Starting phenix.real_space_refine on Mon Mar 11 16:49:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uth_20879/03_2024/6uth_20879.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.220 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: 4 Type Number sf(0) Gaussians S 231 5.16 5 C 36932 2.51 5 N 9975 2.21 5 O 11256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 58394 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "C" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "D" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "E" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "G" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Z" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "M" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "1" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "N" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "2" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "H" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "V" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "I" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "W" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "J" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "X" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "K" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "Y" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1558 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 196} Chain: "O" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "P" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "Q" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "R" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "S" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "T" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "U" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain: "a" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "b" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "c" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "d" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "e" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "f" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Chain: "g" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1692 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ARG O 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG O 28 " occ=0.50 residue: pdb=" N VAL O 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 77 " occ=0.50 residue: pdb=" N ARG P 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG P 28 " occ=0.50 residue: pdb=" N VAL P 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL P 77 " occ=0.50 residue: pdb=" N ARG Q 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG Q 28 " occ=0.50 residue: pdb=" N VAL Q 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL Q 77 " occ=0.50 residue: pdb=" N ARG R 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG R 28 " occ=0.50 residue: pdb=" N VAL R 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL R 77 " occ=0.50 residue: pdb=" N ARG S 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG S 28 " occ=0.50 residue: pdb=" N VAL S 77 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL S 77 " occ=0.50 residue: pdb=" N ARG T 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG T 28 " occ=0.50 residue: pdb=" N ARG U 28 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG U 28 " occ=0.50 Time building chain proxies: 21.84, per 1000 atoms: 0.37 Number of scatterers: 58394 At special positions: 0 Unit cell: (132.25, 133.4, 239.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 231 16.00 O 11256 8.00 N 9975 7.00 C 36932 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: 17.49 Conformation dependent library (CDL) restraints added in 8.7 seconds 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13916 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 56 sheets defined 49.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 81 through 104 Processing helix chain 'A' and resid 108 through 126 removed outlier: 3.710A pdb=" N LEU A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 180 Processing helix chain 'A' and resid 185 through 202 removed outlier: 3.517A pdb=" N SER A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.680A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 81 through 104 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.726A pdb=" N LEU B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.511A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 233 removed outlier: 3.667A pdb=" N VAL B 229 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 Processing helix chain 'C' and resid 81 through 104 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.724A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 Processing helix chain 'C' and resid 185 through 202 removed outlier: 3.513A pdb=" N SER C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.670A pdb=" N VAL C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C 230 " --> pdb=" O GLN C 226 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 81 through 104 Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.716A pdb=" N LEU D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 180 Processing helix chain 'D' and resid 185 through 202 removed outlier: 3.514A pdb=" N SER D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 233 removed outlier: 3.666A pdb=" N VAL D 229 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 230 " --> pdb=" O GLN D 226 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 33 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.716A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 180 Processing helix chain 'E' and resid 185 through 202 removed outlier: 3.514A pdb=" N SER E 200 " --> pdb=" O ALA E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 233 removed outlier: 3.667A pdb=" N VAL E 229 " --> pdb=" O ASP E 225 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 33 Processing helix chain 'F' and resid 81 through 104 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.724A pdb=" N LEU F 112 " --> pdb=" O ASN F 108 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'F' and resid 185 through 202 removed outlier: 3.513A pdb=" N SER F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 233 removed outlier: 3.666A pdb=" N VAL F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS F 230 " --> pdb=" O GLN F 226 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.731A pdb=" N LEU G 112 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 180 Processing helix chain 'G' and resid 185 through 202 removed outlier: 3.514A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 233 removed outlier: 3.675A pdb=" N VAL G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS G 231 " --> pdb=" O GLU G 227 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 90 removed outlier: 4.024A pdb=" N VAL Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 142 removed outlier: 3.834A pdb=" N VAL Z 134 " --> pdb=" O GLY Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 166 Processing helix chain 'Z' and resid 188 through 200 Processing helix chain 'M' and resid 48 through 71 Processing helix chain 'M' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL M 90 " --> pdb=" O MET M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL M 134 " --> pdb=" O GLY M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 166 Processing helix chain 'M' and resid 188 through 200 Processing helix chain '1' and resid 48 through 71 Processing helix chain '1' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL 1 90 " --> pdb=" O MET 1 86 " (cutoff:3.500A) Processing helix chain '1' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL 1 134 " --> pdb=" O GLY 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 166 Processing helix chain '1' and resid 188 through 200 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL N 134 " --> pdb=" O GLY N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 166 Processing helix chain 'N' and resid 188 through 200 Processing helix chain '2' and resid 48 through 71 Processing helix chain '2' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL 2 90 " --> pdb=" O MET 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 130 through 142 removed outlier: 3.834A pdb=" N VAL 2 134 " --> pdb=" O GLY 2 130 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 166 Processing helix chain '2' and resid 188 through 200 Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL H 90 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL H 134 " --> pdb=" O GLY H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 166 Processing helix chain 'H' and resid 188 through 200 Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL V 90 " --> pdb=" O MET V 86 " (cutoff:3.500A) Processing helix chain 'V' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL V 134 " --> pdb=" O GLY V 130 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 166 Processing helix chain 'V' and resid 188 through 200 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL I 90 " --> pdb=" O MET I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'I' and resid 188 through 200 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL W 90 " --> pdb=" O MET W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 142 removed outlier: 3.834A pdb=" N VAL W 134 " --> pdb=" O GLY W 130 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'W' and resid 188 through 200 Processing helix chain 'J' and resid 48 through 71 Processing helix chain 'J' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL J 90 " --> pdb=" O MET J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 142 removed outlier: 3.834A pdb=" N VAL J 134 " --> pdb=" O GLY J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 166 Processing helix chain 'J' and resid 188 through 200 Processing helix chain 'X' and resid 48 through 71 Processing helix chain 'X' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL X 90 " --> pdb=" O MET X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL X 134 " --> pdb=" O GLY X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 166 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'K' and resid 48 through 71 Processing helix chain 'K' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL K 90 " --> pdb=" O MET K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 166 Processing helix chain 'K' and resid 188 through 200 Processing helix chain 'Y' and resid 48 through 71 Processing helix chain 'Y' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL Y 90 " --> pdb=" O MET Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 142 removed outlier: 3.835A pdb=" N VAL Y 134 " --> pdb=" O GLY Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 166 Processing helix chain 'Y' and resid 188 through 200 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.023A pdb=" N VAL L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 142 removed outlier: 3.836A pdb=" N VAL L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 166 Processing helix chain 'L' and resid 188 through 200 Processing helix chain 'O' and resid 21 through 33 removed outlier: 3.624A pdb=" N LYS O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 64 removed outlier: 3.530A pdb=" N ILE O 64 " --> pdb=" O GLN O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 104 Processing helix chain 'O' and resid 108 through 123 removed outlier: 4.126A pdb=" N LEU O 112 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 180 removed outlier: 3.594A pdb=" N ARG O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 199 Processing helix chain 'O' and resid 225 through 231 Processing helix chain 'P' and resid 21 through 33 removed outlier: 3.653A pdb=" N LYS P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 64 removed outlier: 3.536A pdb=" N ILE P 64 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 104 Processing helix chain 'P' and resid 108 through 123 removed outlier: 4.212A pdb=" N LEU P 112 " --> pdb=" O ASN P 108 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 180 removed outlier: 3.590A pdb=" N ARG P 178 " --> pdb=" O SER P 174 " (cutoff:3.500A) Processing helix chain 'P' and resid 185 through 199 Processing helix chain 'P' and resid 225 through 231 Processing helix chain 'Q' and resid 21 through 33 removed outlier: 3.648A pdb=" N LYS Q 33 " --> pdb=" O GLU Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 64 removed outlier: 3.527A pdb=" N ILE Q 64 " --> pdb=" O GLN Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 104 Processing helix chain 'Q' and resid 108 through 123 removed outlier: 4.120A pdb=" N LEU Q 112 " --> pdb=" O ASN Q 108 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 180 removed outlier: 3.593A pdb=" N ARG Q 178 " --> pdb=" O SER Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 225 through 231 Processing helix chain 'R' and resid 21 through 33 removed outlier: 3.620A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.560A pdb=" N ILE R 64 " --> pdb=" O GLN R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 123 removed outlier: 4.116A pdb=" N LEU R 112 " --> pdb=" O ASN R 108 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 removed outlier: 3.600A pdb=" N ARG R 178 " --> pdb=" O SER R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 199 Processing helix chain 'R' and resid 225 through 231 Processing helix chain 'S' and resid 21 through 33 removed outlier: 3.636A pdb=" N LYS S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 64 removed outlier: 3.563A pdb=" N ILE S 64 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 123 removed outlier: 4.135A pdb=" N LEU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 180 removed outlier: 3.595A pdb=" N ARG S 178 " --> pdb=" O SER S 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 185 through 199 Processing helix chain 'S' and resid 225 through 231 Processing helix chain 'T' and resid 21 through 33 removed outlier: 3.628A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 64 removed outlier: 3.537A pdb=" N ILE T 64 " --> pdb=" O GLN T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 104 Processing helix chain 'T' and resid 108 through 123 removed outlier: 4.166A pdb=" N LEU T 112 " --> pdb=" O ASN T 108 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 removed outlier: 3.582A pdb=" N ARG T 178 " --> pdb=" O SER T 174 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 199 Processing helix chain 'T' and resid 225 through 231 Processing helix chain 'U' and resid 21 through 33 removed outlier: 3.622A pdb=" N LYS U 33 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.532A pdb=" N ILE U 64 " --> pdb=" O GLN U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 104 Processing helix chain 'U' and resid 108 through 123 removed outlier: 4.108A pdb=" N LEU U 112 " --> pdb=" O ASN U 108 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 180 removed outlier: 3.602A pdb=" N ARG U 178 " --> pdb=" O SER U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 199 Processing helix chain 'U' and resid 225 through 231 Processing helix chain 'a' and resid 5 through 16 Processing helix chain 'a' and resid 17 through 52 removed outlier: 4.145A pdb=" N THR a 32 " --> pdb=" O TRP a 28 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU a 33 " --> pdb=" O ALA a 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN a 34 " --> pdb=" O ALA a 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS a 62 " --> pdb=" O GLN a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE a 88 " --> pdb=" O GLN a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL a 109 " --> pdb=" O LEU a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 161 removed outlier: 3.818A pdb=" N VAL a 155 " --> pdb=" O ALA a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU a 180 " --> pdb=" O SER a 176 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS a 217 " --> pdb=" O LEU a 213 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS a 218 " --> pdb=" O LEU a 214 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 16 Processing helix chain 'b' and resid 17 through 