Starting phenix.real_space_refine on Tue Mar 26 00:34:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/03_2024/8g6e_29764_updated.pdb" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 282 5.16 5 C 33146 2.51 5 N 8676 2.21 5 O 10162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 230": "OE1" <-> "OE2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 195": "OD1" <-> "OD2" Residue "N TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "P TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 44": "OD1" <-> "OD2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ASP 122": "OD1" <-> "OD2" Residue "U ASP 205": "OD1" <-> "OD2" Residue "V PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X ASP 172": "OD1" <-> "OD2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "b TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 52266 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2006 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain: "B" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1851 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "C" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1938 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "D" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1870 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain: "E" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1867 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain: "F" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1897 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "G" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2025 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain: "H" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1991 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 244} Chain breaks: 1 Chain: "I" Number of atoms: 1703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} bond proxies already assigned to first conformer: 1717 Chain: "J" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1653 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 1 Chain: "K" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "L" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1663 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain: "M" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "N" Number of atoms: 2106 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2095 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 2095 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 2129 Chain: "O" Number of atoms: 2006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2006 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain: "P" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1851 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 7, 'TRANS': 225} Chain: "Q" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1938 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 5, 'TRANS': 236} Chain: "R" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1870 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain: "S" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1867 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 6, 'TRANS': 234} Chain: "T" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1897 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "U" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2025 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 5, 'TRANS': 241} Chain: "V" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1991 Classifications: {'peptide': 246} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 244} Chain breaks: 1 Chain: "W" Number of atoms: 1703 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 221, 1693 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} bond proxies already assigned to first conformer: 1717 Chain: "X" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1653 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain breaks: 1 Chain: "Y" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1614 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 193} Chain: "Z" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1663 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 209} Chain: "a" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1711 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 209} Chain: "b" Number of atoms: 2106 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2095 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 2095 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 2129 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'YRE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "I" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "Y" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "Z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "b" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AHIS I 54 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS I 54 " occ=0.50 residue: pdb=" N AARG N 211 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG N 211 " occ=0.46 residue: pdb=" N AHIS W 54 " occ=0.54 ... (18 atoms not shown) pdb=" NE2BHIS W 54 " occ=0.46 residue: pdb=" N AARG b 211 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG b 211 " occ=0.43 Time building chain proxies: 29.85, per 1000 atoms: 0.57 Number of scatterers: 52266 At special positions: 0 Unit cell: (138.276, 176.364, 138.276, 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 282 16.00 O 10162 8.00 N 8676 7.00 C 33146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.34 Conformation dependent library (CDL) restraints added in 10.3 seconds 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 172 helices and 68 sheets defined 35.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.25 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.639A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 111 Processing helix chain 'A' and resid 117 through 133 removed outlier: 3.769A pdb=" N VAL A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 201 through 220 Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 101 Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.716A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 184 through 198 Processing helix chain 'B' and resid 224 through 232 Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 29 Processing helix chain 'C' and resid 80 through 101 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 168 through 178 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 229 through 242 Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 77 through 98 Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.772A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 194 Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 219 through 236 Processing helix chain 'E' and resid 22 through 29 Processing helix chain 'E' and resid 82 through 103 Processing helix chain 'E' and resid 109 through 124 removed outlier: 5.025A pdb=" N PHE E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 193 through 207 Processing helix chain 'E' and resid 234 through 243 removed outlier: 3.659A pdb=" N VAL E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.805A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.720A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR F 120 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 180 removed outlier: 5.343A pdb=" N HIS F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU F 179 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU F 180 " --> pdb=" O HIS F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.761A pdb=" N SER F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 240 Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 53 through 55 No H-bonds generated for 'chain 'G' and resid 53 through 55' Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.779A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 181 removed outlier: 3.925A pdb=" N LYS G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 189 through 203 removed outlier: 4.136A pdb=" N GLU G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 250 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 49 through 69 Processing helix chain 'H' and resid 94 through 97 No H-bonds generated for 'chain 'H' and resid 94 through 97' Processing helix chain 'H' and resid 129 through 142 Processing helix chain 'H' and resid 190 through 196 Processing helix chain 'H' and resid 203 through 220 Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 131 through 141 Processing helix chain 'I' and resid 148 through 165 Processing helix chain 'J' and resid 3 through 8 removed outlier: 4.239A pdb=" N ASN