Starting phenix.real_space_refine on Sat Jan 18 09:52:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_20879.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_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/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_20879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_20879.map" model { file = "/net/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_20879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uth_20879/01_2025/6uth_20879.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 24.53, per 1000 atoms: 0.42 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 6.1 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: 5.69 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: 29.84 Time building geometry restraints manager: 13.22 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: 0.00 - 3.44: 78272 3.44 - 6.89: 1479 6.89 - 10.33: 124 10.33 - 13.78: 9 13.78 - 17.22: 21 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 3.040 nonbonded pdb=" OG1 THR L 21 " pdb=" O GLU L 23 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR Z 21 " pdb=" O GLU Z 23 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR K 21 " pdb=" O GLU K 23 " model vdw 2.199 3.040 nonbonded pdb=" OG1 THR J 21 " pdb=" O GLU J 23 " model vdw 2.199 3.040 ... (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 Time spend for trying shortcut: 0.39 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } ncs_group { reference = chain '1' selection = chain '2' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 1.910 Check model and map are aligned: 0.350 Set scattering table: 0.440 Process input model: 110.660 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.310 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 42 poor density : 1343 time to evaluate : 5.004 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: 0.6092 time to fit residues: 1352.5748 Evaluate side-chains 956 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 924 time to evaluate : 4.886 ------------------------------------------------------------------------------- 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: 1.9990 chunk 557 optimal weight: 0.9990 chunk 309 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 375 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 576 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 chunk 428 optimal weight: 0.9990 chunk 667 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 D 23 GLN E 23 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN G 23 GLN G 98 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN N 164 GLN V 88 ASN I 30 ASN W 88 ASN K 164 GLN Y 88 ASN O 68 GLN O 98 GLN P 68 GLN Q 68 GLN ** Q 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 GLN R 125 GLN S 68 GLN T 68 GLN 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 ** c 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 g 111 HIS ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 200 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132764 restraints weight = 59533.081| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.32 r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 59164 Z= 0.231 Angle : 0.647 12.737 79905 Z= 0.352 Chirality : 0.043 0.218 9345 Planarity : 0.005 0.063 10262 Dihedral : 6.863 62.771 8372 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.13 % Favored : 96.73 % Rotamer: Outliers : 2.92 % Allowed : 9.94 % Favored : 87.14 % 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: -0.83 (0.09), residues: 7469 helix: 0.99 (0.08), residues: 3437 sheet: -1.28 (0.12), residues: 1407 loop : -2.18 (0.10), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 28 HIS 0.007 0.002 HIS Y 109 PHE 0.015 0.002 PHE D 42 TYR 0.030 0.002 TYR D 8 ARG 0.009 0.001 ARG J 70 *********************** 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 1225 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1042 time to evaluate : 5.000 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: A 144 ILE cc_start: 0.8769 (mm) cc_final: 0.8567 (mt) REVERT: A 223 ILE cc_start: 0.8815 (mt) cc_final: 0.8596 (mt) REVERT: B 35 SER cc_start: 0.7569 (p) cc_final: 0.7226 (t) REVERT: B 72 ASP cc_start: 0.8065 (m-30) cc_final: 0.7837 (t0) REVERT: B 98 GLN cc_start: 0.7703 (mm-40) cc_final: 0.6848 (mt0) REVERT: B 122 GLN cc_start: 0.8228 (mt0) cc_final: 0.7716 (tt0) REVERT: B 167 SER cc_start: 0.8826 (t) cc_final: 0.8443 (p) REVERT: B 188 GLU cc_start: 0.7762 (tp30) cc_final: 0.7521 (tp30) REVERT: C 98 GLN cc_start: 0.7737 (mm-40) cc_final: 0.6910 (mt0) REVERT: C 186 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6372 (mm-30) REVERT: C 195 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7621 (mtmt) REVERT: C 220 LYS cc_start: 0.9071 (mttt) cc_final: 0.8662 (mtpp) REVERT: C 223 ILE cc_start: 0.8806 (mt) cc_final: 0.8601 (mt) REVERT: D 35 SER cc_start: 0.7849 (p) cc_final: 0.7554 (t) REVERT: D 49 ILE cc_start: 0.8471 (tt) cc_final: 0.8235 (mt) REVERT: D 98 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7305 (tt0) REVERT: D 182 GLU cc_start: 0.6923 (mp0) cc_final: 0.6526 (tt0) REVERT: D 220 LYS cc_start: 0.9062 (mttt) cc_final: 0.8656 (mtpp) REVERT: E 35 SER cc_start: 0.7970 (p) cc_final: 0.7558 (t) REVERT: E 98 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7386 (mt0) REVERT: E 231 LYS cc_start: 0.7879 (mttp) cc_final: 0.7071 (ttpt) REVERT: F 40 MET cc_start: 0.8827 (ptp) cc_final: 0.8419 (ptp) REVERT: F 98 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7215 (mt0) REVERT: F 120 MET cc_start: 0.8605 (mtp) cc_final: 0.8377 (mtp) REVERT: F 123 TYR cc_start: 0.9014 (m-80) cc_final: 0.8770 (m-80) REVERT: F 161 LYS cc_start: 0.7556 (mttm) cc_final: 0.7237 (mtmm) REVERT: F 182 GLU cc_start: 0.6955 (mp0) cc_final: 0.6269 (tt0) REVERT: F 188 GLU cc_start: 0.7571 (tp30) cc_final: 0.7368 (tp30) REVERT: F 220 LYS cc_start: 0.8947 (mttt) cc_final: 0.8601 (mtpt) REVERT: G 40 MET cc_start: 0.8581 (ptm) cc_final: 0.8317 (ptp) REVERT: G 98 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7240 (mt0) REVERT: G 109 ILE cc_start: 0.8357 (tt) cc_final: 0.8130 (mp) REVERT: G 220 LYS cc_start: 0.8972 (mttt) cc_final: 0.8603 (mtpp) REVERT: Z 172 MET cc_start: 0.8630 (tpt) cc_final: 0.8422 (tpp) REVERT: M 71 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7528 (mtm-85) REVERT: M 181 LYS cc_start: 0.8624 (tttm) cc_final: 0.8421 (mtmm) REVERT: 1 32 LYS cc_start: 0.8873 (tttp) cc_final: 0.8367 (tttp) REVERT: 1 74 MET cc_start: 0.8675 (ttp) cc_final: 0.8364 (ttm) REVERT: N 59 MET cc_start: 0.8710 (mmm) cc_final: 0.8347 (tpp) REVERT: N 181 LYS cc_start: 0.8471 (tttm) cc_final: 0.8098 (mtmm) REVERT: 2 21 THR cc_start: 0.6464 (OUTLIER) cc_final: 0.6209 (t) REVERT: V 9 LYS cc_start: 0.8352 (mttt) cc_final: 0.8098 (tptp) REVERT: V 21 THR cc_start: 0.6583 (OUTLIER) cc_final: 0.6359 (t) REVERT: V 27 MET cc_start: 0.8491 (ttt) cc_final: 0.8226 (ttt) REVERT: I 14 MET cc_start: 0.8780 (mtm) cc_final: 0.8371 (mtt) REVERT: I 27 MET cc_start: 0.8640 (ttt) cc_final: 0.8292 (ttp) REVERT: I 84 SER cc_start: 0.8838 (m) cc_final: 0.8311 (t) REVERT: I 127 THR cc_start: 0.8852 (p) cc_final: 0.8544 (p) REVERT: I 164 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7895 (mm-40) REVERT: W 164 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7958 (mt0) REVERT: J 27 MET cc_start: 0.8447 (ttt) cc_final: 0.8106 (ttt) REVERT: J 43 MET cc_start: 0.9156 (ttm) cc_final: 0.8907 (ttp) REVERT: J 98 GLN cc_start: 0.8758 (mt0) cc_final: 0.8529 (mt0) REVERT: J 164 GLN cc_start: 0.8166 (mp10) cc_final: 0.7824 (mp10) REVERT: J 180 ARG cc_start: 0.8969 (tpt170) cc_final: 0.8767 (tpp-160) REVERT: J 181 LYS cc_start: 0.8671 (tttm) cc_final: 0.8465 (mtmm) REVERT: J 182 ASP cc_start: 0.7923 (m-30) cc_final: 0.7635 (m-30) REVERT: X 40 TYR cc_start: 0.8510 (m-80) cc_final: 0.8305 (m-80) REVERT: X 180 ARG cc_start: 0.8880 (tpt170) cc_final: 0.8641 (tpt170) REVERT: K 14 MET cc_start: 0.8674 (mtp) cc_final: 0.8467 (mtt) REVERT: K 141 GLN cc_start: 0.8969 (mt0) cc_final: 0.8766 (mt0) REVERT: K 180 ARG cc_start: 0.9037 (tpt170) cc_final: 0.8632 (tpt170) REVERT: K 181 LYS cc_start: 0.8379 (tttm) cc_final: 0.8086 (tttm) REVERT: O 20 ARG cc_start: 0.8791 (mtp180) cc_final: 0.8572 (mtp-110) REVERT: O 40 MET cc_start: 0.8837 (ptp) cc_final: 0.8608 (ptm) REVERT: O 64 ILE cc_start: 0.7894 (pt) cc_final: 0.7620 (pt) REVERT: O 120 MET cc_start: 0.9047 (mtp) cc_final: 0.8714 (mtm) REVERT: O 182 GLU cc_start: 0.7929 (pm20) cc_final: 0.7358 (pt0) REVERT: P 40 MET cc_start: 0.8879 (ptp) cc_final: 0.8635 (ptp) REVERT: P 65 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6802 (pt0) REVERT: P 99 GLU cc_start: 0.7498 (tp30) cc_final: 0.7272 (tt0) REVERT: Q 99 GLU cc_start: 0.7718 (tp30) cc_final: 0.7417 (tt0) REVERT: Q 122 GLN cc_start: 0.8856 (tt0) cc_final: 0.8626 (tt0) REVERT: Q 177 GLU cc_start: 0.7773 (tp30) cc_final: 0.7168 (tp30) REVERT: R 40 MET cc_start: 0.8843 (ptp) cc_final: 0.8435 (ptm) REVERT: R 60 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8372 (mm-30) REVERT: R 122 GLN cc_start: 0.8873 (tt0) cc_final: 0.8599 (tt0) REVERT: R 182 GLU cc_start: 0.7720 (pm20) cc_final: 0.7266 (pt0) REVERT: T 122 GLN cc_start: 0.8883 (tt0) cc_final: 0.8523 (tt0) REVERT: T 177 GLU cc_start: 0.7969 (tp30) cc_final: 0.7316 (tp30) REVERT: T 182 GLU cc_start: 0.7673 (pm20) cc_final: 0.7111 (pt0) REVERT: T 220 LYS cc_start: 0.8761 (mttt) cc_final: 0.8497 (mtpm) REVERT: U 40 MET cc_start: 0.8941 (ptp) cc_final: 0.8662 (ptp) REVERT: U 65 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7412 (mt-10) REVERT: U 99 GLU cc_start: 0.7833 (tp30) cc_final: 0.7543 (tt0) REVERT: a 27 GLU cc_start: 0.7948 (tp30) cc_final: 0.7604 (tp30) REVERT: a 37 GLU cc_start: 0.8267 (tt0) cc_final: 0.7841 (mt-10) REVERT: a 39 ILE cc_start: 0.8588 (mt) cc_final: 0.8312 (mt) REVERT: c 142 MET cc_start: 0.7859 (mmt) cc_final: 0.7554 (mpp) REVERT: d 16 TYR cc_start: 0.8425 (m-80) cc_final: 0.8152 (m-80) REVERT: d 39 ILE cc_start: 0.8472 (mt) cc_final: 0.8151 (mt) REVERT: d 121 GLU cc_start: 0.7776 (pt0) cc_final: 0.7496 (pt0) REVERT: e 27 GLU cc_start: 0.7959 (tp30) cc_final: 0.7498 (tp30) REVERT: f 39 ILE cc_start: 0.8387 (mt) cc_final: 0.8033 (mt) REVERT: g 39 ILE cc_start: 0.8334 (mt) cc_final: 0.8071 (mt) REVERT: g 41 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7870 (mtmm) REVERT: g 142 MET cc_start: 0.8271 (mmm) cc_final: 0.7934 (mpp) REVERT: g 191 MET cc_start: 0.8464 (mmp) cc_final: 0.8231 (mmt) REVERT: g 232 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.6830 (ttp-170) outliers start: 183 outliers final: 80 residues processed: 1179 average time/residue: 0.5900 time to fit residues: 1141.6294 Evaluate side-chains 911 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 827 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 77 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 200 SER 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 137 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 41 THR Chi-restraints excluded: chain M residue 44 THR 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 178 ILE Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 41 THR 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 41 THR Chi-restraints excluded: chain H residue 135 TYR Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain V residue 21 THR 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 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 23 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 72 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 41 THR Chi-restraints excluded: chain Y residue 178 ILE Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain U residue 38 LEU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 393 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 525 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 418 optimal weight: 5.9990 chunk 539 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 535 optimal weight: 5.9990 chunk 641 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 69 GLN Z 73 ASN Z 164 