52 removed outlier: 4.146A pdb=" N THR b 32 " --> pdb=" O TRP b 28 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU b 33 " --> pdb=" O ALA b 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN b 34 " --> pdb=" O ALA b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS b 62 " --> pdb=" O GLN b 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE b 88 " --> pdb=" O GLN b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL b 109 " --> pdb=" O LEU b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 161 removed outlier: 3.818A pdb=" N VAL b 155 " --> pdb=" O ALA b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU b 180 " --> pdb=" O SER b 176 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS b 218 " --> pdb=" O LEU b 214 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 16 Processing helix chain 'c' and resid 17 through 52 removed outlier: 4.146A pdb=" N THR c 32 " --> pdb=" O TRP c 28 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS c 62 " --> pdb=" O GLN c 59 " (cutoff:3.500A) Processing helix chain 'c' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE c 88 " --> pdb=" O GLN c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 123 removed outlier: 3.526A pdb=" N VAL c 109 " --> pdb=" O LEU c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 161 removed outlier: 3.817A pdb=" N VAL c 155 " --> pdb=" O ALA c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU c 180 " --> pdb=" O SER c 176 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS c 217 " --> pdb=" O LEU c 213 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS c 218 " --> pdb=" O LEU c 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 16 Processing helix chain 'd' and resid 17 through 52 removed outlier: 4.145A pdb=" N THR d 32 " --> pdb=" O TRP d 28 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN d 34 " --> pdb=" O ALA d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS d 62 " --> pdb=" O GLN d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE d 88 " --> pdb=" O GLN d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL d 109 " --> pdb=" O LEU d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 143 through 161 removed outlier: 3.817A pdb=" N VAL d 155 " --> pdb=" O ALA d 151 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU d 180 " --> pdb=" O SER d 176 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS d 217 " --> pdb=" O LEU d 213 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS d 218 " --> pdb=" O LEU d 214 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 16 Processing helix chain 'e' and resid 17 through 52 removed outlier: 4.145A pdb=" N THR e 32 " --> pdb=" O TRP e 28 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU e 33 " --> pdb=" O ALA e 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN e 34 " --> pdb=" O ALA e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS e 62 " --> pdb=" O GLN e 59 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE e 88 " --> pdb=" O GLN e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL e 109 " --> pdb=" O LEU e 105 " (cutoff:3.500A) Processing helix chain 'e' and resid 143 through 161 removed outlier: 3.817A pdb=" N VAL e 155 " --> pdb=" O ALA e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU e 180 " --> pdb=" O SER e 176 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS e 217 " --> pdb=" O LEU e 213 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS e 218 " --> pdb=" O LEU e 214 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 16 Processing helix chain 'f' and resid 17 through 52 removed outlier: 4.145A pdb=" N THR f 32 " --> pdb=" O TRP f 28 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU f 33 " --> pdb=" O ALA f 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN f 34 " --> pdb=" O ALA f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS f 62 " --> pdb=" O GLN f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE f 88 " --> pdb=" O GLN f 84 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL f 109 " --> pdb=" O LEU f 105 " (cutoff:3.500A) Processing helix chain 'f' and resid 143 through 161 removed outlier: 3.817A pdb=" N VAL f 155 " --> pdb=" O ALA f 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU f 180 " --> pdb=" O SER f 176 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS f 217 " --> pdb=" O LEU f 213 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS f 218 " --> pdb=" O LEU f 214 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 16 Processing helix chain 'g' and resid 17 through 52 removed outlier: 4.146A pdb=" N THR g 32 " --> pdb=" O TRP g 28 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 62 removed outlier: 3.856A pdb=" N LYS g 62 " --> pdb=" O GLN g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 64 through 94 removed outlier: 3.552A pdb=" N ILE g 88 " --> pdb=" O GLN g 84 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 123 removed outlier: 3.525A pdb=" N VAL g 109 " --> pdb=" O LEU g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 143 through 161 removed outlier: 3.818A pdb=" N VAL g 155 " --> pdb=" O ALA g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 176 through 221 removed outlier: 3.609A pdb=" N LEU g 180 " --> pdb=" O SER g 176 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS g 217 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS g 218 " --> pdb=" O LEU g 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 165 removed outlier: 3.620A pdb=" N GLY A 45 " --> pdb=" O PHE A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 71 removed outlier: 6.148A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 136 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN A 158 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.616A pdb=" N GLY B 45 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 71 removed outlier: 6.119A pdb=" N VAL B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 136 " --> pdb=" O CYS B 151 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 158 " --> pdb=" O ASP B 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.620A pdb=" N GLY C 45 " --> pdb=" O PHE C 42 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 71 removed outlier: 6.106A pdb=" N VAL C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 136 " --> pdb=" O CYS C 151 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 158 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 162 through 165 removed outlier: 3.611A pdb=" N GLY D 45 " --> pdb=" O PHE D 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 67 through 71 removed outlier: 6.095A pdb=" N VAL D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 136 " --> pdb=" O CYS D 151 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 158 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.606A pdb=" N GLY E 45 " --> pdb=" O PHE E 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.098A pdb=" N VAL E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 136 " --> pdb=" O CYS E 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN E 158 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 162 through 165 removed outlier: 3.611A pdb=" N GLY F 45 " --> pdb=" O PHE F 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 67 through 71 removed outlier: 6.084A pdb=" N VAL F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 136 " --> pdb=" O CYS F 151 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN F 158 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.615A pdb=" N GLY G 45 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.141A pdb=" N VAL G 74 " --> pdb=" O ILE G 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 136 " --> pdb=" O CYS G 151 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN G 158 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Z' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR Z 179 " --> pdb=" O GLY Z 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Z' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL Z 110 " --> pdb=" O ASP Z 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR M 179 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR M 41 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU M 100 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL M 110 " --> pdb=" O ASP M 122 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '1' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR 1 179 " --> pdb=" O GLY 1 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR 1 41 " --> pdb=" O ILE 1 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 1 100 " --> pdb=" O THR 1 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL 1 110 " --> pdb=" O ASP 1 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR N 179 " --> pdb=" O GLY N 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU N 100 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL N 110 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR 2 179 " --> pdb=" O GLY 2 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '2' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR 2 41 " --> pdb=" O ILE 2 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU 2 100 " --> pdb=" O THR 2 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL 2 110 " --> pdb=" O ASP 2 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR H 179 " --> pdb=" O GLY H 183 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU H 100 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL H 110 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR V 179 " --> pdb=" O GLY V 183 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU V 100 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL V 110 " --> pdb=" O ASP V 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR I 179 " --> pdb=" O GLY I 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU I 100 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL I 110 " --> pdb=" O ASP I 122 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'W' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR W 179 " --> pdb=" O GLY W 183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU W 100 " --> pdb=" O THR W 44 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL W 110 " --> pdb=" O ASP W 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR J 179 " --> pdb=" O GLY J 183 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU J 100 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL J 110 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 124 through 125 removed outlier: 3.633A pdb=" N THR X 179 " --> pdb=" O GLY X 183 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU X 100 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL X 110 " --> pdb=" O ASP X 122 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.631A pdb=" N THR K 179 " --> pdb=" O GLY K 183 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU K 100 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL K 110 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Y' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR Y 179 " --> pdb=" O GLY Y 183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y' and resid 35 through 38 removed outlier: 6.627A pdb=" N THR Y 41 " --> pdb=" O ILE Y 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU Y 100 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL Y 110 " --> pdb=" O ASP Y 122 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 124 through 125 removed outlier: 3.632A pdb=" N THR L 179 " --> pdb=" O GLY L 183 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 35 through 38 removed outlier: 6.628A pdb=" N THR L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL L 110 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 162 through 165 Processing sheet with id=AE8, first strand: chain 'O' and resid 67 through 69 removed outlier: 3.547A pdb=" N ASN O 158 " --> pdb=" O ASP O 150 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 162 through 165 Processing sheet with id=AF1, first strand: chain 'P' and resid 67 through 69 removed outlier: 3.513A pdb=" N ASN P 158 " --> pdb=" O ASP P 150 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 162 through 165 Processing sheet with id=AF3, first strand: chain 'Q' and resid 67 through 69 removed outlier: 3.531A pdb=" N ASN Q 158 " --> pdb=" O ASP Q 150 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'R' and resid 67 through 69 removed outlier: 3.515A pdb=" N ASN R 158 " --> pdb=" O ASP R 150 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 162 through 165 Processing sheet with id=AF7, first strand: chain 'S' and resid 67 through 69 removed outlier: 3.534A pdb=" N ASN S 158 " --> pdb=" O ASP S 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 162 through 165 Processing sheet with id=AF9, first strand: chain 'T' and resid 67 through 69 removed outlier: 3.518A pdb=" N ASN T 158 " --> pdb=" O ASP T 150 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AG2, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.542A pdb=" N ASN U 158 " --> pdb=" O ASP U 150 " (cutoff:3.500A) 3577 hydrogen bonds defined for protein. 10353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.05 Time building geometry restraints manager: 19.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10726 1.32 - 1.44: 13549 1.44 - 1.56: 34448 1.56 - 1.68: 7 1.68 - 1.80: 434 Bond restraints: 59164 Sorted by residual: bond pdb=" CA TYR g 16 " pdb=" CB TYR g 16 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 1.00e+01 bond pdb=" CA TYR d 16 " pdb=" CB TYR d 16 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 9.89e+00 bond pdb=" CA TYR f 16 " pdb=" CB TYR f 16 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 9.89e+00 bond pdb=" CA TYR a 16 " pdb=" CB TYR a 16 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 9.89e+00 bond pdb=" CA TYR e 16 " pdb=" CB TYR e 16 " ideal model delta sigma weight residual 1.526 1.478 0.048 1.53e-02 4.27e+03 9.88e+00 ... (remaining 59159 not shown) Histogram of bond angle deviations from ideal: 95.23 - 103.97: 662 103.97 - 112.71: 31518 112.71 - 121.45: 33515 121.45 - 130.18: 14069 130.18 - 138.92: 141 Bond angle restraints: 79905 Sorted by residual: angle pdb=" C THR M 21 " pdb=" N MET M 22 " pdb=" CA MET M 22 " ideal model delta sigma weight residual 121.70 138.92 -17.22 1.80e+00 3.09e-01 9.16e+01 angle pdb=" C THR N 21 " pdb=" N MET N 22 " pdb=" CA MET N 22 " ideal model delta sigma weight residual 121.70 138.91 -17.21 1.80e+00 3.09e-01 9.15e+01 angle pdb=" C THR V 21 " pdb=" N MET V 22 " pdb=" CA MET V 22 " ideal model delta sigma weight residual 121.70 138.91 -17.21 1.80e+00 3.09e-01 9.14e+01 angle pdb=" C THR Y 21 " pdb=" N MET Y 22 " pdb=" CA MET Y 22 " ideal model delta sigma weight residual 121.70 138.90 -17.20 1.80e+00 3.09e-01 9.13e+01 angle pdb=" C THR I 21 " pdb=" N MET I 22 " pdb=" CA MET I 22 " ideal model delta sigma weight residual 121.70 138.89 -17.19 1.80e+00 3.09e-01 9.13e+01 ... (remaining 79900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.72: 34493 15.72 - 31.45: 1149 31.45 - 47.17: 387 47.17 - 62.90: 63 62.90 - 78.62: 70 Dihedral angle restraints: 36162 sinusoidal: 14399 harmonic: 21763 Sorted by residual: dihedral pdb=" CA TYR E 8 " pdb=" C TYR E 8 " pdb=" N ASP E 9 " pdb=" CA ASP E 9 " ideal model delta harmonic sigma weight residual -180.00 -111.96 -68.04 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA TYR D 8 " pdb=" C TYR D 8 " pdb=" N ASP D 9 " pdb=" CA ASP D 9 " ideal model delta harmonic sigma weight residual -180.00 -112.02 -67.98 0 5.00e+00 4.00e-02 1.85e+02 dihedral pdb=" CA TYR C 8 " pdb=" C TYR C 8 " pdb=" N ASP C 9 " pdb=" CA ASP C 9 " ideal model delta harmonic sigma weight residual 180.00 -112.19 -67.81 0 5.00e+00 4.00e-02 1.84e+02 ... (remaining 36159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 7412 0.070 - 0.139: 1528 0.139 - 0.209: 317 0.209 - 0.278: 61 0.278 - 0.347: 27 Chirality restraints: 9345 Sorted by residual: chirality pdb=" CB VAL T 74 " pdb=" CA VAL T 74 " pdb=" CG1 VAL T 74 " pdb=" CG2 VAL T 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CB VAL P 74 " pdb=" CA VAL P 74 " pdb=" CG1 VAL P 74 " pdb=" CG2 VAL P 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL Q 74 " pdb=" CA