J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 80 Processing helix chain 'J' and resid 86 through 100 removed outlier: 3.749A pdb=" N ASN J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 166 Processing helix chain 'J' and resid 173 through 190 removed outlier: 3.843A pdb=" N ARG J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 Processing helix chain 'K' and resid 78 through 93 Processing helix chain 'K' and resid 134 through 146 removed outlier: 4.639A pdb=" N SER K 140 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR K 146 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.720A pdb=" N TYR L 90 " --> pdb=" O ILE L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 Processing helix chain 'L' and resid 149 through 166 Processing helix chain 'L' and resid 193 through 200 removed outlier: 3.600A pdb=" N TYR L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 107 Processing helix chain 'M' and resid 113 through 127 removed outlier: 4.069A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 181 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 195 through 212 removed outlier: 3.605A pdb=" N ARG M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 78 Processing helix chain 'N' and resid 82 through 84 No H-bonds generated for 'chain 'N' and resid 82 through 84' Processing helix chain 'N' and resid 88 through 104 Processing helix chain 'N' and resid 126 through 128 No H-bonds generated for 'chain 'N' and resid 126 through 128' Processing helix chain 'N' and resid 156 through 158 No H-bonds generated for 'chain 'N' and resid 156 through 158' Processing helix chain 'N' and resid 179 through 182 Processing helix chain 'N' and resid 184 through 192 removed outlier: 3.586A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 Processing helix chain 'N' and resid 255 through 257 No H-bonds generated for 'chain 'N' and resid 255 through 257' Processing helix chain 'O' and resid 23 through 35 removed outlier: 3.650A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.733A pdb=" N VAL O 130 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 193 Processing helix chain 'O' and resid 201 through 220 Processing helix chain 'O' and resid 226 through 228 No H-bonds generated for 'chain 'O' and resid 226 through 228' Processing helix chain 'O' and resid 246 through 257 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 20 through 30 Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 80 through 101 Processing helix chain 'P' and resid 107 through 122 removed outlier: 3.708A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 184 through 198 Processing helix chain 'P' and resid 224 through 232 Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 29 Processing helix chain 'Q' and resid 80 through 101 Processing helix chain 'Q' and resid 107 through 123 Processing helix chain 'Q' and resid 168 through 178 Processing helix chain 'Q' and resid 185 through 199 Processing helix chain 'Q' and resid 207 through 209 No H-bonds generated for 'chain 'Q' and resid 207 through 209' Processing helix chain 'Q' and resid 229 through 242 Processing helix chain 'R' and resid 17 through 28 Processing helix chain 'R' and resid 77 through 98 Processing helix chain 'R' and resid 104 through 119 Processing helix chain 'R' and resid 165 through 174 removed outlier: 3.654A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 194 Processing helix chain 'R' and resid 201 through 203 No H-bonds generated for 'chain 'R' and resid 201 through 203' Processing helix chain 'R' and resid 219 through 236 Processing helix chain 'S' and resid 22 through 30 removed outlier: 3.511A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 103 Processing helix chain 'S' and resid 109 through 124 removed outlier: 5.013A pdb=" N PHE S 123 " --> pdb=" O LEU S 119 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER S 124 " --> pdb=" O ALA S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 176 through 186 Processing helix chain 'S' and resid 193 through 207 Processing helix chain 'S' and resid 234 through 243 Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.805A pdb=" N ILE T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS T 30 " --> pdb=" O SER T 26 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 105 through 120 removed outlier: 3.735A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR T 120 " --> pdb=" O TYR T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 180 removed outlier: 5.335A pdb=" N HIS T 176 " --> pdb=" O GLU T 172 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU T 177 " --> pdb=" O LYS T 173 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE T 178 " --> pdb=" O ASN T 174 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU T 179 " --> pdb=" O LEU T 175 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU T 180 " --> pdb=" O HIS T 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 197 removed outlier: 3.760A pdb=" N SER T 197 " --> pdb=" O ALA T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 225 through 240 Processing helix chain 'U' and resid 22 through 33 Processing helix chain 'U' and resid 53 through 55 No H-bonds generated for 'chain 'U' and resid 53 through 55' Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 126 removed outlier: 3.779A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR U 126 " --> pdb=" O ILE U 122 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.920A pdb=" N LYS U 181 " --> pdb=" O THR U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 186 No H-bonds generated for 'chain 'U' and resid 184 through 186' Processing helix chain 'U' and resid 189 through 203 removed outlier: 4.152A pdb=" N GLU U 194 " --> pdb=" O ARG U 190 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP U 195 " --> pdb=" O ASP U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 250 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 49 through 70 Processing helix chain 'V' and resid 94 through 97 No H-bonds generated for 'chain 'V' and resid 94 through 97' Processing helix chain 'V' and resid 129 through 142 Processing helix chain 'V' and resid 186 through 196 removed outlier: 5.205A pdb=" N SER V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYR V 192 " --> pdb=" O TYR V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 220 Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 131 through 141 Processing helix chain 'W' and resid 148 through 165 Processing helix chain 'X' and resid 3 through 8 removed outlier: 4.238A pdb=" N ASN X 8 " --> pdb=" O ILE X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 80 Processing helix chain 'X' and resid 86 through 100 removed outlier: 3.748A pdb=" N ASN X 100 " --> pdb=" O ILE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 156 through 166 Processing helix chain 'X' and resid 173 through 190 removed outlier: 3.833A pdb=" N ARG X 190 " --> pdb=" O SER X 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 Processing helix chain 'Y' and resid 78 through 94 removed outlier: 4.165A pdb=" N ARG Y 94 " --> pdb=" O ALA Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 146 removed outlier: 4.766A pdb=" N SER Y 140 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ALA Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR Y 146 " --> pdb=" O LEU Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.721A pdb=" N TYR Z 90 " --> pdb=" O ILE Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 Processing helix chain 'Z' and resid 149 through 166 Processing helix chain 'Z' and resid 193 through 200 removed outlier: 3.592A pdb=" N TYR Z 198 " --> pdb=" O PHE Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 107 Processing helix chain 'a' and resid 113 through 127 removed outlier: 4.067A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 181 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 195 through 212 removed outlier: 3.581A pdb=" N ARG a 212 " --> pdb=" O SER a 208 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 78 Processing helix chain 'b' and resid 82 through 84 No H-bonds generated for 'chain 'b' and resid 82 through 84' Processing helix chain 'b' and resid 88 through 104 Processing helix chain 'b' and resid 126 through 128 No H-bonds generated for 'chain 'b' and resid 126 through 128' Processing helix chain 'b' and resid 156 through 158 No H-bonds generated for 'chain 'b' and resid 156 through 158' Processing helix chain 'b' and resid 179 through 182 Processing helix chain 'b' and resid 184 through 192 removed outlier: 3.605A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 199 through 216 Processing helix chain 'b' and resid 255 through 257 No H-bonds generated for 'chain 'b' and resid 255 through 