GLN 1 36 GLN 1 88 ASN 1 164 GLN N 141 GLN ** 2 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 GLN V 73 ASN V 88 ASN I 30 ASN ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 141 GLN X 88 ASN X 141 GLN K 85 ASN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN L 141 GLN L 164 GLN O 219 ASN S 98 GLN S 158 ASN T 98 GLN c 200 HIS f 200 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.163014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130831 restraints weight = 63246.733| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.08 r_work: 0.3248 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 59164 Z= 0.490 Angle : 0.779 13.502 79905 Z= 0.414 Chirality : 0.048 0.233 9345 Planarity : 0.005 0.093 10262 Dihedral : 6.405 57.857 8335 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 4.47 % Allowed : 12.22 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: -0.42 (0.09), residues: 7469 helix: 1.28 (0.09), residues: 3416 sheet: -1.06 (0.12), residues: 1442 loop : -1.89 (0.10), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 216 HIS 0.008 0.002 HIS Z 28 PHE 0.023 0.003 PHE F 138 TYR 0.025 0.003 TYR B 8 ARG 0.017 0.001 ARG J 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 1153 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 873 time to evaluate : 5.134 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 122 GLN cc_start: 0.8391 (tt0) cc_final: 0.8183 (tt0) REVERT: A 123 TYR cc_start: 0.9277 (m-80) cc_final: 0.8946 (m-80) REVERT: B 122 GLN cc_start: 0.8201 (mt0) cc_final: 0.7809 (tt0) REVERT: C 216 THR cc_start: 0.8633 (m) cc_final: 0.8323 (p) REVERT: C 220 LYS cc_start: 0.8978 (mttt) cc_final: 0.8753 (mttp) REVERT: D 35 SER cc_start: 0.8148 (p) cc_final: 0.7840 (t) REVERT: D 49 ILE cc_start: 0.8515 (tt) cc_final: 0.8258 (mt) REVERT: D 200 SER cc_start: 0.8078 (p) cc_final: 0.7785 (m) REVERT: D 221 TYR cc_start: 0.8373 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: E 105 SER cc_start: 0.8687 (p) cc_final: 0.8399 (t) REVERT: E 178 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.8189 (ttp80) REVERT: F 40 MET cc_start: 0.9010 (ptp) cc_final: 0.8654 (ptp) REVERT: F 160 TYR cc_start: 0.9003 (m-80) cc_final: 0.8764 (m-80) REVERT: G 186 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7093 (tp30) REVERT: G 220 LYS cc_start: 0.8787 (mttt) cc_final: 0.8404 (mtpp) REVERT: Z 38 ASP cc_start: 0.8620 (t0) cc_final: 0.8310 (t0) REVERT: Z 114 ASP cc_start: 0.8168 (p0) cc_final: 0.7913 (p0) REVERT: Z 182 ASP cc_start: 0.7919 (t0) cc_final: 0.7607 (m-30) REVERT: M 4 VAL cc_start: 0.9167 (p) cc_final: 0.8887 (t) REVERT: M 93 MET cc_start: 0.7619 (mmm) cc_final: 0.6793 (mpp) REVERT: N 96 MET cc_start: 0.8585 (mtm) cc_final: 0.8285 (mtt) REVERT: N 181 LYS cc_start: 0.8501 (tttm) cc_final: 0.8291 (tttm) REVERT: 2 21 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6473 (t) REVERT: 2 38 ASP cc_start: 0.8723 (t0) cc_final: 0.8424 (t0) REVERT: H 122 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: V 27 MET cc_start: 0.8725 (ttt) cc_final: 0.8427 (ttt) REVERT: V 29 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8801 (mtmm) REVERT: V 30 ASN cc_start: 0.8698 (t0) cc_final: 0.8411 (t0) REVERT: V 182 ASP cc_start: 0.7969 (m-30) cc_final: 0.7724 (m-30) REVERT: I 27 MET cc_start: 0.8684 (ttt) cc_final: 0.8468 (ttp) REVERT: I 30 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8254 (t0) REVERT: I 71 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7253 (mtt90) REVERT: W 59 MET cc_start: 0.8812 (mmm) cc_final: 0.8413 (mmm) REVERT: W 203 LEU cc_start: 0.2119 (OUTLIER) cc_final: 0.1876 (pp) REVERT: J 27 MET cc_start: 0.8512 (ttt) cc_final: 0.8277 (ttt) REVERT: J 43 MET cc_start: 0.9027 (ttm) cc_final: 0.8826 (ttp) REVERT: J 59 MET cc_start: 0.8893 (mmm) cc_final: 0.8406 (mmm) REVERT: J 93 MET cc_start: 0.7902 (mtm) cc_final: 0.7683 (mtt) REVERT: J 164 GLN cc_start: 0.8145 (mp10) cc_final: 0.7803 (mp10) REVERT: J 203 LEU cc_start: 0.2379 (OUTLIER) cc_final: 0.2177 (tm) REVERT: X 40 TYR cc_start: 0.8659 (m-80) cc_final: 0.8193 (m-80) REVERT: K 17 GLU cc_start: 0.7559 (pp20) cc_final: 0.6728 (pp20) REVERT: K 122 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: K 180 ARG cc_start: 0.9120 (tpt170) cc_final: 0.8767 (tpt170) REVERT: K 181 LYS cc_start: 0.8329 (tttm) cc_final: 0.8071 (tttm) REVERT: Y 110 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8676 (t) REVERT: Y 180 ARG cc_start: 0.9103 (tpt90) cc_final: 0.8892 (tpt170) REVERT: Y 182 ASP cc_start: 0.8010 (t0) cc_final: 0.7514 (m-30) REVERT: L 122 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: O 40 MET cc_start: 0.9052 (ptp) cc_final: 0.8842 (ptp) REVERT: O 99 GLU cc_start: 0.7656 (tt0) cc_final: 0.7225 (tt0) REVERT: O 105 SER cc_start: 0.9020 (p) cc_final: 0.8634 (m) REVERT: O 114 LYS cc_start: 0.7673 (tppt) cc_final: 0.7283 (ttpt) REVERT: O 179 GLU cc_start: 0.8601 (tp30) cc_final: 0.8332 (tp30) REVERT: O 182 GLU cc_start: 0.7939 (pm20) cc_final: 0.7583 (pt0) REVERT: P 40 MET cc_start: 0.9051 (ptp) cc_final: 0.8810 (ptp) REVERT: P 114 LYS cc_start: 0.7536 (tppt) cc_final: 0.7095 (tttm) REVERT: P 182 GLU cc_start: 0.7956 (pm20) cc_final: 0.7720 (pt0) REVERT: Q 105 SER cc_start: 0.8966 (p) cc_final: 0.8644 (m) REVERT: Q 114 LYS cc_start: 0.7503 (tppt) cc_final: 0.7052 (tttm) REVERT: Q 122 GLN cc_start: 0.8868 (tt0) cc_final: 0.8616 (tt0) REVERT: R 114 LYS cc_start: 0.7339 (tppt) cc_final: 0.6975 (tttm) REVERT: R 122 GLN cc_start: 0.8815 (tt0) cc_final: 0.8493 (tt0) REVERT: R 182 GLU cc_start: 0.8000 (pm20) cc_final: 0.7775 (pt0) REVERT: S 40 MET cc_start: 0.9036 (ptp) cc_final: 0.8750 (ptp) REVERT: S 114 LYS cc_start: 0.7668 (tppt) cc_final: 0.7173 (ttpt) REVERT: S 223 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8420 (mm) REVERT: T 122 GLN cc_start: 0.8844 (tt0) cc_final: 0.8362 (tt0) REVERT: T 177 GLU cc_start: 0.8329 (tp30) cc_final: 0.7574 (tp30) REVERT: U 40 MET cc_start: 0.9086 (ptp) cc_final: 0.8788 (ptp) REVERT: U 65 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7258 (tt0) REVERT: U 114 LYS cc_start: 0.7709 (tppt) cc_final: 0.7251 (tttp) REVERT: U 182 GLU cc_start: 0.8152 (pm20) cc_final: 0.7800 (pt0) REVERT: a 27 GLU cc_start: 0.8424 (tp30) cc_final: 0.8042 (tp30) REVERT: b 27 GLU cc_start: 0.8277 (tp30) cc_final: 0.7727 (tp30) REVERT: c 27 GLU cc_start: 0.8441 (tp30) cc_final: 0.8151 (tp30) REVERT: e 27 GLU cc_start: 0.8301 (tp30) cc_final: 0.7689 (tp30) REVERT: e 57 ARG cc_start: 0.7946 (ttm110) cc_final: 0.6993 (ttp80) REVERT: e 217 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8530 (mttt) REVERT: f 45 GLU cc_start: 0.8104 (tt0) cc_final: 0.7806 (mt-10) REVERT: g 142 MET cc_start: 0.8322 (mmm) cc_final: 0.8110 (mmm) outliers start: 280 outliers final: 196 residues processed: 1107 average time/residue: 0.5990 time to fit residues: 1093.3050 Evaluate side-chains 971 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 764 time to evaluate : 5.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 38 LEU 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 212 ILE 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 79 SER Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE 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 74 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 214 SER 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 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 67 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 79 SER 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 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 79 SER 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 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 110 VAL Chi-restraints excluded: chain Z residue 140 SER Chi-restraints excluded: chain Z residue 173 ILE Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU 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 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 110 VAL Chi-restraints excluded: chain 1 residue 129 SER 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 41 THR Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 122 ASP 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 21 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 110 VAL 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 101 VAL Chi-restraints excluded: chain H residue 122 ASP 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 41 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 110 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 7 THR Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 110 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 185 VAL 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 110 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 W residue 203 LEU 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 110 VAL 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 J residue 203 LEU Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 110 VAL 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 93 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 167 SER 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 110 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 41 THR Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 122 ASP 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 38 LEU Chi-restraints excluded: chain O residue 102 THR Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 211 GLU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 38 LEU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain b residue 91 VAL Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 49 THR Chi-restraints excluded: chain c residue 230 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 122 ILE Chi-restraints excluded: chain d residue 230 LEU Chi-restraints excluded: chain e residue 49 THR Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 49 THR Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 140 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 453 optimal weight: 5.9990 chunk 463 optimal weight: 0.8980 chunk 235 optimal weight: 0.6980 chunk 537 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 690 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 chunk 250 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 468 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** ** 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** 1 141 GLN N 30 ASN 2 88 ASN 2 164 GLN H 141 GLN W 88 ASN W 141 GLN W 164 GLN Y 164 GLN L 141 GLN L 164 GLN S 98 GLN ** a 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 185 GLN b 200 HIS ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.154610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120118 restraints weight = 60543.725| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.28 r_work: 0.3195 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 59164 Z= 0.164 Angle : 0.592 12.434 79905 Z= 0.318 Chirality : 0.042 0.200 9345 Planarity : 0.004 0.039 10262 Dihedral : 5.563 54.437 8332 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer: Outliers : 3.44 % Allowed : 14.48 % Favored : 82.09 % 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: 0.30 (0.10), residues: 7469 helix: 1.99 (0.09), residues: 3444 sheet: -0.79 (0.13), residues: 1449 loop : -1.72 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP b 216 HIS 0.007 0.001 HIS W 28 PHE 0.013 0.001 PHE V 111 TYR 0.022 0.001 TYR 2 66 ARG 0.005 0.000 ARG U 20 *********************** 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 1044 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 829 time to evaluate : 5.027 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: A 122 GLN cc_start: 0.8278 (tt0) cc_final: 0.8078 (tt0) REVERT: B 35 SER cc_start: 0.7735 (p) cc_final: 0.7456 (t) REVERT: B 98 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7183 (tt0) REVERT: B 122 GLN cc_start: 0.8068 (mt0) cc_final: 0.7654 (tt0) REVERT: B 167 SER cc_start: 0.8798 (t) cc_final: 0.8438 (p) REVERT: C 98 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7245 (mm-40) REVERT: D 98 