VAL Q 74 " pdb=" CG1 VAL Q 74 " pdb=" CG2 VAL Q 74 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 9342 not shown) Planarity restraints: 10262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE I 25 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.20e+01 pdb=" C PHE I 25 " 0.060 2.00e-02 2.50e+03 pdb=" O PHE I 25 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE I 26 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 25 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C PHE L 25 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE L 25 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE L 26 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 25 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C PHE K 25 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE K 25 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE K 26 " 0.021 2.00e-02 2.50e+03 ... (remaining 10259 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5708 2.74 - 3.28: 56823 3.28 - 3.82: 99211 3.82 - 4.36: 115525 4.36 - 4.90: 199611 Nonbonded interactions: 476878 Sorted by model distance: nonbonded pdb=" OG1 THR 2 21 " pdb=" O GLU 2 23 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR L 21 " pdb=" O GLU L 23 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR Z 21 " pdb=" O GLU Z 23 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR K 21 " pdb=" O GLU K 23 " model vdw 2.199 2.440 nonbonded pdb=" OG1 THR J 21 " pdb=" O GLU J 23 " model vdw 2.199 2.440 ... (remaining 476873 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 '1' selection = chain '2' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = (chain 'A' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'B' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'C' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'D' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'E' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'F' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'G' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'O' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'P' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'Q' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'R' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'S' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'T' and (resid 7 through 65 or resid 67 through 233)) selection = (chain 'U' and (resid 7 through 65 or resid 67 through 233)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.840 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 120.420 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5770 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 : 0.008 0.107 59164 Z= 0.530 Angle : 1.190 17.224 79905 Z= 0.698 Chirality : 0.063 0.347 9345 Planarity : 0.007 0.062 10262 Dihedral : 10.446 78.621 22246 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.38 % Favored : 95.34 % Rotamer: Outliers : 0.67 % Allowed : 5.78 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.67 % 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: -2.57 (0.08), residues: 7469 helix: -0.92 (0.07), residues: 3416 sheet: -1.74 (0.12), residues: 1351 loop : -2.57 (0.10), residues: 2702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP e 28 HIS 0.010 0.004 HIS N 28 PHE 0.027 0.004 PHE C 42 TYR 0.029 0.004 TYR C 224 ARG 0.012 0.001 ARG 2 70 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1343 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.5997 (tt) cc_final: 0.5574 (tt) REVERT: A 144 ILE cc_start: 0.7706 (mm) cc_final: 0.7404 (mt) REVERT: A 220 LYS cc_start: 0.8003 (mttt) cc_final: 0.7772 (mttm) REVERT: B 109 ILE cc_start: 0.6479 (tt) cc_final: 0.6150 (tt) REVERT: B 215 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7334 (tt) REVERT: C 84 ASP cc_start: 0.6738 (m-30) cc_final: 0.6399 (m-30) REVERT: C 105 SER cc_start: 0.7990 (p) cc_final: 0.7300 (t) REVERT: C 141 ILE cc_start: 0.6978 (pp) cc_final: 0.6743 (pp) REVERT: C 220 LYS cc_start: 0.8266 (mttt) cc_final: 0.7828 (mtpt) REVERT: D 109 ILE cc_start: 0.6215 (tt) cc_final: 0.5924 (tt) REVERT: D 220 LYS cc_start: 0.8095 (mttt) cc_final: 0.7656 (mtpp) REVERT: E 161 LYS cc_start: 0.5628 (mttm) cc_final: 0.5402 (mtmt) REVERT: E 220 LYS cc_start: 0.7928 (mttt) cc_final: 0.7703 (mttm) REVERT: F 161 LYS cc_start: 0.5781 (mttm) cc_final: 0.5409 (mtmm) REVERT: F 220 LYS cc_start: 0.7954 (mttt) cc_final: 0.7540 (mtpt) REVERT: G 32 LYS cc_start: 0.6375 (mttt) cc_final: 0.6169 (mtpp) REVERT: G 109 ILE cc_start: 0.6216 (tt) cc_final: 0.5877 (tt) REVERT: G 215 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7259 (tt) REVERT: G 220 LYS cc_start: 0.7915 (mttt) cc_final: 0.7546 (mtpp) REVERT: Z 14 MET cc_start: 0.7960 (mtm) cc_final: 0.7678 (mtm) REVERT: Z 62 GLU cc_start: 0.5916 (tp30) cc_final: 0.5701 (mt-10) REVERT: Z 129 SER cc_start: 0.7743 (m) cc_final: 0.7492 (m) REVERT: Z 145 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7985 (mttp) REVERT: Z 180 ARG cc_start: 0.8055 (tpt170) cc_final: 0.7644 (tpt170) REVERT: M 23 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.4458 (mp0) REVERT: M 32 LYS cc_start: 0.8047 (tttp) cc_final: 0.7784 (tttm) REVERT: M 129 SER cc_start: 0.7709 (m) cc_final: 0.7474 (p) REVERT: M 181 LYS cc_start: 0.8000 (tttm) cc_final: 0.7540 (mtmm) REVERT: 1 32 LYS cc_start: 0.7896 (tttp) cc_final: 0.7416 (tttp) REVERT: 1 43 MET cc_start: 0.7874 (ttm) cc_final: 0.7620 (ttt) REVERT: 1 145 LYS cc_start: 0.8424 (mmtm) cc_final: 0.7979 (mttt) REVERT: 1 146 MET cc_start: 0.8332 (mtt) cc_final: 0.7868 (mtp) REVERT: 1 172 MET cc_start: 0.7777 (tpt) cc_final: 0.7481 (tpp) REVERT: N 23 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.3829 (mp0) REVERT: N 43 MET cc_start: 0.7874 (ttm) cc_final: 0.7613 (ttt) REVERT: N 129 SER cc_start: 0.7956 (m) cc_final: 0.7639 (p) REVERT: N 167 SER cc_start: 0.7594 (p) cc_final: 0.7317 (m) REVERT: N 181 LYS cc_start: 0.7879 (tttm) cc_final: 0.7317 (mtmm) REVERT: 2 23 GLU cc_start: 0.4690 (OUTLIER) cc_final: 0.4163 (mp0) REVERT: 2 43 MET cc_start: 0.7727 (ttm) cc_final: 0.7431 (ttp) REVERT: 2 129 SER cc_start: 0.7504 (m) cc_final: 0.7290 (m) REVERT: 2 145 LYS cc_start: 0.8419 (mmtm) cc_final: 0.8036 (mttp) REVERT: 2 167 SER cc_start: 0.7691 (p) cc_final: 0.7391 (p) REVERT: 2 172 MET cc_start: 0.7828 (tpt) cc_final: 0.7491 (tpt) REVERT: H 23 GLU cc_start: 0.4211 (OUTLIER) cc_final: 0.3330 (mp0) REVERT: H 129 SER cc_start: 0.7568 (m) cc_final: 0.7184 (p) REVERT: H 172 MET cc_start: 0.7710 (tpt) cc_final: 0.7482 (tpt) REVERT: H 181 LYS cc_start: 0.7462 (tttm) cc_final: 0.7172 (tttm) REVERT: V 9 LYS cc_start: 0.7741 (mttt) cc_final: 0.7368 (tptp) REVERT: V 23 GLU cc_start: 0.5118 (OUTLIER) cc_final: 0.4429 (mp0) REVERT: V 27 MET cc_start: 0.6894 (ttt) cc_final: 0.6571 (ttt) REVERT: V 43 MET cc_start: 0.7785 (ttm) cc_final: 0.7262 (ttm) REVERT: V 129 SER cc_start: 0.7723 (m) cc_final: 0.7514 (m) REVERT: V 141 GLN cc_start: 0.7938 (mt0) cc_final: 0.7639 (mt0) REVERT: V 145 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7800 (mttp) REVERT: I 14 MET cc_start: 0.7536 (mtm) cc_final: 0.6944 (mtm) REVERT: I 23 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.4287 (mp0) REVERT: I 27 MET cc_start: 0.6465 (ttt) cc_final: 0.6140 (ttt) REVERT: I 43 MET cc_start: 0.7772 (ttm) cc_final: 0.7485 (ttt) REVERT: I 84 SER cc_start: 0.6779 (m) cc_final: 0.6382 (t) REVERT: I 98 GLN cc_start: 0.7956 (mt0) cc_final: 0.7298 (mt0) REVERT: I 180 ARG cc_start: 0.7967 (tpt170) cc_final: 0.7433 (tpp-160) REVERT: W 23 GLU cc_start: 0.5269 (OUTLIER) cc_final: 0.4387 (mp0) REVERT: W 32 LYS cc_start: 0.8082 (tttp) cc_final: 0.7792 (tttm) REVERT: W 43 MET cc_start: 0.7819 (ttm) cc_final: 0.7333 (ttm) REVERT: W 141 GLN cc_start: 0.7524 (mt0) cc_final: 0.7312 (mt0) REVERT: W 145 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8003 (mttp) REVERT: J 23 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.3819 (mp0) REVERT: J 43 MET cc_start: 0.7675 (ttm) cc_final: 0.7444 (ttt) REVERT: J 62 GLU cc_start: 0.6248 (tp30) cc_final: 0.5973 (tp30) REVERT: J 141 GLN cc_start: 0.7789 (mt0) cc_final: 0.7449 (mt0) REVERT: J 181 LYS cc_start: 0.7546 (tttm) cc_final: 0.7146 (tmtt) REVERT: J 182 ASP cc_start: 0.6782 (m-30) cc_final: 0.6320 (m-30) REVERT: X 23 GLU cc_start: 0.5264 (OUTLIER) cc_final: 0.4836 (mp0) REVERT: X 32 LYS cc_start: 0.7989 (tttp) cc_final: 0.7673 (tttp) REVERT: X 40 TYR cc_start: 0.7155 (m-80) cc_final: 0.6861 (m-80) REVERT: X 43 MET cc_start: 0.7723 (ttm) cc_final: 0.7354 (ttm) REVERT: X 145 LYS cc_start: 0.8290 (mmtm) cc_final: 0.8060 (mtmm) REVERT: X 167 SER cc_start: 0.7658 (p) cc_final: 0.7411 (p) REVERT: X 180 ARG cc_start: 0.7969 (tpt170) cc_final: 0.7241 (tpt170) REVERT: K 9 LYS cc_start: 0.8285 (mttt) cc_final: 0.7813 (tptm) REVERT: K 10 ASP cc_start: 0.6379 (m-30) cc_final: 0.6009 (m-30) REVERT: K 23 GLU cc_start: 0.4142 (OUTLIER) cc_final: 0.3468 (mp0) REVERT: K 27 MET cc_start: 0.6827 (ttt) cc_final: 0.6015 (ttt) REVERT: K 43 MET cc_start: 0.7836 (ttm) cc_final: 0.7620 (ttt) REVERT: K 141 GLN cc_start: 0.7740 (mt0) cc_final: 0.7446 (mt0) REVERT: Y 32 LYS cc_start: 0.8397 (tttp) cc_final: 0.8114 (tttm) REVERT: Y 43 MET cc_start: 0.7930 (ttm) cc_final: 0.7639 (ttt) REVERT: Y 62 GLU cc_start: 0.6482 (tp30) cc_final: 0.6267 (mt-10) REVERT: Y 66 TYR cc_start: 0.6361 (t80) cc_final: 0.6109 (t80) REVERT: Y 145 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8008 (mttp) REVERT: Y 146 MET cc_start: 0.8275 (mtt) cc_final: 0.8027 (mtp) REVERT: Y 164 GLN cc_start: 0.6308 (mm-40) cc_final: 0.5971 (mt0) REVERT: L 23 GLU cc_start: 0.4419 (OUTLIER) cc_final: 0.3692 (mp0) REVERT: L 27 MET cc_start: 0.6843 (ttt) cc_final: 0.6566 (ttt) REVERT: L 129 SER cc_start: 0.7970 (m) cc_final: 0.7619 (p) REVERT: L 141 GLN cc_start: 0.8166 (mt0) cc_final: 0.7963 (mt0) REVERT: L 181 LYS cc_start: 0.7854 (tttm) cc_final: 0.7610 (tmtt) REVERT: O 20 ARG cc_start: 0.6632 (mtp180) cc_final: 0.6191 (mtp-110) REVERT: O 29 GLU cc_start: 0.5505 (mm-30) cc_final: 0.5236 (mt-10) REVERT: O 220 LYS cc_start: 0.7885 (mttt) cc_final: 0.7592 (mttm) REVERT: P 122 GLN cc_start: 0.7079 (tt0) cc_final: 0.6823 (tt0) REVERT: P 220 LYS cc_start: 0.7996 (mttt) cc_final: 0.7642 (mttm) REVERT: Q 159 GLU cc_start: 0.7036 (tt0) cc_final: 0.6833 (tt0) REVERT: Q 177 GLU cc_start: 0.6614 (tp30) cc_final: 0.6413 (tp30) REVERT: R 122 GLN cc_start: 0.7140 (tt0) cc_final: 0.6891 (tt0) REVERT: R 177 GLU cc_start: 0.6550 (tp30) cc_final: 0.5853 (tp30) REVERT: R 220 LYS cc_start: 0.7772 (mttt) cc_final: 0.7329 (mttm) REVERT: R 222 ARG cc_start: 0.7511 (ppt-90) cc_final: 0.7212 (ptt90) REVERT: S 40 MET cc_start: 0.7000 (pmt) cc_final: 0.6792 (ptp) REVERT: S 179 GLU cc_start: 0.7138 (tp30) cc_final: 0.6911 (tp30) REVERT: T 40 MET cc_start: 0.7085 (pmt) cc_final: 0.6719 (ptp) REVERT: T 122 GLN cc_start: 0.7041 (tt0) cc_final: 0.6712 (tt0) REVERT: T 177 GLU cc_start: 0.6408 (tp30) cc_final: 0.5470 (tp30) REVERT: T 220 LYS cc_start: 0.7804 (mttt) cc_final: 0.7343 (mttm) REVERT: U 177 GLU cc_start: 0.6189 (tp30) cc_final: 0.5435 (tp30) REVERT: a 27 GLU cc_start: 0.6033 (tp30) cc_final: 0.5752 (tt0) REVERT: a 39 ILE cc_start: 0.5978 (mt) cc_final: 0.5706 (mt) REVERT: a 101 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6540 (mm-30) REVERT: b 101 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6577 (mm-30) REVERT: b 142 MET cc_start: 0.7692 (mmm) cc_final: 0.7475 (mpp) REVERT: c 27 GLU cc_start: 0.6241 (tp30) cc_final: 0.5923 (tp30) REVERT: c 101 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6934 (mm-30) REVERT: c 103 ASP cc_start: 0.6621 (t70) cc_final: 0.6290 (t70) REVERT: d 39 ILE cc_start: 0.5988 (mt) cc_final: 0.5772 (mt) REVERT: d 101 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7425 (mm-30) REVERT: e 101 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7308 (mm-30) REVERT: f 39 ILE cc_start: 0.5800 (mt) cc_final: 0.5495 (mt) REVERT: f 101 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6774 (mm-30) REVERT: g 41 LYS cc_start: 0.6359 (mmtt) cc_final: 0.6112 (mtmm) REVERT: g 101 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6842 (mm-30) REVERT: g 232 ARG cc_start: 0.5917 (ttp-170) cc_final: 0.5578 (ttp-170) outliers start: 42 outliers final: 19 residues processed: 1377 average time/residue: 0.6047 time to fit residues: 1343.5139 Evaluate side-chains 956 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 924 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain Z residue 23 GLU Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 23 GLU Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 23 GLU Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 23 GLU Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain X residue 23 GLU Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain Y residue 23 GLU Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 178 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 620 optimal weight: 2.9990 chunk 557 optimal weight: 0.8980 chunk 309 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 375 optimal weight: 0.8980 chunk 297 optimal weight: 1.9990 chunk 576 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 350 optimal weight: 4.9990 chunk 428 optimal weight: 2.9990 chunk 667 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN C 23 GLN C 119 GLN D 23 GLN E 23 GLN F 23 GLN G 23 GLN G 98 GLN Z 69 GLN 1 141 GLN N 141 GLN N 164 GLN H 141 GLN V 88 ASN I 30 ASN W 88 ASN J 141 GLN X 141 GLN K 141 GLN K 164 GLN Y 88 ASN L 141 GLN O 68 GLN O 98 GLN O 219 ASN P 68 GLN P 219 ASN Q 68 GLN Q 219 ASN R 68 GLN R 125 GLN R 219 ASN S 68 GLN S 219 ASN T 68 GLN T 219 ASN U 68 GLN U 219 ASN a 72 GLN a 111 HIS ** a 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 200 HIS b 72 GLN b 99 HIS b 111 HIS ** b 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 72 GLN c 111 HIS d 111 HIS ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 200 HIS e 111 HIS ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 200 HIS f 111 HIS ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 200 HIS Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 59164 Z= 0.222 Angle : 0.639 12.415 79905 Z= 0.350 Chirality : 0.043 0.206 9345 Planarity : 0.004 0.057 10262 Dihedral : 6.995 59.932 8372 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.73 % Rotamer: Outliers : 2.78 % Allowed : 10.04 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.87 (0.09), residues: 7469 helix: 0.96 (0.08), residues: 3437 sheet: -1.29 (0.12), residues: 1407 loop : -2.22 (0.10), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 28 HIS 0.006 0.002 HIS 1 28 PHE 0.015 0.002 PHE D 42 TYR 0.030 0.002 TYR E 8 ARG 0.007 0.001 ARG 1 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1012 time to evaluate : 5.