257' Processing sheet with id= A, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= B, first strand: chain 'A' and resid 75 through 77 removed outlier: 3.561A pdb=" N GLY A 83 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 160 through 163 removed outlier: 3.831A pdb=" N GLY B 43 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 155 through 157 removed outlier: 3.538A pdb=" N SER B 69 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 74 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLN B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N TYR B 76 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE B 65 " --> pdb=" O TYR B 76 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 161 through 164 removed outlier: 4.853A pdb=" N LEU C 212 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 65 through 67 Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 62 through 64 removed outlier: 4.122A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 169 through 172 Processing sheet with id= J, first strand: chain 'E' and resid 164 through 167 removed outlier: 4.122A pdb=" N LEU E 155 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N CYS E 76 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N MET E 78 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= L, first strand: chain 'F' and resid 152 through 155 removed outlier: 4.045A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 72 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LYS F 65 " --> pdb=" O ILE F 72 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N MET F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE F 63 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 165 through 168 Processing sheet with id= N, first strand: chain 'G' and resid 76 through 82 removed outlier: 3.878A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 179 through 182 Processing sheet with id= P, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.683A pdb=" N SER H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU H 164 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL H 43 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ARG H 36 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG H 45 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE H 34 " --> pdb=" O ARG H 45 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.484A pdb=" N SER H 22 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ILE H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 124 through 127 Processing sheet with id= S, first strand: chain 'I' and resid 119 through 121 removed outlier: 6.555A pdb=" N CYS I 43 " --> pdb=" O TYR I 36 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR I 36 " --> pdb=" O CYS I 43 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY I 45 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU I 34 " --> pdb=" O GLY I 45 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.048A pdb=" N GLU I 22 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL I 26 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 149 through 153 removed outlier: 5.789A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 143 through 146 removed outlier: 3.922A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER J 56 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL J 53 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS J 46 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU J 55 " --> pdb=" O ILE J 44 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE J 44 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.592A pdb=" N ALA J 31 " --> pdb=" O THR J 36 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N THR J 36 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= Y, first strand: chain 'K' and resid 36 through 39 Processing sheet with id= Z, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.406A pdb=" N ASN K 23 " --> pdb=" O LYS K 27 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS K 27 " --> pdb=" O ASN K 23 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.673A pdb=" N HIS L 178 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS L 186 " --> pdb=" O HIS L 178 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS L 180 " --> pdb=" O TYR L 184 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR L 184 " --> pdb=" O HIS L 180 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 120 through 122 removed outlier: 3.765A pdb=" N ILE L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLY L 43 " --> pdb=" O GLU L 36 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU L 36 " --> pdb=" O GLY L 43 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET L 45 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE L 34 " --> pdb=" O MET L 45 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.208A pdb=" N MET L 22 " --> pdb=" O ILE L 26 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 163 through 167 removed outlier: 5.349A pdb=" N THR M 39 " --> pdb=" O ASP M 54 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 158 through 161 removed outlier: 3.758A pdb=" N LEU M 149 " --> pdb=" O ALA M 161 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN M 136 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE M 80 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS M 73 " --> pdb=" O ILE M 80 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N SER M 82 " --> pdb=" O ILE M 71 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE M 71 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.300A pdb=" N LEU M 59 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'N' and resid 175 through 177 Processing sheet with id= AH, first strand: chain 'N' and resid 170 through 172 removed outlier: 6.164A pdb=" N MET N 52 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LYS N 45 " --> pdb=" O MET N 52 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE N 54 " --> pdb=" O ILE N 43 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE N 43 " --> pdb=" O PHE N 54 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'O' and resid 171 through 174 Processing sheet with id= AJ, first strand: chain 'O' and resid 75 through 77 removed outlier: 3.577A pdb=" N GLY O 83 " --> pdb=" O ILE O 147 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'P' and resid 160 through 163 removed outlier: 3.839A pdb=" N GLY P 43 " --> pdb=" O ALA P 40 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'P' and resid 155 through 157 removed outlier: 3.543A pdb=" N SER P 69 " --> pdb=" O ILE P 72 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE P 74 " --> pdb=" O GLN P 67 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN P 67 " --> pdb=" O ILE P 74 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N TYR P 76 " --> pdb=" O ILE P 65 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE P 65 " --> pdb=" O TYR P 76 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Q' and resid 161 through 164 removed outlier: 4.854A pdb=" N LEU Q 212 " --> pdb=" O LEU Q 227 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id= AO, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AP, first strand: chain 'R' and resid 62 through 64 removed outlier: 4.120A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'S' and resid 169 through 172 Processing sheet with id= AR, first strand: chain 'S' and resid 164 through 167 removed outlier: 4.090A pdb=" N LEU S 155 " --> pdb=" O PHE S 167 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS S 76 " --> pdb=" O SER S 69 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER S 69 " --> pdb=" O CYS S 76 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N MET S 78 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU S 67 " --> pdb=" O MET S 78 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 157 through 160 Processing sheet with id= AT, first strand: chain 'T' and resid 152 through 155 removed outlier: 4.054A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE T 72 " --> pdb=" O LYS T 65 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS T 65 " --> pdb=" O ILE T 72 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N MET T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE T 63 " --> pdb=" O MET T 74 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'U' and resid 165 through 168 Processing sheet with id= AV, first strand: chain 'U' and resid 76 through 82 removed outlier: 3.849A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'V' and resid 179 through 182 Processing sheet with id= AX, first strand: chain 'V' and resid 172 through 176 removed outlier: 3.696A pdb=" N SER V 172 " --> pdb=" O ASN V 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU V 164 " --> pdb=" O LYS V 176 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL V 43 " --> pdb=" O ARG V 36 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG V 36 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG V 45 " --> pdb=" O ILE V 34 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE V 34 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.278A pdb=" N SER V 22 " --> pdb=" O ILE V 26 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE V 26 " --> pdb=" O SER V 22 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'W' and resid 124 through 127 Processing sheet with id= BA, first strand: chain 'W' and resid 119 through 121 removed outlier: 6.557A pdb=" N CYS W 43 " --> pdb=" O TYR W 36 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N TYR W 36 " --> pdb=" O CYS W 43 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY W 45 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU W 34 " --> pdb=" O GLY W 45 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'W' and resid 20 through 22 removed outlier: 6.014A pdb=" N GLU W 22 " --> pdb=" O VAL W 26 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL W 26 " --> pdb=" O GLU W 22 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'X' and resid 149 through 153 removed outlier: 5.795A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA X 198 " --> pdb=" O LEU X 213 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.900A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER X 56 " --> pdb=" O ASN X 108 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL X 53 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS X 46 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU X 55 " --> pdb=" O ILE X 44 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE X 44 " --> pdb=" O LEU X 55 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.585A pdb=" N ALA X 31 " --> pdb=" O THR X 36 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N THR X 36 " --> pdb=" O ALA X 31 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= BG, first strand: chain 'Y' and resid 36 through 39 Processing sheet with id= BH, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.428A pdb=" N ASN Y 23 " --> pdb=" O LYS Y 27 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS Y 27 " --> pdb=" O ASN Y 23 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.652A pdb=" N HIS Z 178 " --> pdb=" O LYS Z 186 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS Z 186 " --> pdb=" O HIS Z 178 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS Z 180 " --> pdb=" O TYR Z 184 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR Z 184 " --> pdb=" O HIS Z 180 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Z' and resid 120 through 122 removed outlier: 3.764A pdb=" N ILE Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLY Z 43 " --> pdb=" O GLU Z 36 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU Z 36 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N MET Z 45 " --> pdb=" O ILE Z 34 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE Z 34 " --> pdb=" O MET Z 45 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.199A pdb=" N MET Z 22 " --> pdb=" O ILE Z 26 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE Z 26 " --> pdb=" O MET Z 22 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 163 through 167 removed outlier: 5.330A pdb=" N THR a 39 " --> pdb=" O ASP a 54 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.761A pdb=" N LEU a 149 " --> pdb=" O ALA a 161 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN a 136 " --> pdb=" O TYR a 152 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE a 80 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS a 73 " --> pdb=" O ILE a 80 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER a 82 " --> pdb=" O ILE a 71 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE a 71 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.294A pdb=" N LEU a 59 " --> pdb=" O ILE a 63 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ILE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 175 through 177 Processing sheet with id= BP, first strand: chain 'b' and resid 170 through 172 removed outlier: 6.148A pdb=" N MET b 52 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS b 45 " --> pdb=" O MET b 52 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE b 54 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ILE b 43 " --> pdb=" O PHE b 54 " (cutoff:3.500A) 2592 hydrogen bonds defined for protein. 7417 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: 21.81 Time building geometry restraints manager: 21.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11067 1.33 - 1.45: 11986 1.45 - 1.57: 29573 1.57 - 1.69: 2 1.69 - 1.82: 402 Bond restraints: 53030 Sorted by residual: bond pdb=" C07 YRE Q 301 " pdb=" C11 YRE Q 301 " ideal model delta sigma weight residual 1.365 1.551 -0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" C07 YRE C 301 " pdb=" C11 YRE C 301 " ideal model delta sigma weight residual 1.365 1.548 -0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C07 YRE L 301 " pdb=" C11 YRE L 301 " ideal model delta sigma weight residual 1.365 1.545 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C02 YRE W 301 " pdb=" N03 YRE W 301 " ideal model delta sigma weight residual 1.523 1.343 0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C07 YRE Z 301 " pdb=" C11 YRE Z 301 " ideal model delta sigma weight residual 1.365 1.544 -0.179 2.00e-02 2.50e+03 8.03e+01 ... (remaining 53025 not shown) Histogram of bond angle deviations from ideal: 99.28 - 106.24: 748 106.24 - 113.20: 28740 113.20 - 120.16: 18867 120.16 - 127.12: 22932 127.12 - 134.08: 339 Bond angle restraints: 71626 Sorted by residual: angle pdb=" C02 YRE L 301 " pdb=" N03 YRE L 301 " pdb=" C04 YRE L 301 " ideal model delta sigma weight residual 109.69 125.00 -15.31 3.00e+00 1.11e-01 2.61e+01 angle pdb=" C02 YRE Z 301 " pdb=" N03 YRE Z 301 " pdb=" C04 YRE Z 301 " ideal model delta sigma weight residual 109.69 124.94 -15.25 3.00e+00 1.11e-01 2.59e+01 angle pdb=" C02 YRE C 301 " pdb=" N03 YRE C 301 " pdb=" C04 YRE C 301 " ideal model delta sigma weight residual 109.69 124.65 -14.96 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C02 YRE Q 301 " pdb=" N03 YRE Q 301 " pdb=" C04 YRE Q 301 " ideal model delta sigma weight residual 109.69 124.34 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C02 YRE W 301 " pdb=" N03 YRE W 301 " pdb=" C04 YRE W 301 " ideal model delta sigma weight residual 109.69 123.16 -13.47 3.00e+00 1.11e-01 2.02e+01 ... (remaining 71621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 30925 35.68 - 71.37: 887 71.37 - 107.05: 106 107.05 - 142.74: 8 142.74 - 178.42: 10 Dihedral angle restraints: 31936 sinusoidal: 12862 harmonic: 19074 Sorted by residual: dihedral pdb=" CA ASN b 111 " pdb=" C ASN b 111 " pdb=" N ASN b 112 " pdb=" CA ASN b 112 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA ASN N 111 " pdb=" C ASN N 111 " pdb=" N ASN N 112 " pdb=" CA ASN N 112 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C15 YRE W 301 " pdb=" C16 YRE W 301 " pdb=" C17 YRE W 301 " pdb=" C18 YRE W 301 " ideal model delta sinusoidal sigma weight residual 107.18 -74.40 -178.42 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 31933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.055: 7978 1.055 - 2.110: 0 2.110 - 3.165: 0 3.165 - 4.219: 0 4.219 - 5.274: 6 Chirality restraints: 7984 Sorted by residual: chirality pdb=" C07 YRE Q 301 " pdb=" C08 YRE Q 301 " pdb=" C11 YRE Q 301 " pdb=" N06 YRE Q 301 " both_signs ideal model delta sigma weight residual False -2.62 2.66 -5.27 2.00e-01 2.50e+01 6.95e+02 chirality pdb=" C07 YRE L 301 " pdb=" C08 YRE L 301 " pdb=" C11 YRE L 301 " pdb=" N06 YRE L 301 " both_signs ideal model delta sigma weight residual False -2.62 2.65 -5.27 2.00e-01 2.50e+01 6.94e+02 chirality pdb=" C07 YRE Z 301 " pdb=" C08 YRE Z 301 " pdb=" C11 YRE Z 301 " pdb=" N06 YRE Z 301 " both_signs ideal model delta sigma weight residual False -2.62 2.65 -5.27 2.00e-01 2.50e+01 6.93e+02 ... (remaining 7981 not shown) Planarity restraints: 9138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE Q 73 " -0.020 2.00e-02 2.50e+03 1.78e-02 5.53e+00 pdb=" CG PHE Q 73 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE Q 73 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE Q 73 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE Q 73 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE Q 73 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE Q 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 73 " 0.020 2.00e-02 2.50e+03 1.75e-02 5.37e+00 pdb=" CG PHE C 73 