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7279 (tt0) REVERT: D 200 SER cc_start: 0.7988 (p) cc_final: 0.7766 (m) REVERT: D 221 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: E 74 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8344 (t) REVERT: E 98 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7223 (tt0) REVERT: E 109 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7912 (mp) REVERT: E 178 ARG cc_start: 0.8384 (ttp-110) cc_final: 0.8170 (ttp80) REVERT: F 40 MET cc_start: 0.8843 (ptp) cc_final: 0.8512 (ptp) REVERT: F 74 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8326 (t) REVERT: G 98 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7451 (mm110) REVERT: G 220 LYS cc_start: 0.8861 (mttt) cc_final: 0.8514 (mtpp) REVERT: Z 27 MET cc_start: 0.8675 (ttt) cc_final: 0.8338 (ttm) REVERT: Z 114 ASP cc_start: 0.8298 (p0) cc_final: 0.8066 (p0) REVERT: Z 182 ASP cc_start: 0.8160 (t0) cc_final: 0.7689 (m-30) REVERT: M 93 MET cc_start: 0.7579 (mmm) cc_final: 0.6486 (mpp) REVERT: 1 182 ASP cc_start: 0.7668 (t0) cc_final: 0.7197 (m-30) REVERT: N 181 LYS cc_start: 0.8399 (tttm) cc_final: 0.8170 (mtmm) REVERT: 2 21 THR cc_start: 0.6398 (OUTLIER) cc_final: 0.6178 (t) REVERT: 2 164 GLN cc_start: 0.7895 (mt0) cc_final: 0.7494 (tt0) REVERT: V 27 MET cc_start: 0.8474 (ttt) cc_final: 0.8249 (ttt) REVERT: I 8 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7751 (mp) REVERT: I 27 MET cc_start: 0.8713 (ttt) cc_final: 0.8419 (ttp) REVERT: I 70 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8468 (mmt180) REVERT: I 71 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7426 (mtt90) REVERT: I 164 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7512 (mp10) REVERT: W 59 MET cc_start: 0.8725 (mmm) cc_final: 0.8362 (mmm) REVERT: W 93 MET cc_start: 0.7619 (mmm) cc_final: 0.7174 (mmp) REVERT: J 27 MET cc_start: 0.8711 (ttt) cc_final: 0.8326 (ttp) REVERT: J 59 MET cc_start: 0.8857 (mmm) cc_final: 0.8386 (mmm) REVERT: X 40 TYR cc_start: 0.8591 (m-80) cc_final: 0.8156 (m-80) REVERT: K 180 ARG cc_start: 0.9060 (tpt170) cc_final: 0.8579 (tpt170) REVERT: K 181 LYS cc_start: 0.8299 (tttm) cc_final: 0.8059 (tttm) REVERT: L 43 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8963 (ttt) REVERT: O 99 GLU cc_start: 0.7936 (tt0) cc_final: 0.7603 (tt0) REVERT: O 179 GLU cc_start: 0.8768 (tp30) cc_final: 0.8318 (tp30) REVERT: O 182 GLU cc_start: 0.7864 (pm20) cc_final: 0.7482 (pt0) REVERT: P 40 MET cc_start: 0.8958 (ptp) cc_final: 0.8689 (ptp) REVERT: P 63 SER cc_start: 0.8830 (t) cc_final: 0.8618 (t) REVERT: P 101 VAL cc_start: 0.8830 (p) cc_final: 0.8574 (t) REVERT: P 182 GLU cc_start: 0.8124 (pm20) cc_final: 0.7827 (pt0) REVERT: P 223 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8717 (mm) REVERT: Q 122 GLN cc_start: 0.8966 (tt0) cc_final: 0.8674 (tt0) REVERT: R 40 MET cc_start: 0.8840 (ptp) cc_final: 0.8466 (ptm) REVERT: R 65 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6807 (pt0) REVERT: R 122 GLN cc_start: 0.8839 (tt0) cc_final: 0.8585 (tt0) REVERT: R 182 GLU cc_start: 0.8102 (pm20) cc_final: 0.7668 (pt0) REVERT: S 29 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7611 (mt-10) REVERT: S 67 ILE cc_start: 0.8397 (tt) cc_final: 0.8096 (mt) REVERT: T 40 MET cc_start: 0.8818 (ptp) cc_final: 0.8452 (ptm) REVERT: T 101 VAL cc_start: 0.8911 (p) cc_final: 0.8578 (t) REVERT: T 122 GLN cc_start: 0.8826 (tt0) cc_final: 0.8478 (tt0) REVERT: T 182 GLU cc_start: 0.8212 (pm20) cc_final: 0.7742 (pt0) REVERT: T 223 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8502 (mm) REVERT: U 48 LEU cc_start: 0.8720 (mt) cc_final: 0.8515 (mp) REVERT: U 65 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7152 (tt0) REVERT: U 99 GLU cc_start: 0.8192 (tt0) cc_final: 0.7893 (tt0) REVERT: U 157 ILE cc_start: 0.8746 (pt) cc_final: 0.8529 (mt) REVERT: U 182 GLU cc_start: 0.8263 (pm20) cc_final: 0.7814 (pt0) REVERT: a 27 GLU cc_start: 0.8224 (tp30) cc_final: 0.7774 (tp30) REVERT: a 217 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8191 (mttt) REVERT: b 27 GLU cc_start: 0.8194 (tp30) cc_final: 0.7981 (tp30) REVERT: c 27 GLU cc_start: 0.8313 (tp30) cc_final: 0.8015 (tp30) REVERT: c 51 ARG cc_start: 0.7754 (tpp80) cc_final: 0.7347 (ttp80) REVERT: c 142 MET cc_start: 0.7968 (mmt) cc_final: 0.7726 (mpp) REVERT: c 204 MET cc_start: 0.8297 (tpp) cc_final: 0.8075 (mmt) REVERT: e 27 GLU cc_start: 0.8107 (tp30) cc_final: 0.7903 (tp30) REVERT: f 45 GLU cc_start: 0.8092 (tt0) cc_final: 0.7790 (mt-10) REVERT: f 84 GLN cc_start: 0.8641 (mt0) cc_final: 0.8312 (mt0) REVERT: f 204 MET cc_start: 0.8049 (tpp) cc_final: 0.7748 (mmp) REVERT: g 204 MET cc_start: 0.8187 (tpp) cc_final: 0.7940 (mmt) outliers start: 215 outliers final: 110 residues processed: 1008 average time/residue: 0.5818 time to fit residues: 969.8441 Evaluate side-chains 900 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 781 time to evaluate : 4.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 221 TYR Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 199 SER 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 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU 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 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 30 ASN 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 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 101 VAL Chi-restraints excluded: chain H residue 135 TYR 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 44 THR 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 8 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 41 THR 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 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 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 101 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 101 VAL Chi-restraints excluded: chain X residue 134 VAL 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 41 THR 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 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 41 THR Chi-restraints excluded: chain Y residue 44 THR 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 43 MET Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 182 GLU Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain e residue 140 ILE 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 297 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 694 optimal weight: 5.9990 chunk 437 optimal weight: 3.9990 chunk 303 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 71 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 164 GLN N 30 ASN H 141 GLN V 88 ASN V 141 GLN W 88 ASN X 88 ASN X 141 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 164 GLN L 164 GLN ** 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** g 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.148684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114008 restraints weight = 61314.183| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.28 r_work: 0.3086 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 59164 Z= 0.290 Angle : 0.632 12.985 79905 Z= 0.337 Chirality : 0.043 0.188 9345 Planarity : 0.004 0.040 10262 Dihedral : 5.550 55.817 8326 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 3.93 % Allowed : 14.72 % Favored : 81.35 % 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: 0.40 (0.10), residues: 7469 helix: 2.00 (0.09), residues: 3458 sheet: -0.63 (0.13), residues: 1442 loop : -1.64 (0.11), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 216 HIS 0.006 0.002 HIS 1 28 PHE 0.011 0.002 PHE C 138 TYR 0.020 0.002 TYR G 8 ARG 0.007 0.000 ARG O 20 *********************** 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 1070 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 824 time to evaluate : 5.170 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: A 105 SER cc_start: 0.8688 (p) cc_final: 0.8458 (t) REVERT: A 231 LYS cc_start: 0.7985 (mttt) cc_final: 0.7044 (pttm) REVERT: B 35 SER cc_start: 0.7850 (p) cc_final: 0.7521 (t) REVERT: B 122 GLN cc_start: 0.8001 (mt0) cc_final: 0.7572 (tt0) REVERT: D 200 SER cc_start: 0.7958 (p) cc_final: 0.7676 (m) REVERT: D 221 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: E 105 SER cc_start: 0.8658 (p) cc_final: 0.8273 (t) REVERT: E 178 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8259 (ttp80) REVERT: F 40 MET cc_start: 0.8838 (ptp) cc_final: 0.8511 (ptp) REVERT: F 221 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.7400 (t80) REVERT: G 220 LYS cc_start: 0.8853 (mttt) cc_final: 0.8474 (mtpp) REVERT: G 230 LYS cc_start: 0.7117 (mtmm) cc_final: 0.6583 (mmtm) REVERT: Z 27 MET cc_start: 0.8625 (ttt) cc_final: 0.8267 (ttm) REVERT: Z 38 ASP cc_start: 0.8674 (t0) cc_final: 0.8371 (t0) REVERT: Z 114 ASP cc_start: 0.8153 (p0) cc_final: 0.7874 (p0) REVERT: Z 182 ASP cc_start: 0.8027 (t0) cc_final: 0.7691 (m-30) REVERT: M 93 MET cc_start: 0.7583 (mmm) cc_final: 0.6662 (mpp) REVERT: 1 182 ASP cc_start: 0.7776 (t0) cc_final: 0.7322 (m-30) REVERT: N 30 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8091 (t0) REVERT: N 68 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8290 (mt) REVERT: N 181 LYS cc_start: 0.8436 (tttm) cc_final: 0.8137 (mtmm) REVERT: 2 21 THR cc_start: 0.6414 (OUTLIER) cc_final: 0.6210 (t) REVERT: 2 182 ASP cc_start: 0.7959 (t0) cc_final: 0.7458 (m-30) REVERT: H 68 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8277 (mt) REVERT: V 27 MET cc_start: 0.8659 (ttt) cc_final: 0.8415 (ttt) REVERT: V 93 MET cc_start: 0.7779 (mmt) cc_final: 0.7517 (mmp) REVERT: V 172 MET cc_start: 0.8677 (tpt) cc_final: 0.8460 (tpt) REVERT: I 8 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7656 (mp) REVERT: I 37 ILE cc_start: 0.8997 (mm) cc_final: 0.8740 (mt) REVERT: I 70 ARG cc_start: 0.8762 (mmp80) cc_final: 0.8392 (mmt180) REVERT: I 164 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7640 (mp10) REVERT: W 27 MET cc_start: 0.8653 (ttt) cc_final: 0.8450 (ttt) REVERT: W 43 MET cc_start: 0.8918 (ttm) cc_final: 0.8680 (ttp) REVERT: W 59 MET cc_start: 0.8694 (mmm) cc_final: 0.8485 (mmm) REVERT: J 27 MET cc_start: 0.8637 (ttt) cc_final: 0.8390 (ttt) REVERT: J 59 MET cc_start: 0.8791 (mmm) cc_final: 0.8361 (mmm) REVERT: J 68 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8232 (mt) REVERT: J 177 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8371 (t) REVERT: X 40 TYR cc_start: 0.8600 (m-80) cc_final: 0.8133 (m-80) REVERT: X 62 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: K 68 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8379 (mt) REVERT: K 164 GLN cc_start: 0.7997 (mp10) cc_final: 0.7753 (mp10) REVERT: K 180 ARG cc_start: 0.9070 (tpt170) cc_final: 0.8604 (tpt170) REVERT: K 181 LYS cc_start: 0.8291 (tttm) cc_final: 0.8011 (tttm) REVERT: Y 182 ASP cc_start: 0.7953 (t0) cc_final: 0.7373 (m-30) REVERT: L 43 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8897 (ttt) REVERT: L 68 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8178 (mt) REVERT: O 99 GLU cc_start: 0.7793 (tt0) cc_final: 0.7451 (tt0) REVERT: O 179 GLU cc_start: 0.8708 (tp30) cc_final: 0.8261 (tp30) REVERT: O 182 GLU cc_start: 0.8136 (pm20) cc_final: 0.7891 (pt0) REVERT: P 40 MET cc_start: 0.8953 (ptp) cc_final: 0.8674 (ptp) REVERT: P 63 SER cc_start: 0.8836 (t) cc_final: 0.8594 (t) REVERT: P 101 VAL cc_start: 0.8813 (p) cc_final: 0.8603 (t) REVERT: P 114 LYS cc_start: 0.7458 (tppt) cc_final: 0.7004 (tttm) REVERT: P 182 GLU cc_start: 0.8115 (pm20) cc_final: 0.7801 (mt-10) REVERT: P 221 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8879 (m-80) REVERT: P 223 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8654 (mm) REVERT: Q 122 GLN cc_start: 0.8911 (tt0) cc_final: 0.8602 (tt0) REVERT: Q 179 GLU cc_start: 0.8621 (tp30) cc_final: 0.8399 (tp30) REVERT: R 40 MET cc_start: 0.8890 (ptp) cc_final: 0.8495 (ptm) REVERT: R 65 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6947 (pt0) REVERT: R 122 GLN cc_start: 0.8740 (tt0) cc_final: 0.8517 (tt0) REVERT: R 182 GLU cc_start: 0.8095 (pm20) cc_final: 0.7719 (pt0) REVERT: R 188 