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 SER cc_start: 0.5926 (p) cc_final: 0.5724 (t) REVERT: A 160 TYR cc_start: 0.7034 (m-80) cc_final: 0.6672 (m-80) REVERT: B 35 SER cc_start: 0.5599 (p) cc_final: 0.5359 (t) REVERT: B 72 ASP cc_start: 0.7518 (m-30) cc_final: 0.7212 (t0) REVERT: B 98 GLN cc_start: 0.5414 (mm-40) cc_final: 0.4781 (mt0) REVERT: B 122 GLN cc_start: 0.6540 (mt0) cc_final: 0.6135 (tt0) REVERT: B 167 SER cc_start: 0.7372 (t) cc_final: 0.7139 (p) REVERT: B 182 GLU cc_start: 0.6102 (mp0) cc_final: 0.5296 (tt0) REVERT: C 98 GLN cc_start: 0.5779 (mm-40) cc_final: 0.5243 (tt0) REVERT: C 220 LYS cc_start: 0.8119 (mttt) cc_final: 0.7685 (mtpp) REVERT: D 98 GLN cc_start: 0.5895 (mm-40) cc_final: 0.5355 (mt0) REVERT: D 182 GLU cc_start: 0.6090 (mp0) cc_final: 0.5633 (tt0) REVERT: D 220 LYS cc_start: 0.8082 (mttt) cc_final: 0.7650 (mtpp) REVERT: E 35 SER cc_start: 0.6246 (p) cc_final: 0.6022 (t) REVERT: E 98 GLN cc_start: 0.6271 (mm-40) cc_final: 0.5861 (mt0) REVERT: F 40 MET cc_start: 0.7161 (ptp) cc_final: 0.6737 (ptp) REVERT: F 98 GLN cc_start: 0.5859 (mm-40) cc_final: 0.5316 (mt0) REVERT: F 182 GLU cc_start: 0.6056 (mp0) cc_final: 0.5386 (tt0) REVERT: F 220 LYS cc_start: 0.7962 (mttt) cc_final: 0.7615 (mtpp) REVERT: G 98 GLN cc_start: 0.5962 (mm-40) cc_final: 0.5517 (mt0) REVERT: G 199 SER cc_start: 0.6587 (p) cc_final: 0.6361 (p) REVERT: G 220 LYS cc_start: 0.8024 (mttt) cc_final: 0.7578 (mtpp) REVERT: Z 62 GLU cc_start: 0.6328 (tp30) cc_final: 0.6066 (mt-10) REVERT: Z 129 SER cc_start: 0.7821 (m) cc_final: 0.7605 (m) REVERT: Z 145 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7999 (mttp) REVERT: Z 164 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6193 (mm-40) REVERT: Z 172 MET cc_start: 0.7861 (tpt) cc_final: 0.7397 (tpp) REVERT: M 9 LYS cc_start: 0.8403 (mttt) cc_final: 0.8034 (tptp) REVERT: M 59 MET cc_start: 0.6390 (mmm) cc_final: 0.6182 (mmt) REVERT: M 62 GLU cc_start: 0.6030 (tp30) cc_final: 0.5793 (tp30) REVERT: M 71 ARG cc_start: 0.6513 (mtm-85) cc_final: 0.6281 (mtm-85) REVERT: M 98 GLN cc_start: 0.7870 (mt0) cc_final: 0.7519 (mt0) REVERT: M 129 SER cc_start: 0.7856 (m) cc_final: 0.7481 (p) REVERT: M 181 LYS cc_start: 0.8044 (tttm) cc_final: 0.7644 (mtmm) REVERT: 1 27 MET cc_start: 0.7528 (ttt) cc_final: 0.7287 (ttt) REVERT: 1 32 LYS cc_start: 0.8127 (tttp) cc_final: 0.7857 (tttp) REVERT: 1 74 MET cc_start: 0.7986 (ttp) cc_final: 0.7600 (ttm) REVERT: 1 145 LYS cc_start: 0.8324 (mmtm) cc_final: 0.7994 (mttt) REVERT: 1 172 MET cc_start: 0.8003 (tpt) cc_final: 0.7719 (tpp) REVERT: N 9 LYS cc_start: 0.8017 (mttt) cc_final: 0.7755 (pttp) REVERT: N 59 MET cc_start: 0.6516 (mmm) cc_final: 0.6286 (tpp) REVERT: N 98 GLN cc_start: 0.8094 (mt0) cc_final: 0.7707 (mt0) REVERT: N 129 SER cc_start: 0.7906 (m) cc_final: 0.7520 (p) REVERT: N 164 GLN cc_start: 0.6276 (mm-40) cc_final: 0.6011 (mp10) REVERT: N 181 LYS cc_start: 0.7841 (tttm) cc_final: 0.7259 (mtmm) REVERT: 2 21 THR cc_start: 0.5029 (OUTLIER) cc_final: 0.4774 (t) REVERT: 2 129 SER cc_start: 0.7768 (m) cc_final: 0.7554 (m) REVERT: 2 172 MET cc_start: 0.7875 (tpt) cc_final: 0.7519 (tpp) REVERT: H 62 GLU cc_start: 0.6246 (tp30) cc_final: 0.6044 (tp30) REVERT: H 71 ARG cc_start: 0.6576 (mtm-85) cc_final: 0.6271 (mtm-85) REVERT: H 129 SER cc_start: 0.8346 (m) cc_final: 0.7915 (p) REVERT: H 180 ARG cc_start: 0.8348 (tpt170) cc_final: 0.8089 (tpp-160) REVERT: V 9 LYS cc_start: 0.7935 (mttt) cc_final: 0.7359 (tptp) REVERT: V 27 MET cc_start: 0.7792 (ttt) cc_final: 0.7449 (ttt) REVERT: V 43 MET cc_start: 0.7872 (ttm) cc_final: 0.7641 (ttm) REVERT: V 141 GLN cc_start: 0.7660 (mt0) cc_final: 0.7447 (mt0) REVERT: V 145 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7926 (mttp) REVERT: V 164 GLN cc_start: 0.6766 (mm-40) cc_final: 0.6377 (mt0) REVERT: I 14 MET cc_start: 0.7291 (mtm) cc_final: 0.6610 (mtt) REVERT: I 27 MET cc_start: 0.7799 (ttt) cc_final: 0.7446 (ttt) REVERT: I 43 MET cc_start: 0.7989 (ttm) cc_final: 0.7786 (ttm) REVERT: I 84 SER cc_start: 0.7125 (m) cc_final: 0.6807 (t) REVERT: I 98 GLN cc_start: 0.8015 (mt0) cc_final: 0.7609 (mt0) REVERT: I 164 GLN cc_start: 0.6607 (mm-40) cc_final: 0.6155 (mm110) REVERT: I 180 ARG cc_start: 0.8021 (tpt170) cc_final: 0.7775 (tpp-160) REVERT: W 32 LYS cc_start: 0.7949 (tttp) cc_final: 0.7706 (tttm) REVERT: W 43 MET cc_start: 0.7892 (ttm) cc_final: 0.7556 (ttp) REVERT: W 59 MET cc_start: 0.6925 (mmm) cc_final: 0.6716 (mmm) REVERT: W 145 LYS cc_start: 0.8522 (mmtm) cc_final: 0.8101 (mttp) REVERT: W 164 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6494 (mt0) REVERT: J 27 MET cc_start: 0.7655 (ttt) cc_final: 0.7285 (ttt) REVERT: J 43 MET cc_start: 0.8036 (ttm) cc_final: 0.7756 (ttp) REVERT: J 98 GLN cc_start: 0.8022 (mt0) cc_final: 0.7405 (mt0) REVERT: J 180 ARG cc_start: 0.8500 (tpt170) cc_final: 0.8260 (tpp-160) REVERT: J 181 LYS cc_start: 0.8114 (tttm) cc_final: 0.7500 (mtmm) REVERT: J 182 ASP cc_start: 0.6701 (m-30) cc_final: 0.6411 (m-30) REVERT: X 40 TYR cc_start: 0.7529 (m-80) cc_final: 0.6950 (m-80) REVERT: X 145 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8062 (mtmm) REVERT: X 180 ARG cc_start: 0.8163 (tpt170) cc_final: 0.7603 (tpt170) REVERT: K 9 LYS cc_start: 0.8029 (mttt) cc_final: 0.7625 (tptp) REVERT: K 22 MET cc_start: 0.4581 (ttt) cc_final: 0.4348 (ttt) REVERT: K 27 MET cc_start: 0.7119 (ttt) cc_final: 0.6857 (ttt) REVERT: K 43 MET cc_start: 0.7968 (ttm) cc_final: 0.7756 (ttp) REVERT: K 141 GLN cc_start: 0.7702 (mt0) cc_final: 0.7438 (mt0) REVERT: K 180 ARG cc_start: 0.8460 (tpt170) cc_final: 0.7876 (tpt170) REVERT: K 181 LYS cc_start: 0.7713 (tttm) cc_final: 0.7392 (tttm) REVERT: K 182 ASP cc_start: 0.6439 (m-30) cc_final: 0.6140 (m-30) REVERT: Y 32 LYS cc_start: 0.8435 (tttp) cc_final: 0.8162 (tttm) REVERT: Y 38 ASP cc_start: 0.7230 (t0) cc_final: 0.7009 (t0) REVERT: Y 62 GLU cc_start: 0.6546 (tp30) cc_final: 0.6115 (mt-10) REVERT: Y 64 GLU cc_start: 0.6767 (tt0) cc_final: 0.5959 (tt0) REVERT: Y 145 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8083 (mttp) REVERT: L 9 LYS cc_start: 0.8040 (mttt) cc_final: 0.7813 (tptm) REVERT: L 21 THR cc_start: 0.4638 (OUTLIER) cc_final: 0.4348 (t) REVERT: L 62 GLU cc_start: 0.6075 (tp30) cc_final: 0.5821 (tp30) REVERT: L 71 ARG cc_start: 0.6736 (ttm110) cc_final: 0.6442 (mtm-85) REVERT: L 181 LYS cc_start: 0.8066 (tttm) cc_final: 0.7739 (tmtt) REVERT: O 20 ARG cc_start: 0.7172 (mtp180) cc_final: 0.6890 (mtp-110) REVERT: O 29 GLU cc_start: 0.5677 (mm-30) cc_final: 0.5419 (mt-10) REVERT: O 60 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7079 (mm-30) REVERT: O 122 GLN cc_start: 0.7703 (tt0) cc_final: 0.7415 (tt0) REVERT: O 182 GLU cc_start: 0.7558 (pm20) cc_final: 0.6677 (pt0) REVERT: P 20 ARG cc_start: 0.7126 (mtp180) cc_final: 0.6888 (mtp85) REVERT: P 40 MET cc_start: 0.7403 (ptp) cc_final: 0.6848 (ptp) REVERT: P 65 GLU cc_start: 0.6210 (mt-10) cc_final: 0.5639 (pt0) REVERT: P 122 GLN cc_start: 0.7612 (tt0) cc_final: 0.7257 (tt0) REVERT: P 182 GLU cc_start: 0.7615 (pm20) cc_final: 0.7363 (pm20) REVERT: P 220 LYS cc_start: 0.7885 (mttt) cc_final: 0.7560 (mttm) REVERT: Q 122 GLN cc_start: 0.7635 (tt0) cc_final: 0.7279 (tt0) REVERT: Q 177 GLU cc_start: 0.6280 (tp30) cc_final: 0.5692 (tp30) REVERT: Q 179 GLU cc_start: 0.7402 (tp30) cc_final: 0.6886 (tp30) REVERT: R 20 ARG cc_start: 0.6973 (mtp180) cc_final: 0.6675 (mtp85) REVERT: R 60 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6888 (mm-30) REVERT: R 122 GLN cc_start: 0.7787 (tt0) cc_final: 0.7455 (tt0) REVERT: R 177 GLU cc_start: 0.6240 (tp30) cc_final: 0.5774 (tp30) REVERT: R 182 GLU cc_start: 0.7213 (pm20) cc_final: 0.6655 (pt0) REVERT: S 179 GLU cc_start: 0.7365 (tp30) cc_final: 0.7129 (tp30) REVERT: T 65 GLU cc_start: 0.6075 (mt-10) cc_final: 0.5283 (pt0) REVERT: T 122 GLN cc_start: 0.7647 (tt0) cc_final: 0.7196 (tt0) REVERT: T 177 GLU cc_start: 0.6197 (tp30) cc_final: 0.5692 (tp30) REVERT: T 220 LYS cc_start: 0.7722 (mttt) cc_final: 0.7198 (mtpm) REVERT: U 40 MET cc_start: 0.7565 (ptp) cc_final: 0.7075 (ptp) REVERT: a 27 GLU cc_start: 0.6098 (tp30) cc_final: 0.5613 (tp30) REVERT: a 101 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6761 (mm-30) REVERT: b 27 GLU cc_start: 0.6303 (tp30) cc_final: 0.5927 (tp30) REVERT: b 121 GLU cc_start: 0.5934 (pt0) cc_final: 0.5679 (pt0) REVERT: c 27 GLU cc_start: 0.6081 (tp30) cc_final: 0.5795 (tp30) REVERT: c 101 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7135 (mm-30) REVERT: c 142 MET cc_start: 0.7632 (mmt) cc_final: 0.6834 (mpp) REVERT: c 232 ARG cc_start: 0.6304 (ttp-170) cc_final: 0.5891 (ttp-170) REVERT: d 39 ILE cc_start: 0.6216 (mt) cc_final: 0.5967 (mt) REVERT: e 27 GLU cc_start: 0.6041 (tp30) cc_final: 0.5807 (tt0) REVERT: f 39 ILE cc_start: 0.6083 (mt) cc_final: 0.5811 (mt) REVERT: g 27 GLU cc_start: 0.6079 (tp30) cc_final: 0.5761 (tp30) REVERT: g 39 ILE cc_start: 0.6321 (mt) cc_final: 0.6119 (mt) REVERT: g 101 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6951 (mm-30) REVERT: g 142 MET cc_start: 0.7743 (mmm) cc_final: 0.7354 (mpp) REVERT: g 232 ARG cc_start: 0.6245 (ttp-170) cc_final: 0.5719 (ttp-170) outliers start: 174 outliers final: 92 residues processed: 1142 average time/residue: 0.5799 time to fit residues: 1091.9237 Evaluate side-chains 956 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 862 time to evaluate : 4.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 41 THR Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain O residue 177 GLU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain a residue 24 VAL Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 122 ILE Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain g residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 370 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 555 optimal weight: 4.9990 chunk 454 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 668 optimal weight: 0.7980 chunk 722 optimal weight: 1.9990 chunk 595 optimal weight: 2.9990 chunk 663 optimal weight: 20.0000 chunk 227 optimal weight: 0.9990 chunk 536 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 88 ASN H 141 GLN V 88 ASN I 30 ASN W 88 ASN W 141 GLN X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 141 GLN L 141 GLN O 98 GLN S 158 ASN T 98 GLN c 200 HIS ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5926 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59164 Z= 0.222 Angle : 0.614 12.474 79905 Z= 0.331 Chirality : 0.042 0.180 9345 Planarity : 0.004 0.045 10262 Dihedral : 5.986 58.050 8347 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 3.64 % Allowed : 11.47 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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 (0.09), residues: 7469 helix: 1.78 (0.09), residues: 3451 sheet: -0.93 (0.12), residues: 1407 loop : -1.91 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 216 HIS 0.007 0.002 HIS W 28 PHE 0.012 0.002 PHE T 232 TYR 0.023 0.002 TYR B 8 ARG 0.009 0.001 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 911 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLN cc_start: 0.6256 (mm-40) cc_final: 0.5734 (mt0) REVERT: B 35 SER cc_start: 0.6109 (p) cc_final: 0.5825 (t) REVERT: B 98 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5503 (mt0) REVERT: B 122 GLN cc_start: 0.6519 (mt0) cc_final: 0.6162 (tt0) REVERT: B 167 SER cc_start: 0.7443 (t) cc_final: 0.7228 (p) REVERT: B 182 GLU cc_start: 0.6292 (mp0) cc_final: 0.5750 (tt0) REVERT: B 188 GLU cc_start: 0.6783 (tp30) cc_final: 0.6566 (tp30) REVERT: B 230 LYS cc_start: 0.6324 (mtmm) cc_final: 0.5838 (mptt) REVERT: C 98 GLN cc_start: 0.5778 (mm-40) cc_final: 0.5376 (mt0) REVERT: C 220 LYS cc_start: 0.7872 (mttt) cc_final: 0.7449 (mtpp) REVERT: D 98 GLN cc_start: 0.5826 (mm-40) cc_final: 0.5607 (mm-40) REVERT: D 182 GLU cc_start: 0.6308 (mp0) cc_final: 0.5925 (tt0) REVERT: D 220 LYS cc_start: 0.7809 (mttt) cc_final: 0.7447 (mtpp) REVERT: E 35 SER cc_start: 0.6286 (p) cc_final: 0.6041 (t) REVERT: E 98 GLN cc_start: 0.6021 (mm-40) cc_final: 0.5763 (tt0) REVERT: E 231 LYS cc_start: 0.7699 (mttp) cc_final: 0.6837 (ttpt) REVERT: F 40 MET cc_start: 0.7188 (ptp) cc_final: 0.6695 (ptp) REVERT: F 98 GLN cc_start: 0.5977 (mm-40) cc_final: 0.5479 (mt0) REVERT: F 182 GLU cc_start: 0.6317 (mp0) cc_final: 0.5673 (tt0) REVERT: F 220 LYS cc_start: 0.7822 (mttt) cc_final: 0.7605 (mttm) REVERT: G 98 GLN cc_start: 0.5816 (mm-40) cc_final: 0.5349 (mt0) REVERT: G 220 LYS cc_start: 0.7829 (mttt) cc_final: 0.7492 (mtpp) REVERT: Z 27 MET cc_start: 0.7605 (ttt) cc_final: 0.7292 (ttt) REVERT: Z 62 GLU cc_start: 0.6276 (tp30) cc_final: 0.5969 (mt-10) REVERT: Z 172 MET cc_start: 0.7703 (tpt) cc_final: 0.7275 (tpp) REVERT: Z 182 ASP cc_start: 0.7449 (t0) cc_final: 0.6661 (m-30) REVERT: M 9 LYS cc_start: 0.8380 (mttt) cc_final: 0.7963 (tptp) REVERT: M 62 GLU cc_start: 0.6130 (tp30) cc_final: 0.5877 (tp30) REVERT: M 93 MET cc_start: 0.5840 (mmm) cc_final: 0.4869 (mpp) REVERT: M 122 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7131 (m-30) REVERT: 1 32 LYS cc_start: 0.8129 (tttp) cc_final: 0.7855 (tttp) REVERT: 1 74 MET cc_start: 0.8134 (ttp) cc_final: 0.7734 (ttm) REVERT: 1 172 MET cc_start: 0.7960 (tpt) cc_final: 0.7702 (tpp) REVERT: N 9 LYS cc_start: 0.7987 (mttt) cc_final: 0.7646 (pttp) REVERT: N 122 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6896 (m-30) REVERT: N 129 SER cc_start: 0.7885 (m) cc_final: 0.7480 (p) REVERT: N 181 LYS cc_start: 0.7843 (tttm) cc_final: 0.7352 (mtmm) REVERT: 2 129 SER cc_start: 0.8110 (m) cc_final: 0.7906 (m) REVERT: 2 172 MET cc_start: 0.7542 (tpt) cc_final: 0.7201 (tpp) REVERT: H 129 SER cc_start: 0.8329 (m) cc_final: 0.7980 (p) REVERT: H 144 GLU cc_start: 0.8220 (pt0) cc_final: 0.7993 (mp0) REVERT: H 181 LYS cc_start: 0.7454 (tttm) cc_final: 0.6786 (mtmm) REVERT: V 27 MET cc_start: 0.7637 (ttt) cc_final: 0.7268 (ttt) REVERT: V 43 MET cc_start: 0.7799 (ttm) cc_final: 0.7252 (ttm) REVERT: V 141 GLN cc_start: 0.7228 (mt0) cc_final: 0.7023 (mt0) REVERT: V 164 GLN cc_start: 0.6739 (mm-40) cc_final: 0.6352 (mt0) REVERT: I 14 MET cc_start: 0.7374 (mtm) cc_final: 0.6838 (mtt) REVERT: I 71 ARG cc_start: 0.5934 (mtm-85) cc_final: 0.5710 (mtt90) REVERT: I 122 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: I 164 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6364 (mm-40) REVERT: I 180 ARG cc_start: 0.8236 (tpt170) cc_final: 0.7863 (tpp-160) REVERT: W 43 MET cc_start: 0.7785 (ttm) cc_final: 0.7556 (ttp) REVERT: W 145 LYS cc_start: 0.8576 (mmtm) cc_final: 0.8246 (mttp) REVERT: W 164 GLN cc_start: 0.6688 (mm-40) cc_final: 0.6397 (mt0) REVERT: J 129 SER cc_start: 0.7716 (m) cc_final: 0.7371 (p) REVERT: J 164 GLN cc_start: 0.6267 (mp10) cc_final: 0.5971 (mp10) REVERT: J 181 LYS cc_start: 0.8051 (tttm) cc_final: 0.7512 (mtmm) REVERT: J 182 ASP cc_start: 0.6871 (m-30) cc_final: 0.6593 (m-30) REVERT: X 27 MET cc_start: 0.7855 (ttt) cc_final: 0.7573 (ttt) REVERT: X 40 TYR cc_start: 0.7643 (m-80) cc_final: 0.6969 (m-80) REVERT: X 62 GLU cc_start: 0.5652 (tp30) cc_final: 0.5237 (mt-10) REVERT: X 66 TYR cc_start: 0.6521 (t80) cc_final: 0.5994 (t80) REVERT: X 129 SER cc_start: 0.8025 (m) cc_final: 0.7802 (m) REVERT: X 180 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7685 (tpt170) REVERT: K 9 LYS cc_start: 0.8063 (mttt) cc_final: 0.7555 (tptm) REVERT: K 14 MET cc_start: 0.7167 (mtp) cc_final: 0.6944 (mtt) REVERT: K 122 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: K 141 GLN cc_start: 0.7591 (mt0) cc_final: 0.7315 (mt0) REVERT: K 180 ARG cc_start: 0.8568 (tpt170) cc_final: 0.8119 (tpt170) REVERT: K 181 LYS cc_start: 0.7576 (tttm) cc_final: 0.7294 (tttm) REVERT: Y 32 LYS cc_start: 0.8407 (tttp) cc_final: 0.8192 (tttp) REVERT: Y 38 ASP cc_start: 0.7639 (t0) cc_final: 0.7398 (t0) REVERT: Y 62 GLU cc_start: 0.6462 (tp30) cc_final: 0.5979 (mt-10) REVERT: Y 145 LYS cc_start: 0.8399 (mmtm) cc_final: 0.8037 (mttp) REVERT: L 21 THR cc_start: 0.4316 (OUTLIER) cc_final: 0.4066 (t) REVERT: L 62 GLU cc_start: 0.5983 (tp30) cc_final: 0.5724 (tp30) REVERT: L 129 SER cc_start: 0.7988 (m) cc_final: 0.7604 (p) REVERT: L 146 MET cc_start: 0.7609 (mtm) cc_final: 0.7148 (ptp) REVERT: O 29 GLU cc_start: 0.5577 (mm-30) cc_final: 0.5315 (mt-10) REVERT: O 122 GLN cc_start: 0.7837 (tt0) cc_final: 0.7600 (tt0) REVERT: O 179 GLU cc_start: 0.7927 (tp30) cc_final: 0.7306 (tp30) REVERT: O 182 GLU cc_start: 0.7648 (pm20) cc_final: 0.6981 (pt0) REVERT: P 40 MET cc_start: 0.7596 (ptp) cc_final: 0.7243 (ptp) REVERT: P 65 GLU cc_start: 0.6341 (mt-10) cc_final: 0.5742 (pt0) REVERT: P 122 GLN cc_start: 0.7655 (tt0) cc_final: 0.7438 (tt0) REVERT: P 179 GLU cc_start: 0.7485 (tp30) cc_final: 0.7239 (tp30) REVERT: P 182 GLU cc_start: 0.7815 (pm20) cc_final: 0.7312 (pt0) REVERT: P 220 LYS cc_start: 0.7988 (mttt) cc_final: 0.7624 (mttm) REVERT: Q 177 GLU cc_start: 0.6252 (tp30) cc_final: 0.5664 (tp30) REVERT: Q 179 GLU cc_start: 0.7551 (tp30) cc_final: 0.7115 (tp30) REVERT: R 20 ARG cc_start: 0.7134 (mtp180) cc_final: 0.6652 (mtp85) REVERT: R 122 GLN cc_start: 0.7797 (tt0) cc_final: 0.7483 (tt0) REVERT: R 177 GLU cc_start: 0.6356 (tp30) cc_final: 0.5868 (tp30) REVERT: R 182 GLU cc_start: 0.7543 (pm20) cc_final: 0.7100 (pt0) REVERT: S 179 GLU cc_start: 0.7455 (tp30) cc_final: 0.6968 (tp30) REVERT: T 40 MET cc_start: 0.7251 (ptp) cc_final: 0.6783 (ptm) REVERT: T 65 GLU cc_start: 0.6288 (mt-10) cc_final: 0.5527 (pt0) REVERT: T 122 GLN cc_start: 0.7544 (tt0) cc_final: 0.7094 (tt0) REVERT: T 177 GLU cc_start: 0.6341 (tp30) cc_final: 0.5766 (tp30) REVERT: T 182 GLU cc_start: 0.7738 (pm20) cc_final: 0.7068 (pt0) REVERT: U 20 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6890 (mtp85) REVERT: U 40 MET cc_start: 0.7930 (ptp) cc_final: 0.7574 (ptp) REVERT: U 177 GLU cc_start: 0.6413 (tp30) cc_final: 0.5538 (tp30) REVERT: U 182 GLU cc_start: 0.7729 (pm20) cc_final: 0.6923 (pt0) REVERT: U 222 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6303 (ptt90) REVERT: a 27 GLU cc_start: 0.6100 (tp30) cc_final: 0.5636 (tp30) REVERT: b 27 GLU cc_start: 0.6264 (tp30) cc_final: 0.5891 (tp30) REVERT: b 121 GLU cc_start: 0.5774 (pt0) cc_final: 0.5524 (pt0) REVERT: c 27 GLU cc_start: 0.6163 (tp30) cc_final: 0.5941 (tp30) REVERT: c 101 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7458 (mm-30) REVERT: c 142 MET cc_start: 0.7577 (mmt) cc_final: 0.6692 (mpp) REVERT: c 232 ARG cc_start: 0.6601 (ttp-170) cc_final: 0.5929 (ttp-170) REVERT: d 18 GLU cc_start: 0.5711 (tm-30) cc_final: 0.5091 (tm-30) REVERT: d 98 GLU cc_start: 0.6705 (tt0) cc_final: 0.6472 (tt0) REVERT: e 18 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5825 (tm-30) REVERT: e 27 GLU cc_start: 0.6189 (tp30) cc_final: 0.5942 (tp30) REVERT: f 45 GLU cc_start: 0.6849 (tt0) cc_final: 0.6447 (mt-10) REVERT: g 37 GLU cc_start: 0.6830 (tt0) cc_final: 0.6567 (mt-10) REVERT: g 39 ILE cc_start: 0.6334 (mt) cc_final: 0.6132 (mt) REVERT: g 61 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7143 (mt-10) REVERT: g 119 GLU cc_start: 0.5877 (mt-10) cc_final: 0.5653 (mt-10) REVERT: g 142 MET cc_start: 0.7583 (mmm) cc_final: 0.7253 (mpp) outliers start: 228 outliers final: 131 residues processed: 1106 average time/residue: 0.5774 time to fit residues: 1049.3956 Evaluate side-chains 940 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 803 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 140 SER Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 140 SER Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 63 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 222 ARG Chi-restraints excluded: chain a residue 121 GLU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain f residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 660 optimal weight: 0.5980 chunk 502 optimal weight: 4.9990 chunk 347 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 449 optimal weight: 6.9990 chunk 671 optimal weight: 0.9990 chunk 710 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 636 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 164 GLN V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 ASN X 88 ASN X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 141 GLN L 30 ASN L 164 GLN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 200 HIS ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 200 HIS ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 59164 Z= 0.202 Angle : 0.584 12.597 79905 Z= 0.312 Chirality : 0.041 0.186 9345 Planarity : 0.004 0.040 10262 Dihedral : 5.669 54.453 8345 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 3.56 % Allowed : 13.49 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.45 (0.10), residues: 7469 helix: 2.13 (0.09), residues: 3458 sheet: -0.48 (0.13), residues: 1302 loop : -1.79 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 216 HIS 0.005 0.001 HIS V 28 PHE 0.011 0.001 PHE E 42 TYR 0.019 0.001 TYR B 8 ARG 0.010 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 842 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 SER cc_start: 0.6073 (p) cc_final: 0.5780 (t) REVERT: B 98 GLN cc_start: 0.5891 (mm-40) cc_final: 0.5452 (tt0) REVERT: B 122 GLN cc_start: 0.6495 (mt0) cc_final: 0.6122 (tt0) REVERT: B 182 GLU cc_start: 0.6386 (mp0) cc_final: 0.5873 (tt0) REVERT: B 230 LYS cc_start: 0.6400 (mtmm) cc_final: 0.6055 (mptt) REVERT: C 98 GLN cc_start: 0.5797 (mm-40) cc_final: 0.5473 (mm-40) REVERT: C 220 LYS cc_start: 0.7839 (mttt) cc_final: 0.7427 (mtpp) REVERT: D 98 GLN cc_start: 0.5829 (mm-40) cc_final: 0.5510 (mm110) REVERT: D 182 GLU cc_start: 0.6327 (mp0) cc_final: 0.5920 (tt0) REVERT: D 220 LYS cc_start: 0.7839 (mttt) cc_final: 0.7544 (mtpp) REVERT: D 221 TYR cc_start: 0.5172 (OUTLIER) cc_final: 0.4861 (m-80) REVERT: E 35 SER cc_start: 0.6328 (p) cc_final: 0.6100 (t) REVERT: E 98 GLN cc_start: 0.5932 (mm-40) cc_final: 0.5467 (tt0) REVERT: F 40 MET cc_start: 0.7211 (ptp) cc_final: 0.6764 (ptp) REVERT: F 182 GLU cc_start: 0.6417 (mp0) cc_final: 0.5753 (tt0) REVERT: G 186 GLU cc_start: 0.5756 (OUTLIER) cc_final: 0.5423 (mm-30) REVERT: G 220 LYS cc_start: 0.7814 (mttt) cc_final: 0.7476 (mtpp) REVERT: Z 62 GLU cc_start: 0.6169 (tp30) cc_final: 0.5844 (mt-10) REVERT: Z 182 ASP cc_start: 0.7431 (t0) cc_final: 0.6606 (m-30) REVERT: M 27 MET cc_start: 0.7631 (ttt) cc_final: 0.7169 (ttp) REVERT: M 62 GLU cc_start: 0.6102 (tp30) cc_final: 0.5869 (tp30) REVERT: M 93 MET cc_start: 0.5903 (mmm) cc_final: 0.4945 (mpp) REVERT: M 164 GLN cc_start: 0.7024 (mm-40) cc_final: 0.6590 (mm110) REVERT: 1 32 LYS cc_start: 0.8098 (tttp) cc_final: 0.7849 (tttp) REVERT: 1 74 MET cc_start: 0.8040 (ttp) cc_final: 0.7635 (ttm) REVERT: 1 144 GLU cc_start: 0.7475 (tt0) cc_final: 0.7130 (mt-10) REVERT: 1 172 MET cc_start: 0.7986 (tpt) cc_final: 0.7728 (tpp) REVERT: 1 203 LEU cc_start: 0.1798 (OUTLIER) cc_final: 0.1597 (pp) REVERT: N 59 MET cc_start: 0.6605 (mmm) cc_final: 0.6388 (mmp) REVERT: N 181 LYS cc_start: 0.7794 (tttm) cc_final: 0.7348 (mtmm) REVERT: 2 43 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7337 (ttp) REVERT: 2 172 MET cc_start: 0.7485 (tpt) cc_final: 0.7227 (tpp) REVERT: 2 182 ASP cc_start: 0.7076 (t0) cc_final: 0.6354 (m-30) REVERT: 2 203 LEU cc_start: 0.2017 (OUTLIER) cc_final: 0.1756 (pp) REVERT: H 129 SER cc_start: 0.8316 (m) cc_final: 0.7968 (p) REVERT: H 144 GLU cc_start: 0.8189 (pt0) cc_final: 0.7985 (mp0) REVERT: H 181 LYS cc_start: 0.7460 (tttm) cc_final: 0.6773 (mtmm) REVERT: V 27 MET cc_start: 0.7667 (ttt) cc_final: 0.7144 (ttt) REVERT: V 43 MET cc_start: 0.7815 (ttm) cc_final: 0.7262 (ttm) REVERT: V 124 TYR cc_start: 0.8901 (p90) cc_final: 0.8579 (p90) REVERT: V 164 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6379 (mt0) REVERT: I 14 MET cc_start: 0.7342 (mtm) cc_final: 0.6601 (mtt) REVERT: I 164 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6355 (mm-40) REVERT: W 43 MET cc_start: 0.7792 (ttm) cc_final: 0.7448 (ttp) REVERT: W 59 MET cc_start: 0.6982 (mmm) cc_final: 0.6729 (mmm) REVERT: W 93 MET cc_start: 0.6512 (mmt) cc_final: 0.6284 (mmt) REVERT: W 144 GLU cc_start: 0.7684 (tt0) cc_final: 0.7219 (mt-10) REVERT: W 164 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6448 (mt0) REVERT: J 122 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: J 129 SER cc_start: 0.7688 (m) cc_final: 0.7357 (p) REVERT: J 181 LYS cc_start: 0.8234 (tttm) cc_final: 0.7660 (mtmm) REVERT: J 182 ASP cc_start: 0.6922 (m-30) cc_final: 0.6630 (m-30) REVERT: X 27 MET cc_start: 0.7849 (ttt) cc_final: 0.7622 (ttt) REVERT: X 40 TYR cc_start: 0.7653 (m-80) cc_final: 0.6865 (m-80) REVERT: X 62 GLU cc_start: 0.5605 (tp30) cc_final: 0.5058 (mt-10) REVERT: X 129 SER cc_start: 0.8053 (m) cc_final: 0.7838 (m) REVERT: X 144 GLU cc_start: 0.7392 (tt0) cc_final: 0.7181 (mt-10) REVERT: X 180 ARG cc_start: 0.8208 (tpt170) cc_final: 0.7507 (tpp-160) REVERT: K 9 LYS cc_start: 0.8040 (mttt) cc_final: 0.7535 (tptm) REVERT: K 141 GLN cc_start: 0.7558 (mt0) cc_final: 0.7176 (mt0) REVERT: K 180 ARG cc_start: 0.8542 (tpt170) cc_final: 0.7997 (tpt170) REVERT: K 181 LYS cc_start: 0.7540 (tttm) cc_final: 0.7252 (tttm) REVERT: Y 32 LYS cc_start: 0.8261 (tttp) cc_final: 0.7990 (tttp) REVERT: Y 62 GLU cc_start: 0.6529 (tp30) cc_final: 0.6020 (mt-10) REVERT: L 21 THR cc_start: 0.4643 (OUTLIER) cc_final: 0.4398 (t) REVERT: L 129 SER cc_start: 0.8008 (m) cc_final: 0.7624 (p) REVERT: O 29 GLU cc_start: 0.5647 (mm-30) cc_final: 0.5396 (mt-10) REVERT: O 40 MET cc_start: 0.7438 (ptp) cc_final: 0.7150 (ptm) REVERT: O 179 GLU cc_start: 0.7931 (tp30) cc_final: 0.7184 (tp30) REVERT: O 182 GLU cc_start: 0.7637 (pm20) cc_final: 0.6931 (pt0) REVERT: P 40 MET cc_start: 0.7612 (ptp) cc_final: 0.7102 (ptp) REVERT: P 65 GLU cc_start: 0.6455 (mt-10) cc_final: 0.5933 (pt0) REVERT: P 122 GLN cc_start: 0.7455 (tt0) cc_final: 0.7241 (tt0) REVERT: P 177 GLU cc_start: 0.7470 (tp30) cc_final: 0.7243 (tp30) REVERT: P 220 LYS cc_start: 0.8042 (mttt) cc_final: 0.7798 (mttm) REVERT: P 223 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7660 (mm) REVERT: Q 122 GLN cc_start: 0.7786 (tt0) cc_final: 0.7369 (tt0) REVERT: Q 177 GLU cc_start: 0.6330 (tp30) cc_final: 0.5747 (tp30) REVERT: R 65 GLU cc_start: 0.6299 (mt-10) cc_final: 0.5588 (pt0) REVERT: R 122 GLN cc_start: 0.7622 (tt0) cc_final: 0.7228 (tt0) REVERT: R 182 GLU cc_start: 0.7715 (pm20) cc_final: 0.7150 (pt0) REVERT: S 20 ARG cc_start: 0.7116 (mtp180) cc_final: 0.5656 (mtp180) REVERT: S 220 LYS cc_start: 0.7884 (mttt) cc_final: 0.7678 (mttm) REVERT: S 223 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7233 (mm) REVERT: T 65 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5614 (pt0) REVERT: T 122 GLN cc_start: 0.7735 (tt0) cc_final: 0.7327 (tt0) REVERT: T 177 GLU cc_start: 0.6413 (tp30) cc_final: 0.5897 (tp30) REVERT: T 182 GLU cc_start: 0.7805 (pm20) cc_final: 0.7209 (pt0) REVERT: T 223 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7179 (mm) REVERT: U 40 MET cc_start: 0.7912 (ptp) cc_final: 0.7474 (ptp) REVERT: U 177 GLU cc_start: 0.6423 (tp30) cc_final: 0.5737 (tp30) REVERT: U 182 GLU cc_start: 0.7817 (pm20) cc_final: 0.7193 (pt0) REVERT: a 27 GLU cc_start: 0.6125 (tp30) cc_final: 0.5617 (tp30) REVERT: b 27 GLU cc_start: 0.6312 (tp30) cc_final: 0.5956 (tp30) REVERT: c 18 GLU cc_start: 0.5984 (tm-30) cc_final: 0.5773 (tm-30) REVERT: c 27 GLU cc_start: 0.6159 (tp30) cc_final: 0.5736 (tt0) REVERT: c 101 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7652 (mm-30) REVERT: c 142 MET cc_start: 0.7523 (mmt) cc_final: 0.7168 (mmt) REVERT: d 18 GLU cc_start: 0.5667 (tm-30) cc_final: 0.5309 (tm-30) REVERT: d 98 GLU cc_start: 0.6760 (tt0) cc_final: 0.6498 (tt0) REVERT: e 18 GLU cc_start: 0.6066 (tm-30) cc_final: 0.5630 (tm-30) REVERT: e 27 GLU cc_start: 0.6205 (tp30) cc_final: 0.5916 (tp30) REVERT: e 51 ARG cc_start: 0.6230 (mmm-85) cc_final: 0.5993 (mtp180) REVERT: e 57 ARG cc_start: 0.6494 (ttm110) cc_final: 0.5558 (ttp80) REVERT: e 142 MET cc_start: 0.7760 (mpp) cc_final: 0.7388 (mpp) REVERT: f 45 GLU cc_start: 0.6867 (tt0) cc_final: 0.6600 (mt-10) REVERT: g 27 GLU cc_start: 0.6056 (tp30) cc_final: 0.5722 (tp30) REVERT: g 191 MET cc_start: 0.5959 (mmt) cc_final: 0.5743 (mmt) REVERT: g 204 MET cc_start: 0.5688 (tpp) cc_final: 0.5465 (mmt) outliers start: 223 outliers final: 140 residues processed: 1033 average time/residue: 0.5975 time to fit residues: 1026.0814 Evaluate side-chains 942 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 792 time to evaluate : 4.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 140 SER Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 140 SER Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 203 LEU Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 43 MET Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 122 ASP Chi-restraints excluded: chain V residue 140 SER Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 140 SER Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 140 SER Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 106 LEU Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 591 optimal weight: 4.9990 chunk 403 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 528 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 606 optimal weight: 1.9990 chunk 491 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 362 optimal weight: 0.7980 chunk 637 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 164 GLN 2 141 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 164 GLN L 141 GLN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59164 Z= 0.201 Angle : 0.573 12.480 79905 Z= 0.307 Chirality : 0.041 0.187 9345 Planarity : 0.003 0.038 10262 Dihedral : 5.523 54.088 8341 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.93 % Allowed : 14.13 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 0.69 (0.10), residues: 7469 helix: 2.30 (0.09), residues: 3458 sheet: -0.31 (0.13), residues: 1302 loop : -1.67 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 216 HIS 0.005 0.001 HIS Z 28 PHE 0.010 0.001 PHE B 42 TYR 0.019 0.001 TYR 2 66 ARG 0.011 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 820 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 SER cc_start: 0.6071 (p) cc_final: 0.5799 (t) REVERT: B 182 GLU cc_start: 0.6524 (mp0) cc_final: 0.6209 (tt0) REVERT: B 230 LYS cc_start: 0.6587 (mtmm) cc_final: 0.6258 (mptt) REVERT: C 98 GLN cc_start: 0.5785 (mm-40) cc_final: 0.5484 (mm-40) REVERT: C 220 LYS cc_start: 0.7827 (mttt) cc_final: 0.7381 (mtpp) REVERT: D 182 GLU cc_start: 0.6426 (mp0) cc_final: 0.5942 (tt0) REVERT: D 221 TYR cc_start: 0.5539 (OUTLIER) cc_final: 0.4827 (m-80) REVERT: E 35 SER cc_start: 0.6398 (p) cc_final: 0.6159 (t) REVERT: E 98 GLN cc_start: 0.5883 (mm-40) cc_final: 0.5486 (tt0) REVERT: F 40 MET cc_start: 0.7229 (ptp) cc_final: 0.6800 (ptp) REVERT: F 182 GLU cc_start: 0.6493 (mp0) cc_final: 0.5868 (tt0) REVERT: G 186 GLU cc_start: 0.5613 (OUTLIER) cc_final: 0.5365 (mm-30) REVERT: G 220 LYS cc_start: 0.7787 (mttt) cc_final: 0.7456 (mtpp) REVERT: Z 62 GLU cc_start: 0.6323 (tp30) cc_final: 0.6000 (mt-10) REVERT: Z 122 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6587 (m-30) REVERT: Z 172 MET cc_start: 0.7618 (tpt) cc_final: 0.7378 (tpt) REVERT: Z 182 ASP cc_start: 0.7399 (t0) cc_final: 0.6705 (m-30) REVERT: M 27 MET cc_start: 0.7629 (ttt) cc_final: 0.7124 (ttp) REVERT: M 93 MET cc_start: 0.5898 (mmm) cc_final: 0.4900 (mpp) REVERT: M 164 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6519 (mm-40) REVERT: 1 74 MET cc_start: 0.8043 (ttp) cc_final: 0.7612 (ttm) REVERT: 1 144 GLU cc_start: 0.7342 (tt0) cc_final: 0.7039 (mt-10) REVERT: 1 172 MET cc_start: 0.7775 (tpt) cc_final: 0.7536 (tpp) REVERT: N 181 LYS cc_start: 0.7865 (tttm) cc_final: 0.7642 (tttm) REVERT: 2 43 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7418 (ttp) REVERT: 2 172 MET cc_start: 0.7638 (tpt) cc_final: 0.7409 (tpp) REVERT: 2 203 LEU cc_start: 0.1993 (OUTLIER) cc_final: 0.1762 (pp) REVERT: H 129 SER cc_start: 0.8293 (m) cc_final: 0.7942 (p) REVERT: H 180 ARG cc_start: 0.8421 (tpt170) cc_final: 0.8140 (tpt170) REVERT: H 181 LYS cc_start: 0.7463 (tttm) cc_final: 0.6749 (mtmm) REVERT: V 43 MET cc_start: 0.7847 (ttm) cc_final: 0.7289 (ttm) REVERT: V 124 TYR cc_start: 0.8920 (p90) cc_final: 0.8558 (p90) REVERT: V 164 GLN cc_start: 0.6729 (mm-40) cc_final: 0.6371 (mt0) REVERT: I 14 MET cc_start: 0.7346 (mtm) cc_final: 0.6520 (mtt) REVERT: I 27 MET cc_start: 0.7794 (ttt) cc_final: 0.7387 (ttp) REVERT: I 101 VAL cc_start: 0.6802 (OUTLIER) cc_final: 0.6590 (t) REVERT: I 164 GLN cc_start: 0.6682 (mm-40) cc_final: 0.6348 (mm-40) REVERT: W 43 MET cc_start: 0.7836 (ttm) cc_final: 0.7537 (ttp) REVERT: J 27 MET cc_start: 0.7736 (ttt) cc_final: 0.7456 (ttt) REVERT: J 122 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: J 129 SER cc_start: 0.7665 (m) cc_final: 0.7279 (p) REVERT: J 181 LYS cc_start: 0.8021 (tttm) cc_final: 0.7552 (mtmm) REVERT: J 182 ASP cc_start: 0.6968 (m-30) cc_final: 0.6670 (m-30) REVERT: X 27 MET cc_start: 0.7872 (ttt) cc_final: 0.7633 (ttt) REVERT: X 40 TYR cc_start: 0.7617 (m-80) cc_final: 0.6853 (m-80) REVERT: X 62 GLU cc_start: 0.5661 (tp30) cc_final: 0.5208 (mt-10) REVERT: X 144 GLU cc_start: 0.7444 (tt0) cc_final: 0.7194 (mt-10) REVERT: X 180 ARG cc_start: 0.8226 (tpt170) cc_final: 0.7766 (tpt170) REVERT: K 141 GLN cc_start: 0.7595 (mt0) cc_final: 0.7279 (mt0) REVERT: K 180 ARG cc_start: 0.8489 (tpt170) cc_final: 0.8034 (tpt170) REVERT: K 181 LYS cc_start: 0.7515 (tttm) cc_final: 0.7245 (tttm) REVERT: Y 32 LYS cc_start: 0.8253 (tttp) cc_final: 0.7990 (tttp) REVERT: L 21 THR cc_start: 0.4447 (OUTLIER) cc_final: 0.4160 (t) REVERT: L 129 SER cc_start: 0.7985 (m) cc_final: 0.7604 (p) REVERT: O 29 GLU cc_start: 0.5623 (mm-30) cc_final: 0.5321 (mt-10) REVERT: O 179 GLU cc_start: 0.7941 (tp30) cc_final: 0.7268 (tp30) REVERT: O 182 GLU cc_start: 0.7711 (pm20) cc_final: 0.7093 (pt0) REVERT: P 40 MET cc_start: 0.7544 (ptp) cc_final: 0.7036 (ptp) REVERT: P 65 GLU cc_start: 0.6466 (mt-10) cc_final: 0.5962 (pt0) REVERT: P 122 GLN cc_start: 0.7552 (tt0) cc_final: 0.7327 (tt0) REVERT: P 177 GLU cc_start: 0.7467 (tp30) cc_final: 0.7188 (tp30) REVERT: P 182 GLU cc_start: 0.7747 (pm20) cc_final: 0.7147 (pt0) REVERT: P 220 LYS cc_start: 0.8061 (mttt) cc_final: 0.7801 (mttm) REVERT: Q 122 GLN cc_start: 0.7803 (tt0) cc_final: 0.7421 (tt0) REVERT: Q 177 GLU cc_start: 0.6509 (tp30) cc_final: 0.5829 (tp30) REVERT: R 65 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5527 (mm-30) REVERT: R 122 GLN cc_start: 0.7647 (tt0) cc_final: 0.7347 (tt0) REVERT: R 182 GLU cc_start: 0.7787 (pm20) cc_final: 0.7212 (pt0) REVERT: S 220 LYS cc_start: 0.7960 (mttt) cc_final: 0.7696 (mttm) REVERT: S 223 ILE cc_start: 0.7661 (OUTLIER) cc_final: 0.7294 (mm) REVERT: T 40 MET cc_start: 0.7214 (ptp) cc_final: 0.6826 (ptt) REVERT: T 65 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5597 (pt0) REVERT: T 122 GLN cc_start: 0.7728 (tt0) cc_final: 0.7317 (tt0) REVERT: T 182 GLU cc_start: 0.7804 (pm20) cc_final: 0.7184 (pt0) REVERT: T 223 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7148 (mm) REVERT: U 40 MET cc_start: 0.7949 (ptp) cc_final: 0.7489 (ptp) REVERT: U 65 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5914 (tt0) REVERT: U 157 ILE cc_start: 0.7571 (pt) cc_final: 0.7326 (mt) REVERT: U 182 GLU cc_start: 0.7851 (pm20) cc_final: 0.7206 (pt0) REVERT: U 223 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7255 (mm) REVERT: a 27 GLU cc_start: 0.6146 (tp30) cc_final: 0.5666 (tp30) REVERT: b 27 GLU cc_start: 0.6212 (tp30) cc_final: 0.5868 (tp30) REVERT: c 27 GLU cc_start: 0.6260 (tp30) cc_final: 0.6005 (tp30) REVERT: c 101 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7691 (mm-30) REVERT: c 142 MET cc_start: 0.7527 (mmt) cc_final: 0.7139 (mmt) REVERT: d 18 GLU cc_start: 0.5661 (tm-30) cc_final: 0.5292 (tm-30) REVERT: d 27 GLU cc_start: 0.5873 (tp30) cc_final: 0.5662 (tp30) REVERT: d 98 GLU cc_start: 0.6761 (tt0) cc_final: 0.6495 (tt0) REVERT: e 18 GLU cc_start: 0.6048 (tm-30) cc_final: 0.5579 (tm-30) REVERT: e 27 GLU cc_start: 0.6131 (tp30) cc_final: 0.5544 (tp30) REVERT: e 51 ARG cc_start: 0.6286 (mmm-85) cc_final: 0.6050 (mtp180) REVERT: e 57 ARG cc_start: 0.6507 (ttm110) cc_final: 0.5701 (ttp80) REVERT: f 45 GLU cc_start: 0.6874 (tt0) cc_final: 0.6598 (mt-10) REVERT: f 51 ARG cc_start: 0.6452 (tpp80) cc_final: 0.6164 (ttp-170) REVERT: g 204 MET cc_start: 0.5492 (tpp) cc_final: 0.5279 (mmt) outliers start: 246 outliers final: 165 residues processed: 1014 average time/residue: 0.5710 time to fit residues: 957.1259 Evaluate side-chains 949 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 773 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 140 SER Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 140 SER Chi-restraints excluded: chain 1 residue 164 GLN Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 43 MET Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 129 SER Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 203 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 164 GLN Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 223 ILE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 239 optimal weight: 1.9990 chunk 639 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 417 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 711 optimal weight: 0.8980 chunk 590 optimal weight: 0.8980 chunk 329 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 164 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN W 88 ASN W 164 GLN X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 59164 Z= 0.213 Angle : 0.572 12.534 79905 Z= 0.306 Chirality : 0.041 0.196 9345 Planarity : 0.003 0.044 10262 Dihedral : 5.430 54.947 8338 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.99 % Allowed : 14.81 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 0.78 (0.10), residues: 7469 helix: 2.36 (0.09), residues: 3465 sheet: -0.33 (0.13), residues: 1344 loop : -1.60 (0.11), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 216 HIS 0.005 0.001 HIS 1 28 PHE 0.011 0.001 PHE B 42 TYR 0.018 0.001 TYR 2 66 ARG 0.013 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 827 time to evaluate : 4.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7670 (t0) REVERT: B 35 SER cc_start: 0.6169 (p) cc_final: 0.5909 (t) REVERT: B 182 GLU cc_start: 0.6581 (mp0) cc_final: 0.6231 (tt0) REVERT: B 188 GLU cc_start: 0.6706 (tp30) cc_final: 0.6488 (tp30) REVERT: B 230 LYS cc_start: 0.6731 (mtmm) cc_final: 0.6473 (mptt) REVERT: D 182 GLU cc_start: 0.6523 (mp0) cc_final: 0.5976 (tt0) REVERT: D 221 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.5235 (m-80) REVERT: E 35 SER cc_start: 0.6444 (p) cc_final: 0.6182 (t) REVERT: E 98 GLN cc_start: 0.5704 (mm-40) cc_final: 0.5305 (tt0) REVERT: E 179 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6452 (mt-10) REVERT: F 40 MET cc_start: 0.7268 (ptp) cc_final: 0.6848 (ptp) REVERT: F 98 GLN cc_start: 0.5844 (mm-40) cc_final: 0.5603 (mm110) REVERT: F 126 TYR cc_start: 0.6326 (m-80) cc_final: 0.5739 (m-80) REVERT: F 182 GLU cc_start: 0.6305 (mp0) cc_final: 0.6066 (tt0) REVERT: F 221 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.6168 (t80) REVERT: G 188 GLU cc_start: 0.6482 (tp30) cc_final: 0.6094 (mt-10) REVERT: G 220 LYS cc_start: 0.7963 (mttt) cc_final: 0.7619 (mtpp) REVERT: G 230 LYS cc_start: 0.6482 (mtmm) cc_final: 0.5984 (mmtm) REVERT: Z 62 GLU cc_start: 0.6247 (tp30) cc_final: 0.5931 (mt-10) REVERT: Z 122 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: Z 172 MET cc_start: 0.7443 (tpt) cc_final: 0.7228 (tpt) REVERT: Z 182 ASP cc_start: 0.7415 (t0) cc_final: 0.6748 (m-30) REVERT: M 27 MET cc_start: 0.7614 (ttt) cc_final: 0.6986 (ttp) REVERT: M 71 ARG cc_start: 0.6267 (mtm-85) cc_final: 0.5990 (mtm-85) REVERT: M 90 VAL cc_start: 0.6759 (OUTLIER) cc_final: 0.6539 (p) REVERT: M 93 MET cc_start: 0.6011 (mmm) cc_final: 0.5362 (mpp) REVERT: M 129 SER cc_start: 0.7809 (m) cc_final: 0.7442 (p) REVERT: 1 144 GLU cc_start: 0.7395 (tt0) cc_final: 0.7090 (mt-10) REVERT: 1 172 MET cc_start: 0.7744 (tpt) cc_final: 0.7539 (tpp) REVERT: 1 182 ASP cc_start: 0.7081 (t0) cc_final: 0.6311 (m-30) REVERT: N 129 SER cc_start: 0.7792 (m) cc_final: 0.7393 (p) REVERT: 2 62 GLU cc_start: 0.6303 (tp30) cc_final: 0.5871 (mt-10) REVERT: 2 172 MET cc_start: 0.7602 (tpt) cc_final: 0.7361 (tpp) REVERT: H 122 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: H 129 SER cc_start: 0.8271 (m) cc_final: 0.7938 (p) REVERT: H 180 ARG cc_start: 0.8412 (tpt170) cc_final: 0.8146 (tpt170) REVERT: H 181 LYS cc_start: 0.7415 (tttm) cc_final: 0.6715 (mtmm) REVERT: V 27 MET cc_start: 0.7761 (ttt) cc_final: 0.7111 (ttt) REVERT: V 43 MET cc_start: 0.7841 (ttm) cc_final: 0.7312 (ttm) REVERT: V 62 GLU cc_start: 0.6137 (tp30) cc_final: 0.5885 (mt-10) REVERT: V 124 TYR cc_start: 0.8912 (p90) cc_final: 0.8637 (p90) REVERT: V 164 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6350 (mt0) REVERT: V 182 ASP cc_start: 0.6394 (m-30) cc_final: 0.6151 (m-30) REVERT: I 14 MET cc_start: 0.7313 (mtm) cc_final: 0.6428 (mtt) REVERT: I 27 MET cc_start: 0.7758 (ttt) cc_final: 0.7428 (ttp) REVERT: I 122 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7367 (m-30) REVERT: I 164 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6361 (mm-40) REVERT: W 43 MET cc_start: 0.7834 (ttm) cc_final: 0.7560 (ttp) REVERT: J 27 MET cc_start: 0.7697 (ttt) cc_final: 0.7334 (ttt) REVERT: J 68 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5690 (mt) REVERT: J 122 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6764 (m-30) REVERT: J 129 SER cc_start: 0.7629 (m) cc_final: 0.7234 (p) REVERT: J 182 ASP cc_start: 0.6937 (m-30) cc_final: 0.6708 (m-30) REVERT: X 27 MET cc_start: 0.7881 (ttt) cc_final: 0.7615 (ttt) REVERT: X 40 TYR cc_start: 0.7615 (m-80) cc_final: 0.6826 (m-80) REVERT: X 62 GLU cc_start: 0.5796 (tp30) cc_final: 0.5110 (mt-10) REVERT: X 144 GLU cc_start: 0.7475 (tt0) cc_final: 0.7187 (mt-10) REVERT: X 173 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7611 (mt) REVERT: X 180 ARG cc_start: 0.8228 (tpt170) cc_final: 0.7788 (tpt170) REVERT: K 129 SER cc_start: 0.8058 (m) cc_final: 0.7734 (p) REVERT: K 141 GLN cc_start: 0.7562 (mt0) cc_final: 0.7179 (mt0) REVERT: K 180 ARG cc_start: 0.8469 (tpt170) cc_final: 0.8085 (tpt170) REVERT: K 181 LYS cc_start: 0.7495 (tttm) cc_final: 0.7237 (tttm) REVERT: Y 32 LYS cc_start: 0.8225 (tttp) cc_final: 0.7976 (tttp) REVERT: L 21 THR cc_start: 0.4737 (OUTLIER) cc_final: 0.4506 (t) REVERT: L 129 SER cc_start: 0.7980 (m) cc_final: 0.7599 (p) REVERT: O 29 GLU cc_start: 0.5630 (mm-30) cc_final: 0.5328 (mt-10) REVERT: O 179 GLU cc_start: 0.8109 (tp30) cc_final: 0.7466 (tp30) REVERT: O 182 GLU cc_start: 0.7833 (pm20) cc_final: 0.7325 (pt0) REVERT: O 230 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6871 (mmmt) REVERT: P 40 MET cc_start: 0.7574 (ptp) cc_final: 0.7099 (ptp) REVERT: P 65 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6001 (pt0) REVERT: P 177 GLU cc_start: 0.7421 (tp30) cc_final: 0.7165 (tp30) REVERT: P 182 GLU cc_start: 0.7718 (pm20) cc_final: 0.7182 (pt0) REVERT: P 220 LYS cc_start: 0.8050 (mttt) cc_final: 0.7777 (mttm) REVERT: Q 122 GLN cc_start: 0.7773 (tt0) cc_final: 0.7367 (tt0) REVERT: Q 125 GLN cc_start: 0.8255 (tt0) cc_final: 0.7150 (tt0) REVERT: Q 177 GLU cc_start: 0.6555 (tp30) cc_final: 0.5907 (tp30) REVERT: R 65 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5686 (pt0) REVERT: R 122 GLN cc_start: 0.7569 (tt0) cc_final: 0.7280 (tt0) REVERT: R 182 GLU cc_start: 0.7741 (pm20) cc_final: 0.7194 (pt0) REVERT: S 126 TYR cc_start: 0.8277 (m-10) cc_final: 0.7824 (m-80) REVERT: S 220 LYS cc_start: 0.8059 (mttt) cc_final: 0.7786 (mttm) REVERT: S 223 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7424 (mm) REVERT: S 230 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6730 (mttm) REVERT: T 40 MET cc_start: 0.7258 (ptp) cc_final: 0.6858 (ptt) REVERT: T 65 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5580 (pt0) REVERT: T 122 GLN cc_start: 0.7695 (tt0) cc_final: 0.6954 (tt0) REVERT: T 126 TYR cc_start: 0.8112 (m-10) cc_final: 0.7880 (m-80) REVERT: T 182 GLU cc_start: 0.7782 (pm20) cc_final: 0.7162 (pt0) REVERT: T 223 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7250 (mm) REVERT: U 40 MET cc_start: 0.7972 (ptp) cc_final: 0.7504 (ptp) REVERT: U 65 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6015 (tt0) REVERT: U 182 GLU cc_start: 0.7938 (pm20) cc_final: 0.7411 (pt0) REVERT: U 222 ARG cc_start: 0.6973 (OUTLIER) cc_final: 0.6729 (ptt90) REVERT: U 230 LYS cc_start: 0.6958 (ttpt) cc_final: 0.6539 (mmmt) REVERT: a 18 GLU cc_start: 0.5904 (tm-30) cc_final: 0.5470 (tm-30) REVERT: a 27 GLU cc_start: 0.6122 (tp30) cc_final: 0.5616 (tp30) REVERT: b 27 GLU cc_start: 0.6122 (tp30) cc_final: 0.5801 (tp30) REVERT: c 27 GLU cc_start: 0.6267 (tp30) cc_final: 0.6031 (tp30) REVERT: c 101 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7814 (mm-30) REVERT: c 142 MET cc_start: 0.7578 (mmt) cc_final: 0.7190 (mpp) REVERT: d 18 GLU cc_start: 0.5662 (tm-30) cc_final: 0.5291 (tm-30) REVERT: d 27 GLU cc_start: 0.5885 (tp30) cc_final: 0.5647 (tp30) REVERT: d 98 GLU cc_start: 0.6717 (tt0) cc_final: 0.6459 (tt0) REVERT: e 18 GLU cc_start: 0.6039 (tm-30) cc_final: 0.5800 (tm-30) REVERT: e 27 GLU cc_start: 0.6206 (tp30) cc_final: 0.5600 (tp30) REVERT: e 57 ARG cc_start: 0.6524 (ttm110) cc_final: 0.5784 (ttp80) REVERT: f 45 GLU cc_start: 0.6878 (tt0) cc_final: 0.6594 (mt-10) REVERT: f 51 ARG cc_start: 0.6484 (tpp80) cc_final: 0.6225 (ttp-170) REVERT: g 27 GLU cc_start: 0.6121 (tp30) cc_final: 0.5845 (tp30) REVERT: g 204 MET cc_start: 0.5766 (tpp) cc_final: 0.5543 (mmt) outliers start: 250 outliers final: 179 residues processed: 1020 average time/residue: 0.5799 time to fit residues: 975.3098 Evaluate side-chains 988 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 795 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 122 ASP Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 172 MET Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 43 MET Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 129 SER Chi-restraints excluded: chain 2 residue 164 GLN Chi-restraints excluded: chain 2 residue 173 ILE Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 122 ASP Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 122 ASP Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 21 THR Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 134 VAL Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 222 ARG Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 201 LEU Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 685 optimal weight: 0.0770 chunk 80 optimal weight: 0.9980 chunk 405 optimal weight: 0.5980 chunk 519 optimal weight: 8.9990 chunk 402 optimal weight: 1.9990 chunk 598 optimal weight: 4.9990 chunk 397 optimal weight: 0.0570 chunk 708 optimal weight: 6.9990 chunk 443 optimal weight: 3.9990 chunk 431 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 164 GLN R 44 ASN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59164 Z= 0.173 Angle : 0.549 12.258 79905 Z= 0.296 Chirality : 0.040 0.238 9345 Planarity : 0.003 0.038 10262 Dihedral : 5.275 54.091 8335 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.28 % Allowed : 15.66 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.10), residues: 7469 helix: 2.49 (0.09), residues: 3465 sheet: -0.25 (0.13), residues: 1365 loop : -1.53 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP g 216 HIS 0.005 0.001 HIS 1 28 PHE 0.010 0.001 PHE B 42 TYR 0.019 0.001 TYR 1 58 ARG 0.011 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 822 time to evaluate : 4.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 SER cc_start: 0.6144 (p) cc_final: 0.5881 (t) REVERT: B 72 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7354 (t0) REVERT: B 182 GLU cc_start: 0.6575 (mp0) cc_final: 0.6251 (tt0) REVERT: D 182 GLU cc_start: 0.6560 (mp0) cc_final: 0.6045 (tt0) REVERT: E 179 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6455 (mt-10) REVERT: F 20 ARG cc_start: 0.6000 (ttp-170) cc_final: 0.5529 (ptm160) REVERT: F 40 MET cc_start: 0.7200 (ptp) cc_final: 0.6786 (ptp) REVERT: F 126 TYR cc_start: 0.6261 (m-80) cc_final: 0.5695 (m-80) REVERT: F 182 GLU cc_start: 0.6331 (mp0) cc_final: 0.6072 (tt0) REVERT: F 221 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5874 (t80) REVERT: G 188 GLU cc_start: 0.6566 (tp30) cc_final: 0.6161 (mt-10) REVERT: G 220 LYS cc_start: 0.7936 (mttt) cc_final: 0.7590 (mtpp) REVERT: Z 27 MET cc_start: 0.7284 (ttt) cc_final: 0.6775 (ttm) REVERT: Z 62 GLU cc_start: 0.6223 (tp30) cc_final: 0.5912 (mt-10) REVERT: Z 122 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6414 (m-30) REVERT: Z 182 ASP cc_start: 0.7409 (t0) cc_final: 0.6738 (m-30) REVERT: M 129 SER cc_start: 0.7797 (m) cc_final: 0.7434 (p) REVERT: 1 93 MET cc_start: 0.6301 (mmt) cc_final: 0.6033 (mmp) REVERT: 1 144 GLU cc_start: 0.7410 (tt0) cc_final: 0.7068 (mt-10) REVERT: 1 182 ASP cc_start: 0.7063 (t0) cc_final: 0.6283 (m-30) REVERT: N 59 MET cc_start: 0.6785 (mmp) cc_final: 0.6457 (mmm) REVERT: 2 43 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7420 (ttp) REVERT: 2 62 GLU cc_start: 0.6255 (tp30) cc_final: 0.5845 (mt-10) REVERT: H 129 SER cc_start: 0.8258 (m) cc_final: 0.7984 (p) REVERT: H 180 ARG cc_start: 0.8402 (tpt170) cc_final: 0.8162 (tpt170) REVERT: H 181 LYS cc_start: 0.7412 (tttm) cc_final: 0.6752 (mtmm) REVERT: V 43 MET cc_start: 0.7802 (ttm) cc_final: 0.7317 (ttm) REVERT: V 62 GLU cc_start: 0.6154 (tp30) cc_final: 0.5909 (mt-10) REVERT: V 124 TYR cc_start: 0.8884 (p90) cc_final: 0.8634 (p90) REVERT: V 164 GLN cc_start: 0.6711 (mm-40) cc_final: 0.6390 (mt0) REVERT: I 14 MET cc_start: 0.7278 (mtm) cc_final: 0.6785 (mtt) REVERT: I 27 MET cc_start: 0.7830 (ttt) cc_final: 0.7568 (ttp) REVERT: I 68 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.5844 (mp) REVERT: I 164 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6387 (mm-40) REVERT: W 43 MET cc_start: 0.7820 (ttm) cc_final: 0.7539 (ttp) REVERT: W 59 MET cc_start: 0.6940 (mmm) cc_final: 0.6680 (tpp) REVERT: W 74 MET