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 73 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 73 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 73 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE C 73 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 73 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 64 " 0.018 2.00e-02 2.50e+03 1.42e-02 4.03e+00 pdb=" CG TYR a 64 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR a 64 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR a 64 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR a 64 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR a 64 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR a 64 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR a 64 " 0.003 2.00e-02 2.50e+03 ... (remaining 9135 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 251 2.53 - 3.13: 40452 3.13 - 3.72: 84994 3.72 - 4.31: 127513 4.31 - 4.90: 208225 Nonbonded interactions: 461435 Sorted by model distance: nonbonded pdb=" O ASN V 104 " pdb=" OD1 ASN V 104 " model vdw 1.943 3.040 nonbonded pdb=" OG1 THR X 60 " pdb=" OG SER Y 122 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR J 60 " pdb=" OG SER K 122 " model vdw 2.235 2.440 nonbonded pdb=" OH TYR N 123 " pdb=" OD2 ASP N 158 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR b 123 " pdb=" OD2 ASP b 158 " model vdw 2.261 2.440 ... (remaining 461430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = (chain 'I' and (resid 1 through 53 or resid 55 through 221 or resid 301)) selection = (chain 'W' and (resid 1 through 53 or resid 55 through 221 or resid 301)) } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = (chain 'N' and (resid 2 through 210 or resid 212 through 265)) selection = (chain 'b' and (resid 2 through 210 or resid 212 through 265)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 14.910 Check model and map are aligned: 0.750 Set scattering table: 0.450 Process input model: 141.190 Find NCS groups from input model: 5.680 Set up NCS constraints: 0.590 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.006 0.186 53030 Z= 0.399 Angle : 0.637 15.314 71626 Z= 0.335 Chirality : 0.150 5.274 7984 Planarity : 0.004 0.045 9138 Dihedral : 17.261 178.424 19740 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.63 % Allowed : 14.48 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.10), residues: 6434 helix: 1.73 (0.10), residues: 2362 sheet: 0.45 (0.13), residues: 1490 loop : -0.35 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Z 55 HIS 0.008 0.001 HIS V 134 PHE 0.040 0.002 PHE Q 73 TYR 0.034 0.002 TYR a 64 ARG 0.005 0.001 ARG E 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 838 time to evaluate : 6.342 Fit side-chains REVERT: A 198 GLN cc_start: 0.4235 (tp40) cc_final: 0.3898 (tp-100) REVERT: B 100 GLN cc_start: 0.7785 (mt0) cc_final: 0.7494 (mt0) REVERT: B 186 ASP cc_start: 0.6776 (m-30) cc_final: 0.6400 (m-30) REVERT: B 209 GLU cc_start: 0.7515 (tt0) cc_final: 0.7174 (mm-30) REVERT: B 228 LYS cc_start: 0.5658 (ttmm) cc_final: 0.5197 (mtpt) REVERT: C 3 ARG cc_start: 0.7306 (ptp90) cc_final: 0.6923 (ptm-80) REVERT: C 176 LYS cc_start: 0.7058 (ttmm) cc_final: 0.6718 (ttpp) REVERT: C 233 GLU cc_start: 0.6688 (mm-30) cc_final: 0.6413 (mm-30) REVERT: D 67 GLU cc_start: 0.7191 (mp0) cc_final: 0.6927 (mp0) REVERT: D 179 ASN cc_start: 0.6915 (m-40) cc_final: 0.6665 (m-40) REVERT: D 213 ASP cc_start: 0.6928 (p0) cc_final: 0.6406 (p0) REVERT: E 62 ASP cc_start: 0.5993 (m-30) cc_final: 0.5758 (m-30) REVERT: E 180 GLU cc_start: 0.6381 (tp30) cc_final: 0.6176 (tt0) REVERT: E 189 LYS cc_start: 0.6176 (mttp) cc_final: 0.5888 (ttmm) REVERT: F 18 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7798 (mtm180) REVERT: F 53 ILE cc_start: 0.6710 (mm) cc_final: 0.6506 (mp) REVERT: F 176 HIS cc_start: 0.6990 (p-80) cc_final: 0.6685 (p90) REVERT: F 234 LYS cc_start: 0.6725 (mtpt) cc_final: 0.6262 (mttm) REVERT: G 213 GLN cc_start: 0.7111 (mp10) cc_final: 0.6703 (mt0) REVERT: I 78 MET cc_start: 0.8736 (ttp) cc_final: 0.8531 (ttt) REVERT: I 216 LYS cc_start: 0.7589 (ptmt) cc_final: 0.7276 (pttt) REVERT: K 20 TYR cc_start: 0.8234 (m-80) cc_final: 0.8003 (m-10) REVERT: K 96 ASN cc_start: 0.5900 (t0) cc_final: 0.5487 (p0) REVERT: L 91 LYS cc_start: 0.7714 (ttpt) cc_final: 0.7490 (ttmt) REVERT: L 191 GLU cc_start: 0.7668 (tt0) cc_final: 0.7446 (tt0) REVERT: L 206 LYS cc_start: 0.7174 (ptpt) cc_final: 0.6556 (mttt) REVERT: M 146 LYS cc_start: 0.7153 (mtpt) cc_final: 0.6866 (tttm) REVERT: N 122 LYS cc_start: 0.7896 (pttt) cc_final: 0.7635 (pttp) REVERT: N 200 GLU cc_start: 0.7100 (mp0) cc_final: 0.6882 (mp0) REVERT: O 8 MET cc_start: 0.4676 (ptm) cc_final: 0.3926 (mmt) REVERT: P 100 GLN cc_start: 0.7749 (mt0) cc_final: 0.7418 (mt0) REVERT: P 169 ASN cc_start: 0.7147 (m-40) cc_final: 0.6798 (m-40) REVERT: P 171 MET cc_start: 0.7598 (mmm) cc_final: 0.7373 (tpp) REVERT: P 186 ASP cc_start: 0.6786 (m-30) cc_final: 0.6465 (m-30) REVERT: Q 3 ARG cc_start: 0.7251 (ptp90) cc_final: 0.6914 (ptm-80) REVERT: R 179 ASN cc_start: 0.6983 (m-40) cc_final: 0.6713 (m-40) REVERT: R 213 ASP cc_start: 0.6866 (p0) cc_final: 0.6353 (p0) REVERT: S 62 ASP cc_start: 0.5939 (m-30) cc_final: 0.5706 (m-30) REVERT: S 135 MET cc_start: 0.8167 (mmt) cc_final: 0.7845 (mmt) REVERT: S 180 GLU cc_start: 0.6426 (tp30) cc_final: 0.6215 (tt0) REVERT: T 41 LYS cc_start: 0.7656 (ptpp) cc_final: 0.7440 (ptpp) REVERT: T 53 ILE cc_start: 0.6850 (mm) cc_final: 0.6604 (mp) REVERT: T 176 HIS cc_start: 0.7007 (p-80) cc_final: 0.6674 (p90) REVERT: T 234 LYS cc_start: 0.6762 (mtpt) cc_final: 0.6411 (mttm) REVERT: U 63 LYS cc_start: 0.6821 (tttp) cc_final: 0.6604 (ttmm) REVERT: U 213 GLN cc_start: 0.7090 (mp10) cc_final: 0.6683 (mt0) REVERT: U 246 GLU cc_start: 0.5928 (pp20) cc_final: 0.5419 (pp20) REVERT: W 78 MET cc_start: 0.8710 (ttp) cc_final: 0.8488 (ttt) REVERT: W 194 MET cc_start: 0.6784 (ptp) cc_final: 0.6543 (pmm) REVERT: W 216 LYS cc_start: 0.7597 (ptmt) cc_final: 0.7285 (pttt) REVERT: X 144 CYS cc_start: 0.8237 (t) cc_final: 0.8000 (p) REVERT: Y 3 THR cc_start: 0.8995 (t) cc_final: 0.8781 (m) REVERT: Y 20 TYR cc_start: 0.8182 (m-80) cc_final: 0.7963 (m-10) REVERT: Y 96 ASN cc_start: 0.5877 (t0) cc_final: 0.5559 (p0) REVERT: Y 109 LYS cc_start: 0.7597 (mmtt) cc_final: 0.7351 (mmmm) REVERT: Y 161 LYS cc_start: 0.8053 (tppp) cc_final: 0.7705 (tptm) REVERT: Z 91 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7558 (ttmt) REVERT: Z 191 GLU cc_start: 0.7646 (tt0) cc_final: 0.7397 (tt0) REVERT: Z 206 LYS cc_start: 0.7134 (ptpt) cc_final: 0.6525 (mttt) REVERT: Z 211 MET cc_start: 0.7326 (mtt) cc_final: 0.6955 (mtt) REVERT: a 112 ASP cc_start: 0.7788 (t0) cc_final: 0.7565 (t0) REVERT: a 146 LYS cc_start: 0.7127 (mtpt) cc_final: 0.6907 (tttt) REVERT: b 122 LYS cc_start: 0.7855 (pttt) cc_final: 0.7586 (pttp) REVERT: b 150 GLU cc_start: 0.5849 (tp30) cc_final: 0.5572 (mm-30) REVERT: b 200 GLU cc_start: 0.7166 (mp0) cc_final: 0.6956 (mp0) outliers start: 36 outliers final: 25 residues processed: 869 average time/residue: 1.7684 time to fit residues: 1898.3396 Evaluate side-chains 703 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 678 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 256 ILE Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain a residue 65 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 538 optimal weight: 3.9990 chunk 483 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 258 optimal weight: 6.9990 chunk 500 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 304 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 579 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 153 ASN D 169 GLN E 227 GLN G 112 HIS G 206 HIS H 208 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN J 80 GLN J 108 ASN J 129 ASN N 125 ASN N 126 ASN O 53 GLN Q 149 HIS R 169 GLN T 227 GLN V 104 ASN V 208 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN X 108 ASN X 129 ASN b 112 ASN b 125 ASN b 126 ASN b 192 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 53030 Z= 0.319 Angle : 0.674 10.939 71626 Z= 0.360 Chirality : 0.049 0.466 7984 Planarity : 0.005 0.053 9138 Dihedral : 11.023 178.111 7340 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 15.30 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.10), residues: 6434 helix: 1.74 (0.10), residues: 2366 sheet: 0.60 (0.13), residues: 1468 loop : -0.29 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 55 HIS 0.007 0.002 HIS H 134 PHE 0.021 0.003 PHE J 102 TYR 0.023 0.002 TYR a 64 ARG 0.007 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 698 time to evaluate : 5.748 Fit side-chains REVERT: A 86 MET cc_start: 0.8438 (mmt) cc_final: 0.8200 (mmt) REVERT: A 198 GLN cc_start: 0.4311 (tp40) cc_final: 0.3979 (tp-100) REVERT: B 100 GLN cc_start: 0.7767 (mt0) cc_final: 0.7481 (mt0) REVERT: B 193 LEU cc_start: 0.7155 (mm) cc_final: 0.6769 (tp) REVERT: B 208 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7423 (pp) REVERT: B 209 GLU cc_start: 0.7481 (tt0) cc_final: 0.7129 (mm-30) REVERT: C 3 ARG cc_start: 0.7328 (ptp90) cc_final: 0.6970 (ptm-80) REVERT: C 176 LYS cc_start: 0.7021 (ttmm) cc_final: 0.6730 (ttpp) REVERT: C 233 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6396 (mm-30) REVERT: D 67 GLU cc_start: 0.7204 (mp0) cc_final: 0.6948 (mp0) REVERT: D 213 ASP cc_start: 0.6914 (p0) cc_final: 0.6386 (p0) REVERT: E 180 GLU cc_start: 0.6441 (tp30) cc_final: 0.6216 (tt0) REVERT: E 189 LYS cc_start: 0.6147 (mttp) cc_final: 0.5887 (ttmm) REVERT: F 18 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7799 (mtm180) REVERT: F 53 ILE cc_start: 0.6750 (mm) cc_final: 0.6508 (mp) REVERT: F 82 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (mmtp) REVERT: F 230 GLU cc_start: 0.6271 (OUTLIER) cc_final: 0.5973 (tm-30) REVERT: G 213 GLN cc_start: 0.7087 (mp10) cc_final: 0.6678 (mt0) REVERT: H 75 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7104 (mtt-85) REVERT: I 216 LYS cc_start: 0.7653 (ptmt) cc_final: 0.7323 (pttt) REVERT: K 96 ASN cc_start: 0.5952 (t0) cc_final: 0.5522 (p0) REVERT: K 109 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7242 (mttp) REVERT: L 91 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7432 (tttt) REVERT: L 189 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: L 206 LYS cc_start: 0.7204 (ptpt) cc_final: 0.6750 (mtmt) REVERT: M 64 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: M 146 LYS cc_start: 0.7207 (mtpt) cc_final: 0.6965 (tttt) REVERT: N 122 LYS cc_start: 0.7893 (pttt) cc_final: 0.7642 (pttp) REVERT: N 200 GLU cc_start: 0.7122 (mp0) cc_final: 0.6909 (mp0) REVERT: O 8 MET cc_start: 0.4688 (ptm) cc_final: 0.3946 (mmt) REVERT: O 86 MET cc_start: 0.8444 (mmt) cc_final: 0.8200 (mmt) REVERT: P 100 GLN cc_start: 0.7780 (mt0) cc_final: 0.7428 (mt0) REVERT: P 169 ASN cc_start: 0.7165 (m-40) cc_final: 0.6835 (m-40) REVERT: Q 3 ARG cc_start: 0.7265 (ptp90) cc_final: 0.6901 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6540 (tmtt) REVERT: Q 80 ASN cc_start: 0.7701 (m-40) cc_final: 0.7440 (t0) REVERT: Q 225 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7755 (tttp) REVERT: R 178 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: R 179 ASN cc_start: 0.6971 (m-40) cc_final: 0.6711 (m-40) REVERT: R 213 ASP cc_start: 0.6916 (p0) cc_final: 0.6382 (p0) REVERT: S 8 TYR cc_start: 0.4360 (OUTLIER) cc_final: 0.4050 (t80) REVERT: S 65 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: S 135 MET cc_start: 0.8147 (mmt) cc_final: 0.7816 (mmt) REVERT: T 53 ILE cc_start: 0.6777 (mm) cc_final: 0.6526 (mp) REVERT: T 96 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8188 (mtpp) REVERT: T 176 HIS cc_start: 0.7030 (p-80) cc_final: 0.6679 (p90) REVERT: T 230 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6062 (tm-30) REVERT: T 234 LYS cc_start: 0.6757 (mtpt) cc_final: 0.6316 (tptm) REVERT: U 63 LYS cc_start: 0.6878 (tttp) cc_final: 0.6622 (ttmm) REVERT: U 213 GLN cc_start: 0.7094 (mp10) cc_final: 0.6672 (mt0) REVERT: U 246 GLU cc_start: 0.5939 (pp20) cc_final: 0.5373 (pp20) REVERT: W 78 MET cc_start: 0.8728 (ttp) cc_final: 0.8512 (ttt) REVERT: W 194 MET cc_start: 0.6578 (ptp) cc_final: 0.6103 (ptp) REVERT: W 216 LYS cc_start: 0.7610 (ptmt) cc_final: 0.7290 (pttt) REVERT: Y 96 ASN cc_start: 0.5837 (t0) cc_final: 0.5546 (p0) REVERT: Y 110 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7149 (ttmm) REVERT: Y 161 LYS cc_start: 0.8032 (tppp) cc_final: 0.7720 (tptm) REVERT: Z 91 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7469 (tttt) REVERT: Z 189 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: Z 206 LYS cc_start: 0.7143 (ptpt) cc_final: 0.6894 (mmtt) REVERT: Z 211 MET cc_start: 0.7348 (mtt) cc_final: 0.6994 (mtt) REVERT: a 64 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8419 (m-80) REVERT: a 146 LYS cc_start: 0.7225 (mtpt) cc_final: 0.6929 (tttt) REVERT: b 106 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8367 (mm) REVERT: b 122 LYS cc_start: 0.7873 (pttt) cc_final: 0.7635 (pttp) REVERT: b 150 GLU cc_start: 0.5835 (tp30) cc_final: 0.5622 (mm-30) REVERT: b 200 GLU cc_start: 0.7178 (mp0) cc_final: 0.6971 (mp0) outliers start: 172 outliers final: 81 residues processed: 828 average time/residue: 1.6693 time to fit residues: 1729.6085 Evaluate side-chains 767 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 668 time to evaluate : 5.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 165 LYS Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 321 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 482 optimal weight: 3.9990 chunk 394 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 580 optimal weight: 0.9990 chunk 627 optimal weight: 1.9990 chunk 516 optimal weight: 3.9990 chunk 575 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 465 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 59 GLN A 153 ASN D 169 GLN F 60 GLN F 176 HIS G 206 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 129 ASN N 125 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN O 59 GLN O 153 ASN Q 149 HIS R 169 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN W 109 GLN X 129 ASN Y 114 GLN Y 177 ASN b 125 ASN b 126 ASN b 192 HIS ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 53030 Z= 0.177 Angle : 0.546 10.122 71626 Z= 0.293 Chirality : 0.044 0.375 7984 Planarity : 0.004 0.048 9138 Dihedral : 10.499 177.861 7330 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.28 % Allowed : 16.51 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.10), residues: 6434 helix: 2.13 (0.10), residues: 2370 sheet: 0.76 (0.13), residues: 1488 loop : -0.16 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 55 HIS 0.006 0.001 HIS Q 149 PHE 0.017 0.002 PHE F 160 TYR 0.016 0.002 TYR a 64 ARG 0.007 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 705 time to evaluate : 5.803 Fit side-chains REVERT: A 86 MET cc_start: 0.8414 (mmt) cc_final: 0.8172 (mmt) REVERT: A 103 GLU cc_start: 0.7652 (tp30) cc_final: 0.7405 (mm-30) REVERT: A 198 GLN cc_start: 0.4265 (tp40) cc_final: 0.3974 (tp-100) REVERT: A 201 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6855 (mm) REVERT: B 100 GLN cc_start: 0.7661 (mt0) cc_final: 0.7391 (mm110) REVERT: B 205 GLU cc_start: 0.5637 (pm20) cc_final: 0.5417 (pm20) REVERT: B 209 GLU cc_start: 0.7491 (tt0) cc_final: 0.7102 (mm-30) REVERT: C 3 ARG cc_start: 0.7306 (ptp90) cc_final: 0.6942 (ptm-80) REVERT: C 176 LYS cc_start: 0.6985 (ttmm) cc_final: 0.6697 (ttpp) REVERT: C 233 GLU cc_start: 0.6522 (mm-30) cc_final: 0.6282 (mm-30) REVERT: D 67 GLU cc_start: 0.7151 (mp0) cc_final: 0.6887 (mp0) REVERT: D 170 GLU cc_start: 0.6214 (pp20) cc_final: 0.6013 (pp20) REVERT: E 180 GLU cc_start: 0.6432 (tp30) cc_final: 0.6220 (tt0) REVERT: E 189 LYS cc_start: 0.6244 (mttp) cc_final: 0.5981 (ttmm) REVERT: E 191 MET cc_start: 0.6828 (mtp) cc_final: 0.6541 (ttp) REVERT: F 230 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: G 213 GLN cc_start: 0.6982 (mp10) cc_final: 0.6675 (mt0) REVERT: J 118 HIS cc_start: 0.5817 (m-70) cc_final: 0.5372 (m-70) REVERT: K 11 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7391 (m-40) REVERT: K 96 ASN cc_start: 0.5819 (t0) cc_final: 0.5412 (p0) REVERT: K 109 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7168 (mttp) REVERT: L 91 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7401 (tttt) REVERT: L 189 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: L 206 LYS cc_start: 0.7169 (ptpt) cc_final: 0.6919 (mmtt) REVERT: M 64 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: M 146 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6876 (tttt) REVERT: N 122 LYS cc_start: 0.7901 (pttt) cc_final: 0.7642 (pttp) REVERT: N 200 GLU cc_start: 0.7105 (mp0) cc_final: 0.6897 (mp0) REVERT: O 8 MET cc_start: 0.4557 (ptm) cc_final: 0.3898 (mmt) REVERT: O 86 MET cc_start: 0.8423 (mmt) cc_final: 0.8178 (mmt) REVERT: P 100 GLN cc_start: 0.7632 (mt0) cc_final: 0.7349 (mm110) REVERT: P 169 ASN cc_start: 0.7148 (m-40) cc_final: 0.6813 (m-40) REVERT: P 186 ASP cc_start: 0.6724 (m-30) cc_final: 0.6473 (m-30) REVERT: Q 3 ARG cc_start: 0.7271 (ptp90) cc_final: 0.6906 (ptm-80) REVERT: Q 225 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7767 (tttp) REVERT: R 4 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: R 179 ASN cc_start: 0.6926 (m-40) cc_final: 0.6670 (m-40) REVERT: R 213 ASP cc_start: 0.6915 (p0) cc_final: 0.6384 (p0) REVERT: S 8 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.4166 (t80) REVERT: S 65 GLU cc_start: 0.5779 (OUTLIER) cc_final: 0.5431 (pm20) REVERT: S 78 MET cc_start: 0.8346 (ptp) cc_final: 0.7804 (mtm) REVERT: S 135 MET cc_start: 0.8121 (mmt) cc_final: 0.7812 (mmt) REVERT: T 16 GLU cc_start: 0.7001 (mp0) cc_final: 0.6647 (mp0) REVERT: T 53 ILE cc_start: 0.6678 (mm) cc_final: 0.6436 (mp) REVERT: T 230 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6088 (tm-30) REVERT: T 234 LYS cc_start: 0.6805 (mtpt) cc_final: 0.6312 (tptm) REVERT: U 213 GLN cc_start: 0.7058 (mp10) cc_final: 0.6654 (mt0) REVERT: U 246 GLU cc_start: 0.5902 (pp20) cc_final: 0.5415 (pp20) REVERT: W 194 MET cc_start: 0.6538 (ptp) cc_final: 0.6073 (ptp) REVERT: W 216 LYS cc_start: 0.7602 (ptmt) cc_final: 0.7287 (pttt) REVERT: X 87 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7881 (mt-10) REVERT: Y 11 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7359 (m110) REVERT: Y 96 ASN cc_start: 0.5811 (t0) cc_final: 0.5517 (p0) REVERT: Y 109 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7135 (mttp) REVERT: Y 110 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7273 (ttmm) REVERT: Z 91 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7449 (tttt) REVERT: Z 189 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: Z 206 LYS cc_start: 0.7113 (ptpt) cc_final: 0.6870 (mmtt) REVERT: Z 211 MET cc_start: 0.7183 (mtt) cc_final: 0.6854 (mtt) REVERT: a 64 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: b 106 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8242 (mm) REVERT: b 122 LYS cc_start: 0.7871 (pttt) cc_final: 0.7631 (pttp) REVERT: b 150 GLU cc_start: 0.5793 (tp30) cc_final: 0.5592 (mm-30) REVERT: b 200 GLU cc_start: 0.7125 (mp0) cc_final: 0.6908 (mp0) REVERT: b 235 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7809 (mt-10) outliers start: 130 outliers final: 66 residues processed: 799 average time/residue: 1.6613 time to fit residues: 1662.4063 Evaluate side-chains 733 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 649 time to evaluate : 5.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain W residue 186 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 573 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 301 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 277 optimal weight: 9.9990 chunk 389 optimal weight: 8.9990 chunk 582 optimal weight: 5.9990 chunk 616 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 552 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN A 179 GLN D 49 ASN F 176 HIS F 218 HIS G 206 HIS G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 129 ASN N 125 ASN N 126 ASN O 53 GLN O 63 GLN O 153 ASN Q 149 HIS R 49 ASN T 176 HIS U 242 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 125 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 53030 Z= 0.322 Angle : 0.666 10.728 71626 Z= 0.356 Chirality : 0.049 0.397 7984 Planarity : 0.005 0.066 9138 Dihedral : 10.730 178.159 7316 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.10 % Allowed : 16.56 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 6434 helix: 1.83 (0.10), residues: 2364 sheet: 0.72 (0.13), residues: 1450 loop : -0.22 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 55 HIS 0.007 0.002 HIS I 61 PHE 0.022 0.003 PHE J 102 TYR 0.023 0.003 TYR a 64 ARG 0.007 0.001 ARG M 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 663 time to evaluate : 5.817 Fit side-chains REVERT: A 198 GLN cc_start: 0.4274 (tp40) cc_final: 0.3976 (tp-100) REVERT: A 201 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6904 (mm) REVERT: B 100 GLN cc_start: 0.7762 (mt0) cc_final: 0.7486 (mt0) REVERT: B 193 LEU cc_start: 0.7107 (mm) cc_final: 0.6733 (tp) REVERT: B 208 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7420 (pp) REVERT: B 209 GLU cc_start: 0.7459 (tt0) cc_final: 0.7213 (mt-10) REVERT: B 228 LYS cc_start: 0.5772 (tptm) cc_final: 0.5461 (mtpt) REVERT: C 3 ARG cc_start: 0.7320 (ptp90) cc_final: 0.6968 (ptm-80) REVERT: C 176 LYS cc_start: 0.6990 (ttmm) cc_final: 0.6734 (ttpp) REVERT: D 67 GLU cc_start: 0.7188 (mp0) cc_final: 0.6935 (mp0) REVERT: E 180 GLU cc_start: 0.6466 (tp30) cc_final: 0.6253 (tt0) REVERT: E 189 LYS cc_start: 0.6177 (mttp) cc_final: 0.5786 (mttm) REVERT: E 191 MET cc_start: 0.6980 (mtp) cc_final: 0.6760 (ttp) REVERT: F 230 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6045 (tm-30) REVERT: G 213 GLN cc_start: 0.7082 (mp10) cc_final: 0.6701 (mt0) REVERT: H 75 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7077 (mtt-85) REVERT: K 96 ASN cc_start: 0.5936 (t0) cc_final: 0.5503 (p0) REVERT: L 91 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7434 (tttt) REVERT: L 189 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: L 206 LYS cc_start: 0.7207 (ptpt) cc_final: 0.6951 (mmtt) REVERT: M 64 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8417 (m-80) REVERT: M 146 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6973 (tttt) REVERT: N 122 LYS cc_start: 0.7873 (pttt) cc_final: 0.7642 (pttp) REVERT: O 8 MET cc_start: 0.4651 (ptm) cc_final: 0.3937 (mmt) REVERT: O 201 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7073 (mm) REVERT: P 100 GLN cc_start: 0.7772 (mt0) cc_final: 0.7434 (mt0) REVERT: P 169 ASN cc_start: 0.7172 (m-40) cc_final: 0.6751 (m-40) REVERT: P 228 LYS cc_start: 0.6192 (OUTLIER) cc_final: 0.5583 (mmmt) REVERT: Q 3 ARG cc_start: 0.7277 (ptp90) cc_final: 0.6902 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6535 (tmtt) REVERT: R 178 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: R 179 ASN cc_start: 0.6961 (m-40) cc_final: 0.6694 (m-40) REVERT: R 213 ASP cc_start: 0.6895 (p0) cc_final: 0.6358 (p0) REVERT: S 8 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.4063 (t80) REVERT: S 65 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.5360 (pm20) REVERT: S 78 MET cc_start: 0.8363 (ptp) cc_final: 0.7866 (mtm) REVERT: S 135 MET cc_start: 0.8152 (mmt) cc_final: 0.7809 (mmt) REVERT: T 53 ILE cc_start: 0.6733 (mm) cc_final: 0.6504 (mp) REVERT: T 96 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8183 (mtpp) REVERT: T 230 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: T 234 LYS cc_start: 0.6801 (mtpt) cc_final: 0.6349 (tptm) REVERT: U 213 GLN cc_start: 0.7051 (mp10) cc_final: 0.6649 (mt0) REVERT: U 246 GLU cc_start: 0.5911 (pp20) cc_final: 0.5385 (pp20) REVERT: V 249 ASN cc_start: 0.6360 (m110) cc_final: 0.5632 (t0) REVERT: W 216 LYS cc_start: 0.7678 (ptmt) cc_final: 0.7352 (pttt) REVERT: X 169 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7549 (tttp) REVERT: Y 109 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7238 (mttp) REVERT: Y 110 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7225 (ttmm) REVERT: Z 53 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8493 (tp) REVERT: Z 73 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7192 (mmtt) REVERT: Z 91 LYS cc_start: 0.7820 (ttpt) cc_final: 0.7504 (tttt) REVERT: Z 189 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7455 (mm-30) REVERT: Z 206 LYS cc_start: 0.7196 (ptpt) cc_final: 0.6939 (mmtt) REVERT: Z 211 MET cc_start: 0.7314 (mtt) cc_final: 0.6965 (mtt) REVERT: a 64 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: b 106 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8269 (mm) REVERT: b 122 LYS cc_start: 0.7885 (pttt) cc_final: 0.7651 (pttp) REVERT: b 200 GLU cc_start: 0.7181 (mp0) cc_final: 0.6976 (mp0) REVERT: b 235 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7876 (mt-10) outliers start: 177 outliers final: 93 residues processed: 789 average time/residue: 1.6377 time to fit residues: 1612.2972 Evaluate side-chains 751 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 635 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 74 MET Chi-restraints excluded: chain F residue 82 LYS Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 228 LYS Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 134 ILE Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 169 LYS Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain Z residue 73 LYS Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 513 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 459 optimal weight: 0.0030 chunk 254 optimal weight: 6.9990 chunk 526 optimal weight: 20.0000 chunk 426 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 4.9990 chunk 553 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 overall best weight: 2.