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7267 (mp0) REVERT: S 67 ILE cc_start: 0.8518 (tt) cc_final: 0.8127 (mt) REVERT: S 114 LYS cc_start: 0.7617 (tppt) cc_final: 0.7197 (tttm) REVERT: S 181 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7816 (ptpp) REVERT: S 223 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8401 (mm) REVERT: S 230 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7621 (mmmt) REVERT: T 101 VAL cc_start: 0.8953 (p) cc_final: 0.8662 (t) REVERT: T 122 GLN cc_start: 0.8663 (tt0) cc_final: 0.8334 (tt0) REVERT: T 182 GLU cc_start: 0.8195 (pm20) cc_final: 0.7861 (pt0) REVERT: T 221 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.7336 (t80) REVERT: T 223 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8504 (mm) REVERT: U 65 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7180 (tt0) REVERT: U 74 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8106 (t) REVERT: U 99 GLU cc_start: 0.7871 (tt0) cc_final: 0.7585 (tt0) REVERT: U 114 LYS cc_start: 0.7556 (tppt) cc_final: 0.7011 (tttm) REVERT: U 182 GLU cc_start: 0.8154 (pm20) cc_final: 0.7855 (pt0) REVERT: U 223 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8660 (mm) REVERT: a 27 GLU cc_start: 0.8251 (tp30) cc_final: 0.7738 (tp30) REVERT: a 217 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8185 (mttt) REVERT: b 27 GLU cc_start: 0.8077 (tp30) cc_final: 0.7795 (tp30) REVERT: c 27 GLU cc_start: 0.8255 (tp30) cc_final: 0.7929 (tp30) REVERT: d 51 ARG cc_start: 0.7670 (mmm-85) cc_final: 0.7429 (mtp180) REVERT: e 27 GLU cc_start: 0.8035 (tp30) cc_final: 0.7428 (tp30) REVERT: f 45 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7692 (mt-10) REVERT: f 84 GLN cc_start: 0.8691 (mt0) cc_final: 0.8346 (mt0) outliers start: 246 outliers final: 173 residues processed: 1020 average time/residue: 0.6380 time to fit residues: 1084.5993 Evaluate side-chains 969 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 775 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 SER 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 88 LEU Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 109 ILE 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 40 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 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 200 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 67 ILE Chi-restraints excluded: chain D residue 79 SER 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 59 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 109 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 E residue 221 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 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 88 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 199 SER 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 43 MET Chi-restraints excluded: chain Z residue 62 GLU 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 8 LEU 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 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 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 30 ASN Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE 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 21 THR Chi-restraints excluded: chain 2 residue 41 THR 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 30 ASN Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 155 VAL 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 41 THR 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 8 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU 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 45 ILE Chi-restraints excluded: chain W residue 104 ILE 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 68 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 178 ILE Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 41 THR Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 134 VAL 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 68 LEU Chi-restraints excluded: chain K residue 93 MET 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 41 THR Chi-restraints excluded: chain Y residue 82 LEU 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 30 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 43 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 101 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 L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR 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 211 GLU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 223 ILE Chi-restraints excluded: chain b 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 45 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 684 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 570 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 435 optimal weight: 1.9990 chunk 585 optimal weight: 5.9990 chunk 547 optimal weight: 1.9990 chunk 495 optimal weight: 4.9990 chunk 427 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** D 226 GLN ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 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** Z 164 GLN 1 36 GLN 1 88 ASN 2 164 GLN V 88 ASN W 141 GLN X 141 GLN K 30 ASN R 219 ASN S 219 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.144904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111506 restraints weight = 61432.720| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.24 r_work: 0.3005 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 59164 Z= 0.427 Angle : 0.708 13.419 79905 Z= 0.376 Chirality : 0.046 0.298 9345 Planarity : 0.004 0.041 10262 Dihedral : 5.804 57.033 8326 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 4.78 % Allowed : 15.13 % Favored : 80.09 % 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: 0.16 (0.09), residues: 7469 helix: 1.75 (0.09), residues: 3430 sheet: -0.50 (0.13), residues: 1400 loop : -1.80 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP c 216 HIS 0.007 0.002 HIS N 28 PHE 0.024 0.002 PHE a 190 TYR 0.022 0.002 TYR C 8 ARG 0.009 0.001 ARG O 20 *********************** 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 1132 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 833 time to evaluate : 5.096 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: A 221 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.7323 (t80) REVERT: A 231 LYS cc_start: 0.8119 (mttt) cc_final: 0.7088 (pttm) REVERT: B 122 GLN cc_start: 0.8270 (mt0) cc_final: 0.7818 (tt0) REVERT: D 200 SER cc_start: 0.8035 (p) cc_final: 0.7714 (m) REVERT: D 221 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: E 40 MET cc_start: 0.8755 (ptm) cc_final: 0.8549 (ptp) REVERT: E 105 SER cc_start: 0.8555 (p) cc_final: 0.8254 (t) REVERT: E 178 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8269 (ttp80) REVERT: E 221 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.7443 (t80) REVERT: F 26 TYR cc_start: 0.8356 (m-10) cc_final: 0.8050 (m-10) REVERT: F 40 MET cc_start: 0.9005 (ptp) cc_final: 0.8668 (ptp) REVERT: F 126 TYR cc_start: 0.8114 (m-80) cc_final: 0.7369 (m-80) REVERT: F 221 TYR cc_start: 0.9104 (OUTLIER) cc_final: 0.7499 (t80) REVERT: G 186 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6935 (tp30) REVERT: G 220 LYS cc_start: 0.8929 (mttt) cc_final: 0.8488 (mtpp) REVERT: G 230 LYS cc_start: 0.7153 (mtmm) cc_final: 0.6812 (mmtm) REVERT: Z 38 ASP cc_start: 0.8916 (t0) cc_final: 0.8497 (t0) REVERT: Z 114 ASP cc_start: 0.8237 (p0) cc_final: 0.7970 (p0) REVERT: Z 164 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: Z 182 ASP cc_start: 0.8148 (t0) cc_final: 0.7724 (m-30) REVERT: M 93 MET cc_start: 0.7654 (mmm) cc_final: 0.6936 (mpp) REVERT: 1 182 ASP cc_start: 0.7813 (t0) cc_final: 0.7302 (m-30) REVERT: N 59 MET cc_start: 0.8976 (mmp) cc_final: 0.8650 (mmm) REVERT: N 68 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (mt) REVERT: N 181 LYS cc_start: 0.8607 (tttm) cc_final: 0.8343 (tttm) REVERT: 2 21 THR cc_start: 0.6962 (OUTLIER) cc_final: 0.6738 (t) REVERT: 2 64 GLU cc_start: 0.8475 (tt0) cc_final: 0.8140 (tt0) REVERT: 2 96 MET cc_start: 0.8242 (mtm) cc_final: 0.7814 (mtp) REVERT: 2 182 ASP cc_start: 0.8086 (t0) cc_final: 0.7455 (m-30) REVERT: V 27 MET cc_start: 0.8914 (ttt) cc_final: 0.8709 (ttt) REVERT: I 37 ILE cc_start: 0.9011 (mm) cc_final: 0.8700 (mt) REVERT: I 70 ARG cc_start: 0.9074 (mmp80) cc_final: 0.8766 (mmt180) REVERT: I 164 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7892 (mp10) REVERT: W 27 MET cc_start: 0.8840 (ttt) cc_final: 0.8637 (ttt) REVERT: W 43 MET cc_start: 0.9136 (ttm) cc_final: 0.8873 (ttp) REVERT: W 59 MET cc_start: 0.8905 (mmm) cc_final: 0.8654 (mmm) REVERT: J 59 MET cc_start: 0.8948 (mmm) cc_final: 0.8625 (mmm) REVERT: J 68 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8323 (mt) REVERT: J 180 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8712 (tpp-160) REVERT: X 40 TYR cc_start: 0.8649 (m-80) cc_final: 0.8266 (m-80) REVERT: X 62 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: X 122 ASP cc_start: 0.8298 (t0) cc_final: 0.8074 (t0) REVERT: K 30 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8390 (t0) REVERT: K 68 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8451 (mt) REVERT: K 164 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: K 181 LYS cc_start: 0.8277 (tttm) cc_final: 0.7961 (tttm) REVERT: Y 62 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7828 (mm-30) REVERT: Y 64 GLU cc_start: 0.8659 (tt0) cc_final: 0.8319 (tt0) REVERT: Y 182 ASP cc_start: 0.8067 (t0) cc_final: 0.7462 (m-30) REVERT: O 99 GLU cc_start: 0.8147 (tt0) cc_final: 0.7851 (tt0) REVERT: O 114 LYS cc_start: 0.7843 (tppt) cc_final: 0.7251 (tttm) REVERT: O 179 GLU cc_start: 0.8799 (tp30) cc_final: 0.8365 (tp30) REVERT: O 182 GLU cc_start: 0.8319 (pm20) cc_final: 0.8096 (pt0) REVERT: O 221 TYR cc_start: 0.9459 (OUTLIER) cc_final: 0.7516 (t80) REVERT: P 40 MET cc_start: 0.9113 (ptp) cc_final: 0.8867 (ptp) REVERT: P 114 LYS cc_start: 0.7633 (tppt) cc_final: 0.6940 (tttm) REVERT: P 182 GLU cc_start: 0.8277 (pm20) cc_final: 0.7921 (mt-10) REVERT: P 221 TYR cc_start: 0.9416 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: P 223 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8716 (mm) REVERT: Q 114 LYS cc_start: 0.7736 (tppt) cc_final: 0.7015 (tttm) REVERT: Q 122 GLN cc_start: 0.8957 (tt0) cc_final: 0.8646 (tt0) REVERT: Q 179 GLU cc_start: 0.8684 (tp30) cc_final: 0.8442 (tp30) REVERT: R 65 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7142 (pt0) REVERT: R 114 LYS cc_start: 0.7450 (tppt) cc_final: 0.6913 (tttm) REVERT: R 122 GLN cc_start: 0.8828 (tt0) cc_final: 0.8576 (tt0) REVERT: R 182 GLU cc_start: 0.8254 (pm20) cc_final: 0.7891 (pt0) REVERT: S 40 MET cc_start: 0.9106 (ptp) cc_final: 0.8839 (ptm) REVERT: S 114 LYS cc_start: 0.7926 (tppt) cc_final: 0.7278 (ttpt) REVERT: S 181 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7801 (ptpp) REVERT: S 221 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.9236 (m-80) REVERT: S 223 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8549 (mm) REVERT: T 122 GLN cc_start: 0.8797 (tt0) cc_final: 0.8427 (tt0) REVERT: T 182 GLU cc_start: 0.8424 (pm20) cc_final: 0.8023 (pt0) REVERT: T 221 TYR cc_start: 0.9464 (OUTLIER) cc_final: 0.7367 (t80) REVERT: T 223 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8662 (mm) REVERT: U 65 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7464 (tt0) REVERT: U 99 GLU cc_start: 0.8189 (tt0) cc_final: 0.7951 (tt0) REVERT: U 114 LYS cc_start: 0.7840 (tppt) cc_final: 0.7147 (tttp) REVERT: U 182 GLU cc_start: 0.8444 (pm20) cc_final: 0.8213 (pt0) REVERT: U 223 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8738 (mm) REVERT: a 18 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7574 (tm-30) REVERT: a 27 GLU cc_start: 0.8493 (tp30) cc_final: 0.7764 (tp30) REVERT: a 121 GLU cc_start: 0.8105 (pt0) cc_final: 0.7749 (pt0) REVERT: b 27 GLU cc_start: 0.8118 (tp30) cc_final: 0.7764 (tp30) REVERT: c 27 GLU cc_start: 0.8360 (tp30) cc_final: 0.7644 (tp30) REVERT: d 51 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7608 (mtp180) REVERT: d 57 ARG cc_start: 0.7644 (ttm110) cc_final: 