cc_start: 0.8029 (ttp) cc_final: 0.7659 (ttm) REVERT: W 144 GLU cc_start: 0.7731 (tt0) cc_final: 0.7230 (mt-10) REVERT: W 164 GLN cc_start: 0.7047 (mt0) cc_final: 0.6538 (tt0) REVERT: J 27 MET cc_start: 0.7676 (ttt) cc_final: 0.7323 (ttt) REVERT: J 129 SER cc_start: 0.7594 (m) cc_final: 0.7208 (p) REVERT: J 139 GLU cc_start: 0.7018 (tp30) cc_final: 0.6672 (tt0) REVERT: J 182 ASP cc_start: 0.6877 (m-30) cc_final: 0.6657 (m-30) REVERT: X 27 MET cc_start: 0.7823 (ttt) cc_final: 0.7581 (ttt) REVERT: X 40 TYR cc_start: 0.7609 (m-80) cc_final: 0.6820 (m-80) REVERT: X 62 GLU cc_start: 0.5762 (tp30) cc_final: 0.5098 (mt-10) REVERT: X 144 GLU cc_start: 0.7586 (tt0) cc_final: 0.7289 (mt-10) REVERT: X 173 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7669 (mt) REVERT: X 180 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7851 (tpt170) REVERT: K 14 MET cc_start: 0.7126 (mtt) cc_final: 0.6870 (mtt) REVERT: K 17 GLU cc_start: 0.4939 (pp20) cc_final: 0.4579 (pp20) REVERT: K 59 MET cc_start: 0.6859 (mmm) cc_final: 0.6572 (mmp) REVERT: K 129 SER cc_start: 0.8040 (m) cc_final: 0.7715 (p) REVERT: K 141 GLN cc_start: 0.7531 (mt0) cc_final: 0.7151 (mt0) REVERT: K 144 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: K 180 ARG cc_start: 0.8465 (tpt170) cc_final: 0.7962 (tpt170) REVERT: K 181 LYS cc_start: 0.7502 (tttm) cc_final: 0.7246 (tttm) REVERT: Y 32 LYS cc_start: 0.8207 (tttp) cc_final: 0.7976 (tttp) REVERT: Y 64 GLU cc_start: 0.7000 (tt0) cc_final: 0.6161 (tt0) REVERT: L 21 THR cc_start: 0.4719 (OUTLIER) cc_final: 0.4500 (t) REVERT: L 129 SER cc_start: 0.7973 (m) cc_final: 0.7595 (p) REVERT: O 29 GLU cc_start: 0.5667 (mm-30) cc_final: 0.5418 (mt-10) REVERT: O 40 MET cc_start: 0.7379 (ptp) cc_final: 0.7095 (ptm) REVERT: O 179 GLU cc_start: 0.7996 (tp30) cc_final: 0.7406 (tp30) REVERT: O 182 GLU cc_start: 0.7818 (pm20) cc_final: 0.7291 (pt0) REVERT: P 40 MET cc_start: 0.7524 (ptp) cc_final: 0.7104 (ptp) REVERT: P 65 GLU cc_start: 0.6157 (mt-10) cc_final: 0.5576 (pt0) REVERT: P 177 GLU cc_start: 0.7425 (tp30) cc_final: 0.7187 (tp30) REVERT: P 182 GLU cc_start: 0.7790 (pm20) cc_final: 0.7175 (pt0) REVERT: P 220 LYS cc_start: 0.8018 (mttt) cc_final: 0.7747 (mttm) REVERT: Q 122 GLN cc_start: 0.7731 (tt0) cc_final: 0.7322 (tt0) REVERT: Q 125 GLN cc_start: 0.8180 (tt0) cc_final: 0.7088 (tt0) REVERT: Q 177 GLU cc_start: 0.6588 (tp30) cc_final: 0.5924 (tp30) REVERT: R 65 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5699 (pt0) REVERT: R 122 GLN cc_start: 0.7494 (tt0) cc_final: 0.7213 (tt0) REVERT: R 182 GLU cc_start: 0.7694 (pm20) cc_final: 0.7148 (pt0) REVERT: S 65 GLU cc_start: 0.6646 (mt-10) cc_final: 0.5900 (pt0) REVERT: S 220 LYS cc_start: 0.8052 (mttt) cc_final: 0.7782 (mttm) REVERT: S 223 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7432 (mm) REVERT: T 40 MET cc_start: 0.7231 (ptp) cc_final: 0.6833 (ptt) REVERT: T 65 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5538 (pt0) REVERT: T 122 GLN cc_start: 0.7682 (tt0) cc_final: 0.6995 (tt0) REVERT: T 182 GLU cc_start: 0.7831 (pm20) cc_final: 0.7205 (pt0) REVERT: T 223 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7274 (mm) REVERT: U 65 GLU cc_start: 0.6371 (mt-10) cc_final: 0.5948 (tt0) REVERT: U 157 ILE cc_start: 0.7660 (pt) cc_final: 0.7388 (mt) REVERT: U 182 GLU cc_start: 0.8037 (pm20) cc_final: 0.7391 (pt0) REVERT: U 222 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.6524 (ptt90) REVERT: a 27 GLU cc_start: 0.6130 (tp30) cc_final: 0.5496 (tp30) REVERT: b 27 GLU cc_start: 0.6091 (tp30) cc_final: 0.5780 (tp30) REVERT: c 18 GLU cc_start: 0.5836 (tm-30) cc_final: 0.5618 (tm-30) REVERT: c 27 GLU cc_start: 0.6242 (tp30) cc_final: 0.6028 (tp30) REVERT: c 101 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7831 (mm-30) REVERT: c 142 MET cc_start: 0.7554 (mmt) cc_final: 0.7146 (mpp) REVERT: d 27 GLU cc_start: 0.5912 (tp30) cc_final: 0.5684 (tp30) REVERT: d 98 GLU cc_start: 0.6704 (tt0) cc_final: 0.6456 (tt0) REVERT: e 27 GLU cc_start: 0.6194 (tp30) cc_final: 0.5597 (tp30) REVERT: e 51 ARG cc_start: 0.6156 (mtp180) cc_final: 0.5563 (mtm180) REVERT: e 57 ARG cc_start: 0.6498 (ttm110) cc_final: 0.5825 (ttp80) REVERT: f 45 GLU cc_start: 0.6868 (tt0) cc_final: 0.6581 (mt-10) REVERT: f 51 ARG cc_start: 0.6436 (tpp80) cc_final: 0.5953 (mtp180) REVERT: g 27 GLU cc_start: 0.6099 (tp30) cc_final: 0.5775 (tp30) outliers start: 205 outliers final: 150 residues processed: 980 average time/residue: 0.5719 time to fit residues: 925.1827 Evaluate side-chains 951 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 790 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 43 MET Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 129 SER Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 222 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 438 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 423 optimal weight: 0.3980 chunk 213 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 450 optimal weight: 4.9990 chunk 482 optimal weight: 0.6980 chunk 350 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 556 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 164 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 59164 Z= 0.196 Angle : 0.562 12.438 79905 Z= 0.301 Chirality : 0.041 0.241 9345 Planarity : 0.003 0.042 10262 Dihedral : 5.272 54.694 8335 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.52 % Allowed : 15.69 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.98 (0.10), residues: 7469 helix: 2.50 (0.09), residues: 3465 sheet: -0.17 (0.13), residues: 1365 loop : -1.49 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 216 HIS 0.005 0.001 HIS 1 28 PHE 0.011 0.001 PHE B 42 TYR 0.018 0.001 TYR 1 58 ARG 0.012 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 816 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6460 (t80) REVERT: A 231 LYS cc_start: 0.7686 (mttt) cc_final: 0.6845 (pttm) REVERT: B 35 SER cc_start: 0.6151 (p) cc_final: 0.5891 (t) REVERT: B 182 GLU cc_start: 0.6648 (mp0) cc_final: 0.6334 (tt0) REVERT: D 182 GLU cc_start: 0.6564 (mp0) cc_final: 0.6059 (tt0) REVERT: E 179 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6769 (mt-10) REVERT: F 126 TYR cc_start: 0.6257 (m-80) cc_final: 0.5682 (m-80) REVERT: F 221 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.5901 (t80) REVERT: G 186 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5426 (tp30) REVERT: G 188 GLU cc_start: 0.6486 (tp30) cc_final: 0.6110 (mt-10) REVERT: G 220 LYS cc_start: 0.7741 (mttt) cc_final: 0.7401 (mtpp) REVERT: Z 62 GLU cc_start: 0.6198 (tp30) cc_final: 0.5890 (mt-10) REVERT: Z 122 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6331 (m-30) REVERT: Z 182 ASP cc_start: 0.7423 (t0) cc_final: 0.6742 (m-30) REVERT: M 129 SER cc_start: 0.7824 (m) cc_final: 0.7471 (p) REVERT: 1 144 GLU cc_start: 0.7481 (tt0) cc_final: 0.7110 (mt-10) REVERT: 1 182 ASP cc_start: 0.7063 (t0) cc_final: 0.6290 (m-30) REVERT: N 59 MET cc_start: 0.6682 (mmp) cc_final: 0.6376 (mmm) REVERT: N 139 GLU cc_start: 0.6926 (tt0) cc_final: 0.6635 (tt0) REVERT: 2 43 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7323 (ttp) REVERT: 2 62 GLU cc_start: 0.6247 (tp30) cc_final: 0.5846 (mt-10) REVERT: 2 182 ASP cc_start: 0.7048 (t0) cc_final: 0.6356 (m-30) REVERT: H 129 SER cc_start: 0.8254 (m) cc_final: 0.7988 (p) REVERT: H 180 ARG cc_start: 0.8410 (tpt170) cc_final: 0.8172 (tpt170) REVERT: H 181 LYS cc_start: 0.7436 (tttm) cc_final: 0.6763 (mtmm) REVERT: V 43 MET cc_start: 0.7800 (ttm) cc_final: 0.7262 (ttm) REVERT: V 62 GLU cc_start: 0.6223 (tp30) cc_final: 0.5918 (mt-10) REVERT: V 124 TYR cc_start: 0.8938 (p90) cc_final: 0.8670 (p90) REVERT: V 164 GLN cc_start: 0.6693 (mm-40) cc_final: 0.6433 (mt0) REVERT: I 14 MET cc_start: 0.7276 (mtm) cc_final: 0.6807 (mtm) REVERT: I 27 MET cc_start: 0.7751 (ttt) cc_final: 0.7423 (ttp) REVERT: I 68 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5724 (mp) REVERT: I 164 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6435 (mm-40) REVERT: W 43 MET cc_start: 0.7839 (ttm) cc_final: 0.7595 (ttp) REVERT: W 164 GLN cc_start: 0.6974 (mt0) cc_final: 0.6382 (tt0) REVERT: J 27 MET cc_start: 0.7656 (ttt) cc_final: 0.7277 (ttt) REVERT: J 129 SER cc_start: 0.7646 (m) cc_final: 0.7267 (p) REVERT: J 139 GLU cc_start: 0.7009 (tp30) cc_final: 0.6638 (tt0) REVERT: X 27 MET cc_start: 0.7806 (ttt) cc_final: 0.7552 (ttt) REVERT: X 40 TYR cc_start: 0.7614 (m-80) cc_final: 0.6809 (m-80) REVERT: X 62 GLU cc_start: 0.5758 (tp30) cc_final: 0.5342 (mm-30) REVERT: X 144 GLU cc_start: 0.7587 (tt0) cc_final: 0.7237 (mt-10) REVERT: X 173 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7672 (mt) REVERT: X 180 ARG cc_start: 0.8298 (tpt170) cc_final: 0.7873 (tpt170) REVERT: K 14 MET cc_start: 0.7200 (mtt) cc_final: 0.6840 (mtt) REVERT: K 17 GLU cc_start: 0.5009 (pp20) cc_final: 0.4630 (pp20) REVERT: K 27 MET cc_start: 0.7329 (ttt) cc_final: 0.6982 (ttt) REVERT: K 129 SER cc_start: 0.8044 (m) cc_final: 0.7723 (p) REVERT: K 141 GLN cc_start: 0.7510 (mt0) cc_final: 0.7121 (mt0) REVERT: K 144 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: K 180 ARG cc_start: 0.8446 (tpt170) cc_final: 0.7972 (tpt170) REVERT: K 181 LYS cc_start: 0.7502 (tttm) cc_final: 0.7211 (tttm) REVERT: Y 32 LYS cc_start: 0.8205 (tttp) cc_final: 0.7977 (tttp) REVERT: Y 64 GLU cc_start: 0.7215 (tt0) cc_final: 0.6317 (tt0) REVERT: L 129 SER cc_start: 0.7972 (m) cc_final: 0.7601 (p) REVERT: O 29 GLU cc_start: 0.5678 (mm-30) cc_final: 0.5402 (mt-10) REVERT: O 179 GLU cc_start: 0.8030 (tp30) cc_final: 0.7450 (tp30) REVERT: O 182 GLU cc_start: 0.8081 (pm20) cc_final: 0.7717 (pm20) REVERT: O 221 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7035 (t80) REVERT: O 230 LYS cc_start: 0.7257 (ttpt) cc_final: 0.7026 (mttp) REVERT: P 40 MET cc_start: 0.7551 (ptp) cc_final: 0.7131 (ptp) REVERT: P 65 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5587 (pt0) REVERT: P 177 GLU cc_start: 0.7392 (tp30) cc_final: 0.7173 (tp30) REVERT: P 182 GLU cc_start: 0.7679 (pm20) cc_final: 0.7150 (pt0) REVERT: P 220 LYS cc_start: 0.8028 (mttt) cc_final: 0.7738 (mttm) REVERT: P 221 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.6958 (m-80) REVERT: Q 122 GLN cc_start: 0.7718 (tt0) cc_final: 0.7323 (tt0) REVERT: Q 125 GLN cc_start: 0.8164 (tt0) cc_final: 0.7095 (tt0) REVERT: R 40 MET cc_start: 0.7347 (ptt) cc_final: 0.6719 (ptm) REVERT: R 65 GLU cc_start: 0.6371 (mt-10) cc_final: 0.5727 (pt0) REVERT: R 122 GLN cc_start: 0.7344 (tt0) cc_final: 0.7056 (tt0) REVERT: R 182 GLU cc_start: 0.7759 (pm20) cc_final: 0.7249 (pt0) REVERT: S 126 TYR cc_start: 0.8303 (m-10) cc_final: 0.7861 (m-80) REVERT: S 220 LYS cc_start: 0.8118 (mttt) cc_final: 0.7846 (mttm) REVERT: S 223 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7451 (mm) REVERT: S 230 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6749 (mttp) REVERT: T 65 GLU cc_start: 0.6256 (mt-10) cc_final: 0.5643 (pt0) REVERT: T 122 GLN cc_start: 0.7373 (tt0) cc_final: 0.6991 (tt0) REVERT: T 182 GLU cc_start: 0.7834 (pm20) cc_final: 0.7220 (pt0) REVERT: T 221 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6338 (t80) REVERT: T 223 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7312 (mm) REVERT: U 65 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6132 (tt0) REVERT: U 157 ILE cc_start: 0.7664 (pt) cc_final: 0.7361 (mt) REVERT: U 182 GLU cc_start: 0.7959 (pm20) cc_final: 0.7439 (pt0) REVERT: a 27 GLU cc_start: 0.6256 (tp30) cc_final: 0.5535 (tp30) REVERT: a 121 GLU cc_start: 0.5295 (pt0) cc_final: 0.4961 (pt0) REVERT: b 27 GLU cc_start: 0.6178 (tp30) cc_final: 0.5858 (tp30) REVERT: c 18 GLU cc_start: 0.5881 (tm-30) cc_final: 0.5658 (tm-30) REVERT: c 27 GLU cc_start: 0.6242 (tp30) cc_final: 0.6027 (tp30) REVERT: c 101 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7860 (mm-30) REVERT: c 142 MET cc_start: 0.7585 (mmt) cc_final: 0.7105 (mpp) REVERT: d 27 GLU cc_start: 0.6056 (tp30) cc_final: 0.5814 (tp30) REVERT: d 98 GLU cc_start: 0.6701 (tt0) cc_final: 0.6453 (tt0) REVERT: e 27 GLU cc_start: 0.6229 (tp30) cc_final: 0.5619 (tp30) REVERT: e 51 ARG cc_start: 0.6209 (mtp180) cc_final: 0.5621 (mtm180) REVERT: e 57 ARG cc_start: 0.6542 (ttm110) cc_final: 0.5898 (ttp80) REVERT: f 45 GLU cc_start: 0.6873 (tt0) cc_final: 0.6590 (mt-10) REVERT: f 51 ARG cc_start: 0.6451 (tpp80) cc_final: 0.5961 (mtp180) REVERT: g 27 GLU cc_start: 0.6171 (tp30) cc_final: 0.5823 (tp30) REVERT: g 62 LYS cc_start: 0.7889 (tttt) cc_final: 0.7214 (pptt) outliers start: 220 outliers final: 171 residues processed: 987 average time/residue: 0.5750 time to fit residues: 936.2439 Evaluate side-chains 980 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 796 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 43 MET Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 122 ASP Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 43 MET Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 129 SER Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 41 THR Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 23 GLU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 31 VAL Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 24 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 644 optimal weight: 8.9990 chunk 678 optimal weight: 0.2980 chunk 619 optimal weight: 0.7980 chunk 660 optimal weight: 0.4980 chunk 397 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 518 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 596 optimal weight: 4.9990 chunk 624 optimal weight: 8.9990 chunk 657 optimal weight: 0.0040 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN W 36 GLN ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 125 GLN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5921 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 59164 Z= 0.153 Angle : 0.545 13.844 79905 Z= 0.292 Chirality : 0.040 0.282 9345 Planarity : 0.003 0.037 10262 Dihedral : 5.147 53.704 8335 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.51 % Allowed : 16.75 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.10), residues: 7469 helix: 2.64 (0.09), residues: 3465 sheet: -0.18 (0.13), residues: 1421 loop : -1.53 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP f 28 HIS 0.004 0.001 HIS I 28 PHE 0.010 0.001 PHE B 42 TYR 0.023 0.001 TYR 1 58 ARG 0.007 0.000 ARG M 70 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 814 time to evaluate : 5.