.005 0.000 ARG C 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20013.12 seconds wall clock time: 353 minutes 9.35 seconds (21189.35 seconds total)