0.6872 (ttp80) REVERT: e 27 GLU cc_start: 0.8296 (tp30) cc_final: 0.7627 (tp30) REVERT: e 57 ARG cc_start: 0.7793 (ttm110) cc_final: 0.6818 (ttp80) REVERT: e 84 GLN cc_start: 0.8818 (mt0) cc_final: 0.8482 (mt0) REVERT: e 142 MET cc_start: 0.8219 (mpp) cc_final: 0.7900 (mpp) REVERT: e 217 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8436 (mttt) REVERT: f 45 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: g 27 GLU cc_start: 0.8464 (tp30) cc_final: 0.8163 (tp30) outliers start: 299 outliers final: 229 residues processed: 1070 average time/residue: 0.5742 time to fit residues: 1020.5489 Evaluate side-chains 1025 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 774 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 109 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 107 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR 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 79 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE 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 67 ILE Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 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 67 ILE Chi-restraints excluded: chain E residue 74 VAL 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 109 ILE Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 141 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 E residue 221 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 88 LEU 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 186 GLU Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 ILE 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 45 ILE Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 164 GLN Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 48 LEU 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 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 M residue 185 VAL Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 55 LEU Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 129 SER 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 8 LEU Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE 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 21 THR Chi-restraints excluded: chain 2 residue 41 THR Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE 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 30 ASN Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 101 VAL 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 41 THR Chi-restraints excluded: chain V residue 101 VAL Chi-restraints excluded: chain V residue 104 ILE 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 8 LEU Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 41 THR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 138 LEU Chi-restraints excluded: chain I residue 140 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 VAL 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 45 ILE Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE 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 6 ILE Chi-restraints excluded: chain J residue 23 GLU Chi-restraints excluded: chain J residue 41 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 177 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 45 ILE Chi-restraints excluded: chain X residue 62 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 104 ILE Chi-restraints excluded: chain X residue 134 VAL 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 30 ASN Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 93 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 140 SER 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 12 VAL Chi-restraints excluded: chain Y residue 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 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 30 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 68 LEU 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 L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 59 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 221 TYR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 33 LYS Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain P residue 223 ILE Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 221 TYR 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 R residue 211 GLU Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain S residue 106 LEU Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 221 TYR 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 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 74 VAL Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain U residue 223 ILE Chi-restraints excluded: chain a residue 230 LEU Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b 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 45 GLU Chi-restraints excluded: chain f residue 122 ILE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain g 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 520 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 715 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 540 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** Z 164 GLN 2 164 GLN H 141 GLN W 141 GLN X 164 GLN Q 219 ASN T 23 GLN T 44 ASN U 44 ASN U 125 GLN ** 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.148056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113763 restraints weight = 61132.944| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.27 r_work: 0.3127 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 59164 Z= 0.236 Angle : 0.614 12.660 79905 Z= 0.328 Chirality : 0.042 0.249 9345 Planarity : 0.004 0.042 10262 Dihedral : 5.476 55.631 8326 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.01 % Rotamer: Outliers : 3.98 % Allowed : 16.63 % Favored : 79.39 % 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: 0.46 (0.10), residues: 7469 helix: 2.04 (0.09), residues: 3444 sheet: -0.35 (0.13), residues: 1358 loop : -1.71 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 216 HIS 0.007 0.001 HIS 1 28 PHE 0.014 0.001 PHE a 190 TYR 0.023 0.001 TYR 1 58 ARG 0.007 0.000 ARG g 57 *********************** 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 1084 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 835 time to evaluate : 5.092 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: A 160 TYR cc_start: 0.8931 (m-80) cc_final: 0.8477 (m-80) REVERT: A 221 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7258 (t80) REVERT: A 231 LYS cc_start: 0.8149 (mttt) cc_final: 0.7103 (pttm) REVERT: B 35 SER cc_start: 0.7960 (p) cc_final: 0.7578 (t) REVERT: B 98 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7240 (tt0) REVERT: B 122 GLN cc_start: 0.8190 (mt0) cc_final: 0.7752 (tt0) REVERT: C 109 ILE cc_start: 0.8373 (tt) cc_final: 0.8084 (mp) REVERT: D 200 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7940 (m) REVERT: D 230 LYS cc_start: 0.7538 (mmtm) cc_final: 0.7295 (mmtm) REVERT: E 35 SER cc_start: 0.8291 (p) cc_final: 0.7889 (t) REVERT: F 40 MET cc_start: 0.8890 (ptp) cc_final: 0.8549 (ptp) REVERT: F 98 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7491 (mm110) REVERT: F 120 MET cc_start: 0.8361 (mtp) cc_final: 0.8140 (mtp) REVERT: F 221 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.7460 (t80) REVERT: G 220 LYS cc_start: 0.8918 (mttt) cc_final: 0.8503 (mtpp) REVERT: G 230 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6853 (mmtm) REVERT: Z 27 MET cc_start: 0.8705 (ttt) cc_final: 0.8410 (ttm) REVERT: Z 38 ASP cc_start: 0.8675 (t0) cc_final: 0.8454 (t0) REVERT: Z 114 ASP cc_start: 0.8258 (p0) cc_final: 0.7979 (p0) REVERT: Z 164 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: Z 182 ASP cc_start: 0.8223 (t0) cc_final: 0.7746 (m-30) REVERT: M 93 MET cc_start: 0.7524 (mmm) cc_final: 0.6648 (mpp) REVERT: 1 182 ASP cc_start: 0.7801 (t0) cc_final: 0.7322 (m-30) REVERT: N 59 MET cc_start: 0.8868 (mmp) cc_final: 0.8548 (mmm) REVERT: V 27 MET cc_start: 0.8805 (ttt) cc_final: 0.8601 (ttt) REVERT: I 37 ILE cc_start: 0.9023 (mm) cc_final: 0.8743 (mt) REVERT: I 70 ARG cc_start: 0.8897 (mmp80) cc_final: 0.8625 (mmt180) REVERT: I 164 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7754 (mp10) REVERT: W 43 MET cc_start: 0.9136 (ttm) cc_final: 0.8850 (ttp) REVERT: W 59 MET cc_start: 0.8880 (mmm) cc_final: 0.8624 (mmm) REVERT: W 173 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8492 (mt) REVERT: J 59 MET cc_start: 0.8908 (mmm) cc_final: 0.8553 (mmm) REVERT: J 177 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8541 (t) REVERT: X 40 TYR cc_start: 0.8624 (m-80) cc_final: 0.8339 (m-80) REVERT: K 141 GLN cc_start: 0.8978 (mt0) cc_final: 0.8772 (mt0) REVERT: K 180 ARG cc_start: 0.8964 (tpt170) cc_final: 0.8603 (tpt170) REVERT: K 181 LYS cc_start: 0.8250 (tttm) cc_final: 0.8011 (tttm) REVERT: Y 182 ASP cc_start: 0.8039 (t0) cc_final: 0.7402 (m-30) REVERT: O 99 GLU cc_start: 0.8117 (tt0) cc_final: 0.7754 (tt0) REVERT: O 114 LYS cc_start: 0.7793 (tppt) cc_final: 0.7283 (tttm) REVERT: O 179 GLU cc_start: 0.8716 (tp30) cc_final: 0.8317 (tp30) REVERT: O 182 GLU cc_start: 0.8189 (pm20) cc_final: 0.7936 (pt0) REVERT: P 101 VAL cc_start: 0.8846 (p) cc_final: 0.8577 (t) REVERT: P 114 LYS cc_start: 0.7525 (tppt) cc_final: 0.6926 (tttm) REVERT: P 182 GLU cc_start: 0.8252 (pm20) cc_final: 0.7891 (mt-10) REVERT: P 221 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8982 (m-80) REVERT: Q 122 GLN cc_start: 0.8958 (tt0) cc_final: 0.8651 (tt0) REVERT: Q 125 GLN cc_start: 0.9387 (tt0) cc_final: 0.8749 (tt0) REVERT: R 40 MET cc_start: 0.8801 (ptp) cc_final: 0.8419 (ptm) REVERT: R 65 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7131 (pt0) REVERT: R 122 GLN cc_start: 0.8855 (tt0) cc_final: 0.8605 (tt0) REVERT: R 182 GLU cc_start: 0.8133 (pm20) cc_final: 0.7786 (pt0) REVERT: S 40 MET cc_start: 0.9025 (ptp) cc_final: 0.8754 (ptm) REVERT: S 67 ILE cc_start: 0.8591 (tt) cc_final: 0.7913 (mt) REVERT: S 114 LYS cc_start: 0.7917 (tppt) cc_final: 0.7365 (ttpt) REVERT: S 125 GLN cc_start: 0.9195 (tt0) cc_final: 0.8511 (tt0) REVERT: S 181 LYS cc_start: 0.8281 (mtmt) cc_final: 0.8032 (ptpp) REVERT: S 223 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8563 (mm) REVERT: T 40 MET cc_start: 0.8927 (ptp) cc_final: 0.8556 (ptm) REVERT: T 101 VAL cc_start: 0.8941 (p) cc_final: 0.8570 (t) REVERT: T 122 GLN cc_start: 0.8687 (tt0) cc_final: 0.8296 (tt0) REVERT: T 125 GLN cc_start: 0.9296 (tt0) cc_final: 0.8727 (tt0) REVERT: T 182 GLU cc_start: 0.8307 (pm20) cc_final: 0.7911 (pt0) REVERT: T 221 TYR cc_start: 0.9391 (OUTLIER) cc_final: 0.7575 (t80) REVERT: T 223 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8670 (mm) REVERT: U 65 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7487 (tt0) REVERT: U 99 GLU cc_start: 0.8146 (tt0) cc_final: 0.7911 (tt0) REVERT: U 114 LYS cc_start: 0.7713 (tppt) cc_final: 0.7073 (tttp) REVERT: U 182 GLU cc_start: 0.8492 (pm20) cc_final: 0.8189 (pt0) REVERT: a 18 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7393 (tm-30) REVERT: a 27 GLU cc_start: 0.8437 (tp30) cc_final: 0.7730 (tp30) REVERT: a 39 ILE cc_start: 0.8641 (mt) cc_final: 0.8370 (mt) REVERT: a 217 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8280 (mttt) REVERT: b 27 GLU cc_start: 0.8039 (tp30) cc_final: 0.7690 (tp30) REVERT: c 27 GLU cc_start: 0.8374 (tp30) cc_final: 0.7667 (tp30) REVERT: c 142 MET cc_start: 0.7864 (mmt) cc_final: 0.7245 (mpp) REVERT: d 51 ARG cc_start: 0.7849 (mmm-85) cc_final: 0.7564 (mtp85) REVERT: e 27 GLU cc_start: 0.8218 (tp30) cc_final: 0.7570 (tp30) REVERT: e 57 ARG cc_start: 0.7779 (ttm110) cc_final: 0.6877 (ttp80) REVERT: e 84 GLN cc_start: 0.8821 (mt0) cc_final: 0.8451 (mt0) REVERT: e 86 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7873 (mm-30) REVERT: e 121 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7404 (mt-10) REVERT: e 142 MET cc_start: 0.8080 (mpp) cc_final: 0.7831 (mpp) REVERT: e 217 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8388 (mttt) REVERT: f 45 GLU cc_start: 0.8136 (tt0) cc_final: 0.7838 (mt-10) REVERT: f 204 MET cc_start: 0.8216 (tpp) cc_final: 0.7935 (mmp) REVERT: g 204 MET cc_start: 0.8312 (tpp) cc_final: 0.8003 (mmt) outliers start: 249 outliers final: 189 residues processed: 1028 average time/residue: 0.5760 time to fit residues: 976.7128 Evaluate side-chains 996 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 797 time to evaluate : 6.