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7628 (mttt) cc_final: 0.6803 (pttm) REVERT: B 35 SER cc_start: 0.6118 (p) cc_final: 0.5874 (t) REVERT: B 72 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7256 (t0) REVERT: B 182 GLU cc_start: 0.6654 (mp0) cc_final: 0.6382 (tt0) REVERT: D 182 GLU cc_start: 0.6592 (mp0) cc_final: 0.6073 (tt0) REVERT: E 179 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6746 (mt-10) REVERT: F 20 ARG cc_start: 0.6146 (ttp-170) cc_final: 0.5698 (ptm160) REVERT: F 179 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6589 (mt-10) REVERT: G 188 GLU cc_start: 0.6424 (tp30) cc_final: 0.6048 (mt-10) REVERT: G 220 LYS cc_start: 0.7644 (mttt) cc_final: 0.7305 (mtpp) REVERT: Z 62 GLU cc_start: 0.6054 (tp30) cc_final: 0.5708 (mt-10) REVERT: Z 182 ASP cc_start: 0.7366 (t0) cc_final: 0.6645 (m-30) REVERT: M 129 SER cc_start: 0.7772 (m) cc_final: 0.7443 (p) REVERT: 1 144 GLU cc_start: 0.7576 (tt0) cc_final: 0.7183 (mt-10) REVERT: 1 182 ASP cc_start: 0.7069 (t0) cc_final: 0.6314 (m-30) REVERT: N 59 MET cc_start: 0.6586 (mmp) cc_final: 0.6262 (mmm) REVERT: N 181 LYS cc_start: 0.7886 (tttm) cc_final: 0.7500 (mtmm) REVERT: 2 62 GLU cc_start: 0.6239 (tp30) cc_final: 0.5827 (mt-10) REVERT: 2 182 ASP cc_start: 0.7026 (t0) cc_final: 0.6324 (m-30) REVERT: H 129 SER cc_start: 0.7980 (m) cc_final: 0.7713 (p) REVERT: H 180 ARG cc_start: 0.8438 (tpt170) cc_final: 0.8226 (tpt170) REVERT: H 181 LYS cc_start: 0.7421 (tttm) cc_final: 0.6774 (mtmm) REVERT: V 43 MET cc_start: 0.7789 (ttm) cc_final: 0.7307 (ttm) REVERT: V 59 MET cc_start: 0.6363 (mmm) cc_final: 0.6106 (tpp) REVERT: V 62 GLU cc_start: 0.6171 (tp30) cc_final: 0.5883 (mt-10) REVERT: V 124 TYR cc_start: 0.8899 (p90) cc_final: 0.8667 (p90) REVERT: V 164 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6494 (mt0) REVERT: I 14 MET cc_start: 0.7240 (mtm) cc_final: 0.6766 (mtm) REVERT: I 27 MET cc_start: 0.7527 (ttt) cc_final: 0.7246 (ttp) REVERT: I 71 ARG cc_start: 0.6578 (mtt90) cc_final: 0.6197 (mtm-85) REVERT: I 164 GLN cc_start: 0.6689 (mm-40) cc_final: 0.6435 (mm-40) REVERT: I 180 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.7927 (tpp-160) REVERT: W 43 MET cc_start: 0.7822 (ttm) cc_final: 0.7546 (ttp) REVERT: W 59 MET cc_start: 0.6804 (mmm) cc_final: 0.6521 (tpp) REVERT: W 74 MET cc_start: 0.7921 (ttp) cc_final: 0.7596 (ttm) REVERT: W 144 GLU cc_start: 0.7788 (tt0) cc_final: 0.7255 (mt-10) REVERT: W 146 MET cc_start: 0.7884 (mtp) cc_final: 0.7670 (ptp) REVERT: W 164 GLN cc_start: 0.6589 (mt0) cc_final: 0.6088 (tt0) REVERT: J 129 SER cc_start: 0.7607 (m) cc_final: 0.7226 (p) REVERT: J 139 GLU cc_start: 0.6836 (tp30) cc_final: 0.6441 (tt0) REVERT: X 27 MET cc_start: 0.7770 (ttt) cc_final: 0.7454 (ttm) REVERT: X 40 TYR cc_start: 0.7583 (m-80) cc_final: 0.6889 (m-80) REVERT: X 62 GLU cc_start: 0.5722 (tp30) cc_final: 0.5377 (mm-30) REVERT: X 144 GLU cc_start: 0.7694 (tt0) cc_final: 0.7367 (mt-10) REVERT: X 180 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7878 (tpt170) REVERT: X 182 ASP cc_start: 0.6929 (t0) cc_final: 0.6229 (m-30) REVERT: K 14 MET cc_start: 0.7216 (mtt) cc_final: 0.6762 (mtt) REVERT: K 17 GLU cc_start: 0.5147 (pp20) cc_final: 0.4885 (pp20) REVERT: K 59 MET cc_start: 0.7027 (mmm) cc_final: 0.6732 (mmp) REVERT: K 129 SER cc_start: 0.7874 (m) cc_final: 0.7528 (p) REVERT: K 141 GLN cc_start: 0.7426 (mt0) cc_final: 0.7136 (mt0) REVERT: K 144 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: K 180 ARG cc_start: 0.8353 (tpt170) cc_final: 0.7895 (tpt170) REVERT: K 181 LYS cc_start: 0.7456 (tttm) cc_final: 0.7226 (tttm) REVERT: Y 32 LYS cc_start: 0.8238 (tttp) cc_final: 0.8002 (tttp) REVERT: Y 64 GLU cc_start: 0.7007 (tt0) cc_final: 0.6080 (tt0) REVERT: L 88 ASN cc_start: 0.7509 (t0) cc_final: 0.7258 (t0) REVERT: L 129 SER cc_start: 0.7956 (m) cc_final: 0.7598 (p) REVERT: O 29 GLU cc_start: 0.5662 (mm-30) cc_final: 0.5404 (mt-10) REVERT: O 40 MET cc_start: 0.7344 (ptp) cc_final: 0.7067 (ptm) REVERT: O 67 ILE cc_start: 0.6283 (tt) cc_final: 0.5931 (mt) REVERT: O 179 GLU cc_start: 0.8018 (tp30) cc_final: 0.7525 (tp30) REVERT: O 182 GLU cc_start: 0.8013 (pm20) cc_final: 0.7758 (pm20) REVERT: O 221 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.6884 (t80) REVERT: P 40 MET cc_start: 0.7590 (ptp) cc_final: 0.7260 (ptp) REVERT: P 65 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5570 (pt0) REVERT: P 177 GLU cc_start: 0.7400 (tp30) cc_final: 0.7181 (tp30) REVERT: P 182 GLU cc_start: 0.7579 (pm20) cc_final: 0.7220 (pt0) REVERT: P 220 LYS cc_start: 0.7979 (mttt) cc_final: 0.7708 (mttm) REVERT: P 221 TYR cc_start: 0.7328 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: Q 125 GLN cc_start: 0.8125 (tt0) cc_final: 0.7034 (tt0) REVERT: Q 177 GLU cc_start: 0.7261 (tp30) cc_final: 0.6695 (tp30) REVERT: Q 179 GLU cc_start: 0.7494 (tp30) cc_final: 0.7116 (tp30) REVERT: R 65 GLU cc_start: 0.6486 (mt-10) cc_final: 0.5734 (pt0) REVERT: R 182 GLU cc_start: 0.7755 (pm20) cc_final: 0.7257 (pt0) REVERT: S 220 LYS cc_start: 0.8077 (mttt) cc_final: 0.7815 (mttm) REVERT: S 223 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7458 (mm) REVERT: T 40 MET cc_start: 0.7219 (ptp) cc_final: 0.6829 (ptt) REVERT: T 65 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5635 (pt0) REVERT: T 122 GLN cc_start: 0.7488 (tt0) cc_final: 0.7097 (tt0) REVERT: T 182 GLU cc_start: 0.7913 (pm20) cc_final: 0.7335 (pt0) REVERT: T 221 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6706 (t80) REVERT: T 223 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7243 (mm) REVERT: U 65 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6114 (tt0) REVERT: U 67 ILE cc_start: 0.5862 (tt) cc_final: 0.5430 (mt) REVERT: U 157 ILE cc_start: 0.7526 (pt) cc_final: 0.7299 (mt) REVERT: U 182 GLU cc_start: 0.7922 (pm20) cc_final: 0.7429 (pt0) REVERT: a 27 GLU cc_start: 0.6126 (tp30) cc_final: 0.5430 (tp30) REVERT: a 103 ASP cc_start: 0.7436 (t0) cc_final: 0.7121 (t0) REVERT: b 27 GLU cc_start: 0.6116 (tp30) cc_final: 0.5806 (tp30) REVERT: c 18 GLU cc_start: 0.5755 (tm-30) cc_final: 0.5323 (tm-30) REVERT: c 27 GLU cc_start: 0.6269 (tp30) cc_final: 0.6068 (tp30) REVERT: c 101 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7764 (mm-30) REVERT: c 142 MET cc_start: 0.7530 (mmt) cc_final: 0.7036 (mpp) REVERT: d 27 GLU cc_start: 0.6080 (tp30) cc_final: 0.5826 (tp30) REVERT: d 98 GLU cc_start: 0.6696 (tt0) cc_final: 0.6464 (tt0) REVERT: e 27 GLU cc_start: 0.6131 (tp30) cc_final: 0.5573 (tp30) REVERT: e 51 ARG cc_start: 0.6175 (mtp180) cc_final: 0.5940 (ttp-170) REVERT: f 45 GLU cc_start: 0.6858 (tt0) cc_final: 0.6567 (mt-10) REVERT: f 51 ARG cc_start: 0.6392 (ttp80) cc_final: 0.5935 (mtp180) REVERT: g 27 GLU cc_start: 0.6129 (tp30) cc_final: 0.5789 (tp30) REVERT: g 62 LYS cc_start: 0.7828 (tttt) cc_final: 0.7167 (pptt) outliers start: 157 outliers final: 122 residues processed: 944 average time/residue: 0.5756 time to fit residues: 900.6833 Evaluate side-chains 885 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 756 time to evaluate : 4.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 200 SER Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 27 MET Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 164 GLN Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 433 optimal weight: 2.9990 chunk 698 optimal weight: 9.9990 chunk 426 optimal weight: 6.9990 chunk 331 optimal weight: 0.9980 chunk 485 optimal weight: 6.9990 chunk 732 optimal weight: 5.9990 chunk 673 optimal weight: 0.9980 chunk 583 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 450 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 88 ASN 2 164 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN W 36 GLN J 141 GLN X 164 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 59164 Z= 0.245 Angle : 0.593 12.627 79905 Z= 0.315 Chirality : 0.042 0.287 9345 Planarity : 0.004 0.037 10262 Dihedral : 5.280 54.520 8332 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.54 % Allowed : 17.18 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.10), residues: 7469 helix: 2.50 (0.09), residues: 3444 sheet: -0.03 (0.14), residues: 1379 loop : -1.51 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 216 HIS 0.008 0.001 HIS c 200 PHE 0.011 0.001 PHE G 42 TYR 0.017 0.001 TYR 1 58 ARG 0.007 0.000 ARG M 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14938 Ramachandran restraints generated. 7469 Oldfield, 0 Emsley, 7469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 820 time to evaluate : 5.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LYS cc_start: 0.7629 (mttt) cc_final: 0.6784 (pttm) REVERT: B 35 SER cc_start: 0.6177 (p) cc_final: 0.5921 (t) REVERT: B 72 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7249 (t0) REVERT: B 122 GLN cc_start: 0.6611 (mt0) cc_final: 0.6245 (tt0) REVERT: B 182 GLU cc_start: 0.6649 (mp0) cc_final: 0.6383 (tt0) REVERT: D 182 GLU cc_start: 0.6622 (mp0) cc_final: 0.6111 (tt0) REVERT: E 179 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6695 (mt-10) REVERT: F 123 TYR cc_start: 0.7583 (m-80) cc_final: 0.7372 (m-80) REVERT: F 179 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6519 (mt-10) REVERT: F 221 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5915 (t80) REVERT: G 186 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5563 (tp30) REVERT: G 188 GLU cc_start: 0.6453 (tp30) cc_final: 0.6048 (mt-10) REVERT: G 220 LYS cc_start: 0.7736 (mttt) cc_final: 0.7381 (mtpp) REVERT: Z 27 MET cc_start: 0.7338 (ttt) cc_final: 0.6894 (ttm) REVERT: Z 182 ASP cc_start: 0.7424 (t0) cc_final: 0.6723 (m-30) REVERT: M 129 SER cc_start: 0.7827 (m) cc_final: 0.7496 (p) REVERT: 1 182 ASP cc_start: 0.7051 (t0) cc_final: 0.6379 (m-30) REVERT: N 59 MET cc_start: 0.6851 (mmp) cc_final: 0.6538 (mmm) REVERT: N 181 LYS cc_start: 0.7902 (tttm) cc_final: 0.7574 (mtmm) REVERT: 2 62 GLU cc_start: 0.6299 (tp30) cc_final: 0.5856 (mt-10) REVERT: 2 182 ASP cc_start: 0.7042 (t0) cc_final: 0.6335 (m-30) REVERT: H 129 SER cc_start: 0.8220 (m) cc_final: 0.7973 (p) REVERT: H 180 ARG cc_start: 0.8405 (tpt170) cc_final: 0.8164 (tpt170) REVERT: V 43 MET cc_start: 0.7830 (ttm) cc_final: 0.7287 (ttm) REVERT: V 62 GLU cc_start: 0.6244 (tp30) cc_final: 0.5924 (mt-10) REVERT: V 124 TYR cc_start: 0.8949 (p90) cc_final: 0.8723 (p90) REVERT: V 164 GLN cc_start: 0.6681 (mm-40) cc_final: 0.6451 (mt0) REVERT: I 14 MET cc_start: 0.7255 (mtm) cc_final: 0.6769 (mtm) REVERT: I 27 MET cc_start: 0.7847 (ttt) cc_final: 0.7479 (ttp) REVERT: I 71 ARG cc_start: 0.6645 (mtt90) cc_final: 0.6347 (mtm-85) REVERT: I 180 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.7868 (tpp-160) REVERT: W 43 MET cc_start: 0.7863 (ttm) cc_final: 0.7643 (ttp) REVERT: W 164 GLN cc_start: 0.6617 (mt0) cc_final: 0.6089 (tt0) REVERT: J 27 MET cc_start: 0.7712 (ttt) cc_final: 0.7509 (ttt) REVERT: J 129 SER cc_start: 0.7670 (m) cc_final: 0.7329 (p) REVERT: J 139 GLU cc_start: 0.7072 (tp30) cc_final: 0.6559 (tt0) REVERT: J 141 GLN cc_start: 0.7628 (mt0) cc_final: 0.7320 (mt0) REVERT: X 27 MET cc_start: 0.7820 (ttt) cc_final: 0.7542 (ttt) REVERT: X 40 TYR cc_start: 0.7599 (m-80) cc_final: 0.6700 (m-80) REVERT: X 62 GLU cc_start: 0.5845 (tp30) cc_final: 0.5163 (mt-10) REVERT: X 180 ARG cc_start: 0.8309 (tpt170) cc_final: 0.7792 (tpt170) REVERT: K 14 MET cc_start: 0.7329 (mtt) cc_final: 0.6867 (mtt) REVERT: K 129 SER cc_start: 0.8078 (m) cc_final: 0.7773 (p) REVERT: K 141 GLN cc_start: 0.7516 (mt0) cc_final: 0.7125 (mt0) REVERT: K 144 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: K 180 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7947 (tpt170) REVERT: K 181 LYS cc_start: 0.7492 (tttm) cc_final: 0.7246 (tttm) REVERT: Y 32 LYS cc_start: 0.8201 (tttp) cc_final: 0.7975 (tttp) REVERT: Y 64 GLU cc_start: 0.7194 (tt0) cc_final: 0.6235 (tt0) REVERT: L 129 SER cc_start: 0.7913 (m) cc_final: 0.7559 (p) REVERT: O 29 GLU cc_start: 0.5709 (mm-30) cc_final: 0.5425 (mt-10) REVERT: O 40 MET cc_start: 0.7503 (ptp) cc_final: 0.7186 (ptm) REVERT: O 179 GLU cc_start: 0.7944 (tp30) cc_final: 0.7381 (tp30) REVERT: O 182 GLU cc_start: 0.7994 (pm20) cc_final: 0.7745 (pm20) REVERT: O 221 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.6862 (t80) REVERT: O 230 LYS cc_start: 0.7277 (ttpt) cc_final: 0.7001 (mttp) REVERT: P 40 MET cc_start: 0.7618 (ptp) cc_final: 0.7165 (ptp) REVERT: P 65 GLU cc_start: 0.6513 (mt-10) cc_final: 0.6065 (pt0) REVERT: P 182 GLU cc_start: 0.7616 (pm20) cc_final: 0.7242 (pt0) REVERT: P 220 LYS cc_start: 0.8020 (mttt) cc_final: 0.7720 (mttm) REVERT: P 221 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7055 (m-80) REVERT: Q 122 GLN cc_start: 0.7705 (tt0) cc_final: 0.7318 (tt0) REVERT: Q 125 GLN cc_start: 0.8203 (tt0) cc_final: 0.7522 (tt0) REVERT: R 40 MET cc_start: 0.7496 (ptt) cc_final: 0.7036 (ptm) REVERT: R 65 GLU cc_start: 0.6648 (mt-10) cc_final: 0.5922 (pt0) REVERT: R 122 GLN cc_start: 0.7377 (tt0) cc_final: 0.7096 (tt0) REVERT: R 182 GLU cc_start: 0.7777 (pm20) cc_final: 0.7315 (pt0) REVERT: S 126 TYR cc_start: 0.8339 (m-10) cc_final: 0.7868 (m-80) REVERT: S 181 LYS cc_start: 0.6865 (mtmt) cc_final: 0.6617 (mtmm) REVERT: S 220 LYS cc_start: 0.8146 (mttt) cc_final: 0.7873 (mttm) REVERT: S 223 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7336 (mm) REVERT: S 230 LYS cc_start: 0.7067 (ttpt) cc_final: 0.6790 (mttt) REVERT: T 65 GLU cc_start: 0.6279 (mt-10) cc_final: 0.5672 (pt0) REVERT: T 122 GLN cc_start: 0.7560 (tt0) cc_final: 0.7202 (tt0) REVERT: T 182 GLU cc_start: 0.7939 (pm20) cc_final: 0.7381 (pt0) REVERT: T 221 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.6712 (t80) REVERT: T 223 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7373 (mm) REVERT: U 65 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6188 (tt0) REVERT: U 182 GLU cc_start: 0.8153 (pm20) cc_final: 0.7780 (pt0) REVERT: U 230 LYS cc_start: 0.7095 (ttpt) cc_final: 0.6650 (mmmt) REVERT: a 27 GLU cc_start: 0.6241 (tp30) cc_final: 0.5509 (tp30) REVERT: a 57 ARG cc_start: 0.6618 (tpp-160) cc_final: 0.6250 (mmm-85) REVERT: a 121 GLU cc_start: 0.5254 (pt0) cc_final: 0.4923 (pt0) REVERT: b 27 GLU cc_start: 0.6226 (tp30) cc_final: 0.5898 (tp30) REVERT: c 18 GLU cc_start: 0.5891 (tm-30) cc_final: 0.5661 (tm-30) REVERT: c 27 GLU cc_start: 0.6255 (tp30) cc_final: 0.6043 (tp30) REVERT: c 101 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7774 (mm-30) REVERT: d 27 GLU cc_start: 0.6072 (tp30) cc_final: 0.5826 (tp30) REVERT: d 98 GLU cc_start: 0.6707 (tt0) cc_final: 0.6461 (tt0) REVERT: e 27 GLU cc_start: 0.6255 (tp30) cc_final: 0.5653 (tp30) REVERT: e 51 ARG cc_start: 0.6528 (mtp180) cc_final: 0.6274 (ttp-170) REVERT: e 57 ARG cc_start: 0.6551 (ttm110) cc_final: 0.5924 (ttp80) REVERT: f 45 GLU cc_start: 0.6883 (tt0) cc_final: 0.6593 (mt-10) REVERT: f 51 ARG cc_start: 0.6456 (ttp80) cc_final: 0.5963 (mtp180) REVERT: g 27 GLU cc_start: 0.6165 (tp30) cc_final: 0.5803 (tp30) outliers start: 159 outliers final: 130 residues processed: 942 average time/residue: 0.5773 time to fit residues: 899.0973 Evaluate side-chains 927 residues out of total 6258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 788 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 221 TYR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 215 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 221 TYR Chi-restraints excluded: chain Z residue 12 VAL Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 23 GLU Chi-restraints excluded: chain M residue 72 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 178 ILE Chi-restraints excluded: chain 1 residue 185 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 185 VAL Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 140 SER Chi-restraints excluded: chain 2 residue 178 ILE Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 140 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 178 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain I residue 7 THR Chi-restraints excluded: chain I residue 23 GLU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain I residue 179 THR Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 134 VAL Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 43 MET Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 140 SER Chi-restraints excluded: chain X residue 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 144 GLU Chi-restraints excluded: chain K residue 164 GLN Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 178 ILE Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain Y residue 185 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 172 MET Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 463 optimal weight: 2.9990 chunk 621 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 537 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 584 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 599 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 164 GLN ** H 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 ASN ** V 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 ASN T 44 ASN U 44 ASN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.161324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128528 restraints weight = 60996.006| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.11 r_work: 0.3313 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 59164 Z= 0.215 Angle : 0.577 14.939 79905 Z= 0.307 Chirality : 0.041 0.232 9345 Planarity : 0.003 0.037 10262 Dihedral : 5.245 54.405 8332 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.56 % Allowed : 17.32 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.99 (0.10), residues: 7469 helix: 2.50 (0.09), residues: 3465 sheet: -0.13 (0.13), residues: 1421 loop : -1.53 (0.11), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP a 216 HIS 0.006 0.001 HIS 1 28 PHE 0.011 0.001 PHE G 42 TYR 0.015 0.001 TYR 2 58 ARG 0.007 0.000 ARG M 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15294.86 seconds wall clock time: 268 minutes 15.98 seconds (16095.98 seconds total)