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 SER 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 107 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR Chi-restraints excluded: chain C residue 74 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 200 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 109 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 200 SER Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 109 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 221 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 88 LEU 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 199 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 43 MET Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 104 ILE Chi-restraints excluded: chain Z residue 164 GLN Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 44 THR Chi-restraints excluded: chain M residue 48 LEU 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 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 45 ILE Chi-restraints excluded: chain 1 residue 90 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 129 SER 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 104 ILE 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 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE 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 30 ASN 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 104 ILE 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 8 LEU Chi-restraints excluded: chain I residue 138 LEU 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 W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE 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 41 THR Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain J residue 177 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 101 VAL Chi-restraints excluded: chain X residue 104 ILE 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 93 MET Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 144 GLU 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 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 104 ILE 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 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 L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 63 SER Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 223 ILE Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 140 ILE 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 140 ILE Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 735 random chunks: chunk 334 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 403 optimal weight: 0.2980 chunk 230 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 664 optimal weight: 4.9990 chunk 536 optimal weight: 0.0770 chunk 491 optimal weight: 1.9990 chunk 547 optimal weight: 0.9980 chunk 623 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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** Z 164 GLN M 88 ASN N 30 ASN V 88 ASN V 141 GLN V 164 GLN W 141 GLN X 141 GLN X 164 GLN R 23 GLN R 44 ASN T 44 ASN T 219 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.147028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112549 restraints weight = 61415.245| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.28 r_work: 0.3149 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5037 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= 0.209 Angle : 0.594 12.513 79905 Z= 0.319 Chirality : 0.042 0.228 9345 Planarity : 0.004 0.042 10262 Dihedral : 5.305 55.471 8323 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.77 % Allowed : 16.86 % Favored : 79.37 % 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: 0.64 (0.10), residues: 7469 helix: 2.20 (0.09), residues: 3444 sheet: -0.28 (0.13), residues: 1358 loop : -1.63 (0.11), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP f 216 HIS 0.006 0.001 HIS V 28 PHE 0.013 0.001 PHE a 190 TYR 0.022 0.001 TYR 1 58 ARG 0.008 0.000 ARG S 20 *********************** 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 1057 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 821 time to evaluate : 5.139 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: A 160 TYR cc_start: 0.8919 (m-80) cc_final: 0.8466 (m-80) REVERT: A 221 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7197 (t80) REVERT: A 231 LYS cc_start: 0.8227 (mttt) cc_final: 0.7153 (pttm) REVERT: B 35 SER cc_start: 0.7983 (p) cc_final: 0.7601 (t) REVERT: B 122 GLN cc_start: 0.8136 (mt0) cc_final: 0.7705 (tt0) REVERT: D 67 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7705 (pp) REVERT: D 200 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.8008 (m) REVERT: E 35 SER cc_start: 0.8274 (p) cc_final: 0.7851 (t) REVERT: E 109 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7963 (mp) REVERT: F 40 MET cc_start: 0.8828 (ptp) cc_final: 0.8608 (ptp) REVERT: F 120 MET cc_start: 0.8367 (mtp) cc_final: 0.8159 (mtp) REVERT: F 174 SER cc_start: 0.7706 (t) cc_final: 0.7467 (m) REVERT: F 221 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.7468 (t80) REVERT: G 152 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.6950 (t0) REVERT: G 188 GLU cc_start: 0.7630 (tp30) cc_final: 0.7303 (mt-10) REVERT: G 220 LYS cc_start: 0.8907 (mttt) cc_final: 0.8486 (mtpp) REVERT: G 230 LYS cc_start: 0.7095 (mtmm) cc_final: 0.6877 (mmtm) REVERT: Z 114 ASP cc_start: 0.8270 (p0) cc_final: 0.7981 (p0) REVERT: Z 164 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7908 (mt0) REVERT: Z 182 ASP cc_start: 0.8205 (t0) cc_final: 0.7706 (m-30) REVERT: M 59 MET cc_start: 0.8852 (mmm) cc_final: 0.8528 (mmm) REVERT: M 93 MET cc_start: 0.7414 (mmm) cc_final: 0.6631 (mpp) REVERT: 1 27 MET cc_start: 0.8722 (ttt) cc_final: 0.8466 (ttt) REVERT: N 59 MET cc_start: 0.8824 (mmp) cc_final: 0.8442 (mmm) REVERT: 2 96 MET cc_start: 0.8184 (mtm) cc_final: 0.7755 (mtp) REVERT: V 62 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7785 (mm-30) REVERT: I 70 ARG cc_start: 0.8862 (mmp80) cc_final: 0.8628 (mmt180) REVERT: I 164 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7751 (mp10) REVERT: W 59 MET cc_start: 0.8821 (mmm) cc_final: 0.8599 (mmm) REVERT: J 59 MET cc_start: 0.8895 (mmm) cc_final: 0.8530 (mmm) REVERT: J 177 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8538 (t) REVERT: X 40 TYR cc_start: 0.8599 (m-80) cc_final: 0.8227 (m-80) REVERT: K 180 ARG cc_start: 0.9024 (tpt170) cc_final: 0.8638 (tpt170) REVERT: K 181 LYS cc_start: 0.8266 (tttm) cc_final: 0.8011 (tttm) REVERT: Y 144 GLU cc_start: 0.8251 (tt0) cc_final: 0.7975 (mt-10) REVERT: Y 182 ASP cc_start: 0.8081 (t0) cc_final: 0.7421 (m-30) REVERT: O 99 GLU cc_start: 0.8095 (tt0) cc_final: 0.7815 (tt0) REVERT: O 114 LYS cc_start: 0.7769 (tppt) cc_final: 0.7236 (tttm) REVERT: O 179 GLU cc_start: 0.8763 (tp30) cc_final: 0.8389 (tp30) REVERT: O 182 GLU cc_start: 0.8234 (pm20) cc_final: 0.8005 (pt0) REVERT: P 101 VAL cc_start: 0.8994 (p) cc_final: 0.8622 (t) REVERT: P 182 GLU cc_start: 0.8160 (pm20) cc_final: 0.7829 (mt-10) REVERT: P 221 TYR cc_start: 0.9281 (OUTLIER) cc_final: 0.8952 (m-80) REVERT: Q 122 GLN cc_start: 0.8931 (tt0) cc_final: 0.8613 (tt0) REVERT: Q 125 GLN cc_start: 0.9349 (tt0) cc_final: 0.8752 (tt0) REVERT: R 40 MET cc_start: 0.8772 (ptp) cc_final: 0.8348 (ptm) REVERT: R 65 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7092 (pt0) REVERT: R 101 VAL cc_start: 0.8895 (p) cc_final: 0.8610 (t) REVERT: R 122 GLN cc_start: 0.8810 (tt0) cc_final: 0.8539 (tt0) REVERT: R 182 GLU cc_start: 0.8118 (pm20) cc_final: 0.7786 (pt0) REVERT: S 40 MET cc_start: 0.9017 (ptp) cc_final: 0.8767 (ptm) REVERT: S 67 ILE cc_start: 0.8461 (tt) cc_final: 0.7839 (mt) REVERT: S 114 LYS cc_start: 0.7894 (tppt) cc_final: 0.7375 (ttpt) REVERT: S 125 GLN cc_start: 0.9142 (tt0) cc_final: 0.8450 (tt0) REVERT: S 181 LYS cc_start: 0.8289 (mtmt) cc_final: 0.8043 (ptpp) REVERT: S 223 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8639 (mm) REVERT: T 40 MET cc_start: 0.8908 (ptp) cc_final: 0.8521 (ptm) REVERT: T 101 VAL cc_start: 0.8895 (p) cc_final: 0.8512 (t) REVERT: T 122 GLN cc_start: 0.8671 (tt0) cc_final: 0.8319 (tt0) REVERT: T 125 GLN cc_start: 0.9264 (tt0) cc_final: 0.8712 (tt0) REVERT: T 182 GLU cc_start: 0.8304 (pm20) cc_final: 0.7924 (pt0) REVERT: T 221 TYR cc_start: 0.9390 (OUTLIER) cc_final: 0.7580 (t80) REVERT: T 223 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8746 (mm) REVERT: U 65 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7398 (tt0) REVERT: U 99 GLU cc_start: 0.8180 (tt0) cc_final: 0.7962 (tt0) REVERT: U 114 LYS cc_start: 0.7671 (tppt) cc_final: 0.7036 (tttp) REVERT: U 182 GLU cc_start: 0.8449 (pm20) cc_final: 0.8169 (pt0) REVERT: U 221 TYR cc_start: 0.9379 (OUTLIER) cc_final: 0.7608 (t80) REVERT: a 18 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7378 (tm-30) REVERT: a 27 GLU cc_start: 0.8438 (tp30) cc_final: 0.7752 (tp30) REVERT: a 217 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8221 (mttt) REVERT: b 27 GLU cc_start: 0.8050 (tp30) cc_final: 0.7691 (tp30) REVERT: c 27 GLU cc_start: 0.8365 (tp30) cc_final: 0.7669 (tp30) REVERT: c 142 MET cc_start: 0.7697 (mmt) cc_final: 0.7314 (mpp) REVERT: d 51 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7502 (mtp85) REVERT: e 27 GLU cc_start: 0.8214 (tp30) cc_final: 0.7576 (tp30) REVERT: e 57 ARG cc_start: 0.7738 (ttm110) cc_final: 0.6824 (ttp80) REVERT: e 84 GLN cc_start: 0.8799 (mt0) cc_final: 0.8438 (mt0) REVERT: e 86 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7721 (mm-30) REVERT: e 121 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7202 (mt-10) REVERT: e 142 MET cc_start: 0.8154 (mpp) cc_final: 0.7948 (mpp) REVERT: f 45 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: f 84 GLN cc_start: 0.8656 (mt0) cc_final: 0.8380 (mt0) REVERT: f 204 MET cc_start: 0.8192 (tpp) cc_final: 0.7951 (mmp) REVERT: g 57 ARG cc_start: 0.7540 (ttm110) cc_final: 0.6863 (ttp80) REVERT: g 204 MET cc_start: 0.8279 (tpp) cc_final: 0.8058 (mmt) outliers start: 236 outliers final: 186 residues processed: 999 average time/residue: 0.5811 time to fit residues: 957.2061 Evaluate side-chains 1000 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 800 time to evaluate : 4.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 79 SER 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 107 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 221 TYR 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 79 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 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 67 ILE 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 200 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 109 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 221 TYR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 199 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 43 MET Chi-restraints excluded: chain Z residue 62 GLU Chi-restraints excluded: chain Z residue 101 VAL Chi-restraints excluded: chain Z residue 164 GLN Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 48 LEU 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 173 ILE Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 43 MET Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 90 VAL Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 129 SER 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 30 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE 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 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 139 GLU 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 30 ASN Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 155 VAL 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 104 ILE 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 8 LEU 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 177 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE 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 173 ILE Chi-restraints excluded: chain J residue 177 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 104 ILE 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 93 MET 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 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 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 164 GLN Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 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 101 VAL Chi-restraints excluded: chain L residue 173 ILE 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 31 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 174 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 221 TYR Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 211 GLU Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 107 VAL 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 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain c residue 140 ILE Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain f residue 45 GLU Chi-restraints excluded: chain g residue 140 ILE 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 596 optimal weight: 0.7980 chunk 565 optimal weight: 0.6980 chunk 344 optimal weight: 0.3980 chunk 506 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 695 optimal weight: 0.7980 chunk 341 optimal weight: 2.9990 chunk 591 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 336 optimal weight: 2.9990 chunk 525 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 1 88 ASN 2 164 GLN H 141 GLN V 36 GLN V 88 ASN V 141 GLN W 141 GLN X 141 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 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.158586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123604 restraints weight = 59996.632| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.36 r_work: 0.3132 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2964 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2964 r_free = 0.2964 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2964 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.5121 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= 0.176 Angle : 0.576 12.249 79905 Z= 0.310 Chirality : 0.041 0.207 9345 Planarity : 0.004 0.042 10262 Dihedral : 5.158 55.081 8323 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.21 % Allowed : 17.61 % Favored : 79.18 % 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: 0.79 (0.10), residues: 7469 helix: 2.33 (0.09), residues: 3465 sheet: -0.25 (0.13), residues: 1379 loop : -1.58 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP f 28 HIS 0.007 0.001 HIS N 28 PHE 0.010 0.001 PHE A 42 TYR 0.022 0.001 TYR 1 58 ARG 0.007 0.000 ARG S 20 *********************** 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 1010 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 809 time to evaluate : 5.172 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: A 221 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7181 (t80) REVERT: B 35 SER cc_start: 0.7935 (p) cc_final: 0.7506 (t) REVERT: B 98 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7247 (tt0) REVERT: B 122 GLN cc_start: 0.8084 (mt0) cc_final: 0.7686 (tt0) REVERT: B 152 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7230 (t0) REVERT: C 60 GLU cc_start: 0.8650 (tp30) cc_final: 0.8071 (tp30) REVERT: D 200 SER cc_start: 0.8211 (OUTLIER) cc_final: 0.8007 (m) REVERT: E 35 SER cc_start: 0.8192 (p) cc_final: 0.7742 (t) REVERT: E 109 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7962 (mp) REVERT: E 179 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7553 (mt-10) REVERT: F 40 MET cc_start: 0.8778 (ptp) cc_final: 0.8378 (ptp) REVERT: F 120 MET cc_start: 0.8263 (mtp) cc_final: 0.8054 (mtp) REVERT: F 221 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7362 (t80) REVERT: G 152 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.6868 (t0) REVERT: G 188 GLU cc_start: 0.7558 (tp30) cc_final: 0.7207 (mt-10) REVERT: G 220 LYS cc_start: 0.8792 (mttt) cc_final: 0.8355 (mtpp) REVERT: Z 27 MET cc_start: 0.8533 (ttt) cc_final: 0.8263 (ttm) REVERT: Z 114 ASP cc_start: 0.8269 (p0) cc_final: 0.8024 (p0) REVERT: Z 164 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: Z 182 ASP cc_start: 0.8213 (t0) cc_final: 0.7689 (m-30) REVERT: M 59 MET cc_start: 0.8845 (mmm) cc_final: 0.8486 (mmm) REVERT: 1 182 ASP cc_start: 0.7884 (t0) cc_final: 0.7255 (m-30) REVERT: N 59 MET cc_start: 0.8797 (mmp) cc_final: 0.8411 (mmm) REVERT: 2 62 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: 2 96 MET cc_start: 0.8094 (mtm) cc_final: 0.7647 (mtp) REVERT: I 8 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7609 (mp) REVERT: I 9 LYS cc_start: 0.8446 (ptpt) cc_final: 0.7908 (pttp) REVERT: I 70 ARG cc_start: 0.8799 (mmp80) cc_final: 0.8594 (mmt180) REVERT: I 164 GLN cc_start: 0.8053 (mm-40) cc_final: 0.7708 (mp10) REVERT: W 59 MET cc_start: 0.8784 (mmm) cc_final: 0.8582 (mmm) REVERT: W 144 GLU cc_start: 0.7906 (tt0) cc_final: 0.7606 (mt-10) REVERT: J 59 MET cc_start: 0.8857 (mmm) cc_final: 0.8496 (mmm) REVERT: K 141 GLN cc_start: 0.8972 (mt0) cc_final: 0.8741 (mt0) REVERT: K 144 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: K 180 ARG cc_start: 0.9043 (tpt170) cc_final: 0.8720 (tpt170) REVERT: K 181 LYS cc_start: 0.8183 (tttm) cc_final: 0.7920 (tttm) REVERT: Y 7 THR cc_start: 0.9340 (m) cc_final: 0.9125 (t) REVERT: Y 64 GLU cc_start: 0.8713 (tt0) cc_final: 0.8255 (tt0) REVERT: Y 144 GLU cc_start: 0.8200 (tt0) cc_final: 0.7942 (mt-10) REVERT: Y 182 ASP cc_start: 0.8081 (t0) cc_final: 0.7396 (m-30) REVERT: O 99 GLU cc_start: 0.8057 (tt0) cc_final: 0.7751 (tt0) REVERT: O 179 GLU cc_start: 0.8696 (tp30) cc_final: 0.8286 (tp30) REVERT: O 182 GLU cc_start: 0.8242 (pm20) cc_final: 0.7926 (mt-10) REVERT: O 230 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7217 (mttp) REVERT: P 101 VAL cc_start: 0.9018 (p) cc_final: 0.8669 (t) REVERT: P 182 GLU cc_start: 0.8136 (pm20) cc_final: 0.7753 (mt-10) REVERT: P 221 TYR cc_start: 0.9235 (OUTLIER) cc_final: 0.8903 (m-80) REVERT: Q 122 GLN cc_start: 0.8920 (tt0) cc_final: 0.8590 (tt0) REVERT: Q 125 GLN cc_start: 0.9290 (tt0) cc_final: 0.8678 (tt0) REVERT: R 65 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7093 (tt0) REVERT: R 122 GLN cc_start: 0.8767 (tt0) cc_final: 0.8502 (tt0) REVERT: R 182 GLU cc_start: 0.8096 (pm20) cc_final: 0.7679 (mt-10) REVERT: S 40 MET cc_start: 0.8950 (ptp) cc_final: 0.8676 (ptm) REVERT: S 67 ILE cc_start: 0.8341 (tt) cc_final: 0.7737 (mt) REVERT: S 101 VAL cc_start: 0.9054 (p) cc_final: 0.8783 (t) REVERT: S 125 GLN cc_start: 0.9055 (tt0) cc_final: 0.8385 (tt0) REVERT: S 177 GLU cc_start: 0.8657 (tp30) cc_final: 0.8419 (tp30) REVERT: S 181 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8011 (ptpp) REVERT: S 223 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8682 (mm) REVERT: T 40 MET cc_start: 0.8890 (ptp) cc_final: 0.8505 (ptm) REVERT: T 101 VAL cc_start: 0.8833 (p) cc_final: 0.8410 (t) REVERT: T 122 GLN cc_start: 0.8639 (tt0) cc_final: 0.8284 (tt0) REVERT: T 125 GLN cc_start: 0.9185 (tt0) cc_final: 0.8637 (tt0) REVERT: T 182 GLU cc_start: 0.8357 (pm20) cc_final: 0.7960 (pt0) REVERT: T 221 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7587 (t80) REVERT: T 223 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8724 (mm) REVERT: U 65 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7343 (tt0) REVERT: U 67 ILE cc_start: 0.8218 (tt) cc_final: 0.7323 (mt) REVERT: U 99 GLU cc_start: 0.8169 (tt0) cc_final: 0.7926 (tt0) REVERT: U 182 GLU cc_start: 0.8492 (pm20) cc_final: 0.8244 (mp0) REVERT: U 221 TYR cc_start: 0.9348 (OUTLIER) cc_final: 0.7560 (t80) REVERT: a 18 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7284 (tm-30) REVERT: a 27 GLU cc_start: 0.8404 (tp30) cc_final: 0.7711 (tp30) REVERT: a 55 TYR cc_start: 0.8169 (m-10) cc_final: 0.7926 (m-80) REVERT: a 217 LYS cc_start: 0.8393 (ttmt) cc_final: 0.8155 (mttt) REVERT: b 27 GLU cc_start: 0.7936 (tp30) cc_final: 0.7570 (tp30) REVERT: b 70 VAL cc_start: 0.7916 (t) cc_final: 0.7689 (p) REVERT: c 27 GLU cc_start: 0.8344 (tp30) cc_final: 0.7646 (tp30) REVERT: c 51 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7590 (ttp80) REVERT: c 142 MET cc_start: 0.7680 (mmt) cc_final: 0.7289 (mpp) REVERT: d 51 ARG cc_start: 0.7714 (mmm-85) cc_final: 0.7500 (mtp85) REVERT: d 142 MET cc_start: 0.8073 (mpp) cc_final: 0.7302 (mpp) REVERT: e 27 GLU cc_start: 0.8186 (tp30) cc_final: 0.7555 (tp30) REVERT: e 57 ARG cc_start: 0.7656 (ttm110) cc_final: 0.6746 (ttp80) REVERT: e 84 GLN cc_start: 0.8730 (mt0) cc_final: 0.8371 (mt0) REVERT: f 45 GLU cc_start: 0.8057 (tt0) cc_final: 0.7750 (mt-10) REVERT: f 51 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7346 (ttp-170) REVERT: f 84 GLN cc_start: 0.8618 (mt0) cc_final: 0.8347 (mt0) REVERT: g 142 MET cc_start: 0.8246 (mmm) cc_final: 0.7905 (mpp) outliers start: 201 outliers final: 161 residues processed: 965 average time/residue: 0.5831 time to fit residues: 932.3010 Evaluate side-chains 955 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 779 time to evaluate : 5.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 ILE 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 152 ASP 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 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 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 88 LEU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 109 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 38 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 221 TYR 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 104 ILE Chi-restraints excluded: chain Z residue 164 GLN Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 48 LEU 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 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 129 SER 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 30 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE 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 62 GLU Chi-restraints excluded: chain 2 residue 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE 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 101 VAL Chi-restraints excluded: chain H residue 155 VAL 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 104 ILE 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 8 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain J residue 135 TYR 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 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 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 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 164 GLN Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 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 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 178 ILE Chi-restraints excluded: chain L residue 179 THR 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 P residue 31 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 221 TYR Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR 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 R residue 211 GLU Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 107 VAL 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 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain e residue 140 ILE Chi-restraints excluded: chain e residue 230 LEU Chi-restraints excluded: chain g 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 538 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 723 optimal weight: 4.9990 chunk 411 optimal weight: 0.8980 chunk 634 optimal weight: 6.9990 chunk 297 optimal weight: 1.9990 chunk 518 optimal weight: 0.9990 chunk 436 optimal weight: 2.9990 chunk 666 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 613 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** D 226 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 1 88 ASN N 30 ASN 2 164 GLN V 88 ASN V 141 GLN I 30 ASN X 88 ASN X 141 GLN K 30 ASN ** L 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.146935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113523 restraints weight = 61169.183| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.23 r_work: 0.3070 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 59164 Z= 0.312 Angle : 0.643 12.881 79905 Z= 0.342 Chirality : 0.044 0.226 9345 Planarity : 0.004 0.042 10262 Dihedral : 5.401 56.702 8323 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.23 % Allowed : 17.67 % Favored : 79.10 % 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: 0.63 (0.10), residues: 7469 helix: 2.16 (0.09), residues: 3437 sheet: -0.24 (0.13), residues: 1379 loop : -1.61 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 216 HIS 0.007 0.002 HIS V 28 PHE 0.018 0.002 PHE a 190 TYR 0.019 0.002 TYR 1 58 ARG 0.010 0.001 ARG 2 165 ********************** 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 1009 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 807 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7305 (t80) REVERT: B 122 GLN cc_start: 0.8193 (mt0) cc_final: 0.7749 (tt0) REVERT: C 60 GLU cc_start: 0.8747 (tp30) cc_final: 0.8158 (tp30) REVERT: D 200 SER cc_start: 0.8221 (p) cc_final: 0.7952 (m) REVERT: E 35 SER cc_start: 0.8181 (p) cc_final: 0.7708 (t) REVERT: E 179 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 40 MET cc_start: 0.8869 (ptp) cc_final: 0.8574 (ptp) REVERT: F 174 SER cc_start: 0.7704 (t) cc_final: 0.7489 (m) REVERT: F 221 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7485 (t80) REVERT: G 188 GLU cc_start: 0.7610 (tp30) cc_final: 0.7235 (mt-10) REVERT: G 220 LYS cc_start: 0.8808 (mttt) cc_final: 0.8372 (mtpp) REVERT: G 230 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7287 (mppt) REVERT: Z 27 MET cc_start: 0.8681 (ttt) cc_final: 0.8464 (ttm) REVERT: Z 114 ASP cc_start: 0.8249 (p0) cc_final: 0.7967 (p0) REVERT: Z 164 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7693 (mm-40) REVERT: Z 182 ASP cc_start: 0.8172 (t0) cc_final: 0.7611 (m-30) REVERT: M 59 MET cc_start: 0.8849 (mmm) cc_final: 0.8569 (mmp) REVERT: 1 182 ASP cc_start: 0.7940 (t0) cc_final: 0.7408 (m-30) REVERT: N 59 MET cc_start: 0.8864 (mmp) cc_final: 0.8418 (mmm) REVERT: 2 96 MET cc_start: 0.8168 (mtm) cc_final: 0.7780 (mtp) REVERT: 2 182 ASP cc_start: 0.8012 (t0) cc_final: 0.7420 (m-30) REVERT: V 62 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7942 (mm-30) REVERT: I 70 ARG cc_start: 0.8966 (mmp80) cc_final: 0.8698 (mmt180) REVERT: I 164 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7855 (mp10) REVERT: J 59 MET cc_start: 0.8927 (mmm) cc_final: 0.8549 (mmm) REVERT: X 40 TYR cc_start: 0.8620 (m-80) cc_final: 0.8148 (m-80) REVERT: K 30 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8612 (t0) REVERT: K 180 ARG cc_start: 0.9113 (tpt170) cc_final: 0.8715 (tpt170) REVERT: K 181 LYS cc_start: 0.8255 (tttm) cc_final: 0.8010 (tttm) REVERT: Y 7 THR cc_start: 0.9280 (m) cc_final: 0.9033 (t) REVERT: Y 144 GLU cc_start: 0.8299 (tt0) cc_final: 0.8034 (mt-10) REVERT: Y 182 ASP cc_start: 0.8135 (t0) cc_final: 0.7417 (m-30) REVERT: O 99 GLU cc_start: 0.8083 (tt0) cc_final: 0.7814 (tt0) REVERT: O 114 LYS cc_start: 0.7758 (tppt) cc_final: 0.7225 (tttm) REVERT: O 230 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7350 (mttt) REVERT: P 101 VAL cc_start: 0.8966 (p) cc_final: 0.8739 (t) REVERT: P 114 LYS cc_start: 0.7622 (tppt) cc_final: 0.6951 (tttm) REVERT: P 182 GLU cc_start: 0.8344 (pm20) cc_final: 0.8000 (mt-10) REVERT: P 221 TYR cc_start: 0.9348 (OUTLIER) cc_final: 0.8952 (m-80) REVERT: P 223 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8851 (mm) REVERT: Q 122 GLN cc_start: 0.8979 (tt0) cc_final: 0.8661 (tt0) REVERT: R 40 MET cc_start: 0.8907 (ptp) cc_final: 0.8570 (ptm) REVERT: R 65 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7097 (tt0) REVERT: R 182 GLU cc_start: 0.8254 (pm20) cc_final: 0.7902 (pt0) REVERT: R 230 LYS cc_start: 0.7747 (mmmt) cc_final: 0.6988 (mttm) REVERT: S 40 MET cc_start: 0.9065 (ptp) cc_final: 0.8824 (ptm) REVERT: S 67 ILE cc_start: 0.8453 (tt) cc_final: 0.7950 (mt) REVERT: S 101 VAL cc_start: 0.9035 (p) cc_final: 0.8789 (t) REVERT: S 114 LYS cc_start: 0.7935 (tppt) cc_final: 0.7360 (ttpt) REVERT: S 125 GLN cc_start: 0.9130 (tt0) cc_final: 0.8482 (tt0) REVERT: S 181 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8062 (ptpp) REVERT: S 223 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8644 (mm) REVERT: T 101 VAL cc_start: 0.8932 (p) cc_final: 0.8598 (t) REVERT: T 122 GLN cc_start: 0.8750 (tt0) cc_final: 0.8413 (tt0) REVERT: T 182 GLU cc_start: 0.8489 (pm20) cc_final: 0.8129 (pt0) REVERT: T 221 TYR cc_start: 0.9452 (OUTLIER) cc_final: 0.7663 (t80) REVERT: T 223 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8756 (mm) REVERT: U 65 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7552 (tt0) REVERT: U 99 GLU cc_start: 0.8117 (tt0) cc_final: 0.7870 (tt0) REVERT: U 114 LYS cc_start: 0.7770 (tppt) cc_final: 0.7077 (tttp) REVERT: a 18 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7428 (tm-30) REVERT: a 27 GLU cc_start: 0.8470 (tp30) cc_final: 0.7740 (tp30) REVERT: a 39 ILE cc_start: 0.8568 (mt) cc_final: 0.8353 (mt) REVERT: b 27 GLU cc_start: 0.8075 (tp30) cc_final: 0.7700 (tp30) REVERT: c 27 GLU cc_start: 0.8369 (tp30) cc_final: 0.7666 (tp30) REVERT: d 51 ARG cc_start: 0.7741 (mmm-85) cc_final: 0.7519 (mtp85) REVERT: d 57 ARG cc_start: 0.7580 (ttm110) cc_final: 0.6856 (ttp80) REVERT: e 27 GLU cc_start: 0.8260 (tp30) cc_final: 0.7562 (tp30) REVERT: e 57 ARG cc_start: 0.7672 (ttm110) cc_final: 0.6761 (ttp80) REVERT: e 84 GLN cc_start: 0.8762 (mt0) cc_final: 0.8435 (mt0) REVERT: f 45 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: f 51 ARG cc_start: 0.7808 (ttp80) cc_final: 0.7444 (ttp-170) REVERT: f 57 ARG cc_start: 0.7593 (ttm110) cc_final: 0.6695 (ttp80) REVERT: g 27 GLU cc_start: 0.8424 (tp30) cc_final: 0.8075 (tp30) outliers start: 202 outliers final: 175 residues processed: 963 average time/residue: 0.5729 time to fit residues: 913.6110 Evaluate side-chains 982 residues out of total 6258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 797 time to evaluate : 5.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 221 TYR Chi-restraints excluded: chain B residue 38 LEU 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 221 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 200 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 109 ILE Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 221 TYR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 221 TYR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 221 TYR 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 104 ILE Chi-restraints excluded: chain Z residue 155 VAL Chi-restraints excluded: chain Z residue 164 GLN Chi-restraints excluded: chain Z residue 178 ILE Chi-restraints excluded: chain Z residue 185 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 41 THR Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 48 LEU 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 177 VAL Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 39 THR Chi-restraints excluded: chain 1 residue 41 THR Chi-restraints excluded: chain 1 residue 45 ILE Chi-restraints excluded: chain 1 residue 101 VAL Chi-restraints excluded: chain 1 residue 104 ILE Chi-restraints excluded: chain 1 residue 129 SER 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 30 ASN Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 104 ILE 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 101 VAL Chi-restraints excluded: chain 2 residue 104 ILE Chi-restraints excluded: chain 2 residue 139 GLU 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 101 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 VAL 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 104 ILE 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 8 LEU Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 178 ILE Chi-restraints excluded: chain W residue 12 VAL Chi-restraints excluded: chain W residue 45 ILE Chi-restraints excluded: chain W residue 101 VAL Chi-restraints excluded: chain W residue 104 ILE Chi-restraints excluded: chain W residue 178 ILE Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 101 VAL Chi-restraints excluded: chain J residue 104 ILE 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 178 ILE Chi-restraints excluded: chain X residue 185 VAL Chi-restraints excluded: chain K residue 30 ASN 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 144 GLU 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 41 THR Chi-restraints excluded: chain Y residue 44 THR Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 104 ILE Chi-restraints excluded: chain Y residue 164 GLN Chi-restraints excluded: chain Y residue 173 ILE Chi-restraints excluded: chain Y residue 175 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 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 L residue 179 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain O residue 31 VAL Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 107 VAL Chi-restraints excluded: chain O residue 174 SER Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 107 VAL Chi-restraints excluded: chain P residue 120 MET 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 31 VAL Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain Q residue 63 SER Chi-restraints excluded: chain Q residue 70 ILE Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain Q residue 221 TYR 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 R residue 211 GLU Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 107 VAL 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 221 TYR Chi-restraints excluded: chain T residue 223 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 107 VAL Chi-restraints excluded: chain U residue 221 TYR Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b 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 45 GLU Chi-restraints excluded: chain g residue 140 ILE Chi-restraints excluded: chain g residue 230 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.9039 > 50: distance: 29 - 170: 31.597 distance: 32 - 167: 36.649 distance: 95 - 99: 29.352 distance: 99 - 100: 12.789 distance: 100 - 101: 12.541 distance: 100 - 103: 24.727 distance: 101 - 102: 15.107 distance: 101 - 111: 11.197 distance: 103 - 104: 4.813 distance: 104 - 106: 7.300 distance: 105 - 107: 23.098 distance: 106 - 108: 33.750 distance: 107 - 109: 16.561 distance: 108 - 109: 4.393 distance: 109 - 110: 34.956 distance: 111 - 112: 18.269 distance: 112 - 113: 20.104 distance: 113 - 114: 16.244 distance: 113 - 115: 9.269 distance: 115 - 116: 35.912 distance: 117 - 119: 9.799 distance: 119 - 120: 42.011 distance: 120 - 121: 41.927 distance: 120 - 123: 23.609 distance: 121 - 122: 42.184 distance: 121 - 126: 65.889 distance: 123 - 124: 19.885 distance: 123 - 125: 16.888 distance: 126 - 127: 56.679 distance: 127 - 130: 12.069 distance: 128 - 129: 52.037 distance: 128 - 137: 58.133 distance: 130 - 131: 28.731 distance: 131 - 132: 7.498 distance: 132 - 133: 47.507 distance: 133 - 134: 23.744 distance: 134 - 135: 44.047 distance: 134 - 136: 11.217 distance: 137 - 138: 3.483 distance: 137 - 143: 18.738 distance: 138 - 139: 16.586 distance: 138 - 141: 18.928 distance: 139 - 140: 19.901 distance: 139 - 144: 48.212 distance: 141 - 142: 38.835 distance: 142 - 143: 29.629 distance: 144 - 145: 44.373 distance: 145 - 146: 42.842 distance: 145 - 148: 54.494 distance: 146 - 147: 35.762 distance: 146 - 156: 48.313 distance: 148 - 149: 25.470 distance: 149 - 150: 16.517 distance: 149 - 151: 23.100 distance: 150 - 152: 15.095 distance: 153 - 154: 13.698 distance: 154 - 155: 11.258 distance: 156 - 157: 31.845 distance: 157 - 158: 21.523 distance: 158 - 159: 42.482 distance: 158 - 160: 24.667 distance: 160 - 161: 25.665 distance: 161 - 162: 20.238 distance: 161 - 164: 25.101 distance: 162 - 163: 28.579 distance: 162 - 167: 8.493 distance: 164 - 166: 11.897 distance: 168 - 169: 44.425 distance: 168 - 171: 17.971 distance: 169 - 170: 50.404 distance: 169 - 173: 29.030 distance: 171 - 172: 16.100