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN F 176 HIS G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 118 HIS J 129 ASN K 114 GLN N 125 ASN N 126 ASN O 63 GLN Q 149 HIS R 49 ASN T 176 HIS ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 125 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 53030 Z= 0.170 Angle : 0.535 10.105 71626 Z= 0.289 Chirality : 0.044 0.372 7984 Planarity : 0.004 0.049 9138 Dihedral : 10.356 178.312 7316 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.40 % Allowed : 17.61 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.10), residues: 6434 helix: 2.14 (0.10), residues: 2380 sheet: 0.83 (0.13), residues: 1468 loop : -0.13 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 55 HIS 0.007 0.001 HIS Q 149 PHE 0.016 0.002 PHE M 129 TYR 0.016 0.001 TYR a 64 ARG 0.006 0.000 ARG M 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 668 time to evaluate : 5.479 Fit side-chains REVERT: A 198 GLN cc_start: 0.4180 (tp40) cc_final: 0.3887 (tp-100) REVERT: B 100 GLN cc_start: 0.7665 (mt0) cc_final: 0.7396 (mm110) REVERT: B 205 GLU cc_start: 0.5618 (pm20) cc_final: 0.5413 (pm20) REVERT: B 209 GLU cc_start: 0.7475 (tt0) cc_final: 0.7191 (mt-10) REVERT: C 3 ARG cc_start: 0.7299 (ptp90) cc_final: 0.6935 (ptm-80) REVERT: C 17 ARG cc_start: 0.6723 (OUTLIER) cc_final: 0.6060 (mtm180) REVERT: C 176 LYS cc_start: 0.6981 (ttmm) cc_final: 0.6724 (ttpp) REVERT: D 67 GLU cc_start: 0.7129 (mp0) cc_final: 0.6868 (mp0) REVERT: D 171 PHE cc_start: 0.7785 (t80) cc_final: 0.7479 (t80) REVERT: E 180 GLU cc_start: 0.6436 (tp30) cc_final: 0.6212 (tt0) REVERT: E 189 LYS cc_start: 0.6255 (mttp) cc_final: 0.5859 (mttm) REVERT: E 191 MET cc_start: 0.6927 (mtp) cc_final: 0.6706 (ttp) REVERT: E 201 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8044 (mt) REVERT: E 236 ASP cc_start: 0.6616 (m-30) cc_final: 0.6288 (m-30) REVERT: F 230 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6075 (tm-30) REVERT: G 213 GLN cc_start: 0.6965 (mp10) cc_final: 0.6658 (mt0) REVERT: I 194 MET cc_start: 0.6636 (ptp) cc_final: 0.6168 (ptp) REVERT: K 11 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7396 (m-40) REVERT: K 96 ASN cc_start: 0.5786 (t0) cc_final: 0.5389 (p0) REVERT: L 91 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7397 (tttt) REVERT: L 189 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7356 (mm-30) REVERT: L 206 LYS cc_start: 0.7175 (ptpt) cc_final: 0.6938 (mmtt) REVERT: M 64 TYR cc_start: 0.9187 (OUTLIER) cc_final: 0.8334 (m-80) REVERT: M 146 LYS cc_start: 0.7125 (mtpt) cc_final: 0.6837 (tttt) REVERT: N 122 LYS cc_start: 0.7906 (pttt) cc_final: 0.7649 (pttp) REVERT: O 8 MET cc_start: 0.4601 (ptm) cc_final: 0.3924 (mmt) REVERT: O 201 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6975 (mm) REVERT: P 1 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4161 (ptt) REVERT: P 100 GLN cc_start: 0.7623 (mt0) cc_final: 0.7338 (mm110) REVERT: P 169 ASN cc_start: 0.7137 (m-40) cc_final: 0.6804 (m-40) REVERT: Q 3 ARG cc_start: 0.7317 (ptp90) cc_final: 0.6961 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6862 (OUTLIER) cc_final: 0.6491 (tmtt) REVERT: Q 225 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7758 (tttp) REVERT: R 4 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: R 178 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5789 (mt-10) REVERT: R 179 ASN cc_start: 0.6934 (m-40) cc_final: 0.6680 (m-40) REVERT: S 8 TYR cc_start: 0.4421 (OUTLIER) cc_final: 0.4104 (t80) REVERT: S 65 GLU cc_start: 0.5720 (OUTLIER) cc_final: 0.5380 (pm20) REVERT: S 78 MET cc_start: 0.8362 (ptp) cc_final: 0.7849 (mtm) REVERT: S 135 MET cc_start: 0.8127 (mmt) cc_final: 0.7806 (mmt) REVERT: T 16 GLU cc_start: 0.7017 (mp0) cc_final: 0.6664 (mp0) REVERT: T 53 ILE cc_start: 0.6687 (mm) cc_final: 0.6440 (mp) REVERT: T 96 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8164 (mtpp) REVERT: T 230 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: T 234 LYS cc_start: 0.6800 (mtpt) cc_final: 0.6308 (tptm) REVERT: U 213 GLN cc_start: 0.7037 (mp10) cc_final: 0.6616 (mt0) REVERT: U 246 GLU cc_start: 0.5871 (pp20) cc_final: 0.5386 (pp20) REVERT: W 216 LYS cc_start: 0.7598 (ptmt) cc_final: 0.7294 (pttt) REVERT: Y 11 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7331 (m110) REVERT: Y 96 ASN cc_start: 0.5842 (t0) cc_final: 0.5580 (p0) REVERT: Y 109 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7181 (mttp) REVERT: Y 110 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7235 (ttmm) REVERT: Y 161 LYS cc_start: 0.8000 (tppp) cc_final: 0.7744 (tptm) REVERT: Z 91 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7444 (tttt) REVERT: Z 189 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7329 (mm-30) REVERT: Z 206 LYS cc_start: 0.7144 (ptpt) cc_final: 0.6900 (mmtt) REVERT: a 64 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: b 106 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8234 (mm) REVERT: b 122 LYS cc_start: 0.7919 (pttt) cc_final: 0.7678 (pttp) REVERT: b 200 GLU cc_start: 0.7127 (mp0) cc_final: 0.6910 (mp0) REVERT: b 235 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7829 (mt-10) outliers start: 137 outliers final: 65 residues processed: 766 average time/residue: 1.4678 time to fit residues: 1405.6246 Evaluate side-chains 734 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 646 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain L residue 189 GLU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 181 ASP Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 84 ASP Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 207 optimal weight: 20.0000 chunk 555 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 362 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 617 optimal weight: 0.2980 chunk 512 optimal weight: 10.0000 chunk 285 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 324 optimal weight: 0.0670 overall best weight: 2.2724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 153 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN G 206 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 118 HIS J 129 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN Q 149 HIS U 242 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 125 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 53030 Z= 0.179 Angle : 0.540 10.015 71626 Z= 0.291 Chirality : 0.044 0.379 7984 Planarity : 0.004 0.052 9138 Dihedral : 10.282 178.360 7314 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.36 % Allowed : 17.82 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.10), residues: 6434 helix: 2.20 (0.10), residues: 2378 sheet: 0.87 (0.13), residues: 1488 loop : -0.10 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 55 HIS 0.007 0.001 HIS Q 149 PHE 0.016 0.002 PHE a 129 TYR 0.019 0.002 TYR A 255 ARG 0.007 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 657 time to evaluate : 4.604 Fit side-chains REVERT: A 103 GLU cc_start: 0.7628 (tp30) cc_final: 0.7392 (mm-30) REVERT: A 198 GLN cc_start: 0.4153 (tp40) cc_final: 0.3856 (tp-100) REVERT: B 100 GLN cc_start: 0.7657 (mt0) cc_final: 0.7387 (mt0) REVERT: B 205 GLU cc_start: 0.5622 (pm20) cc_final: 0.5405 (pm20) REVERT: B 209 GLU cc_start: 0.7485 (tt0) cc_final: 0.7162 (mt-10) REVERT: C 3 ARG cc_start: 0.7304 (ptp90) cc_final: 0.6940 (ptm-80) REVERT: C 17 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6081 (mtm180) REVERT: C 176 LYS cc_start: 0.6931 (ttmm) cc_final: 0.6680 (ttpp) REVERT: D 67 GLU cc_start: 0.7120 (mp0) cc_final: 0.6871 (mp0) REVERT: E 180 GLU cc_start: 0.6419 (tp30) cc_final: 0.6207 (tt0) REVERT: E 189 LYS cc_start: 0.6263 (mttp) cc_final: 0.5871 (mttm) REVERT: E 191 MET cc_start: 0.6914 (mtp) cc_final: 0.6697 (ttp) REVERT: F 230 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: G 213 GLN cc_start: 0.6955 (mp10) cc_final: 0.6634 (mt0) REVERT: H 75 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7004 (mtt-85) REVERT: I 194 MET cc_start: 0.6639 (ptp) cc_final: 0.6166 (ptp) REVERT: K 11 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7411 (m-40) REVERT: K 96 ASN cc_start: 0.5765 (t0) cc_final: 0.5320 (p0) REVERT: L 53 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8501 (tp) REVERT: L 91 LYS cc_start: 0.7745 (ttpt) cc_final: 0.7425 (tttt) REVERT: L 206 LYS cc_start: 0.7179 (ptpt) cc_final: 0.6936 (mmtt) REVERT: M 64 TYR cc_start: 0.9190 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: M 146 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6830 (tttt) REVERT: N 122 LYS cc_start: 0.7896 (pttt) cc_final: 0.7642 (pttp) REVERT: O 8 MET cc_start: 0.4607 (ptm) cc_final: 0.3924 (mmt) REVERT: O 201 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6970 (mm) REVERT: P 1 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.4177 (ptt) REVERT: P 100 GLN cc_start: 0.7633 (mt0) cc_final: 0.7351 (mm110) REVERT: P 169 ASN cc_start: 0.7141 (m-40) cc_final: 0.6813 (m-40) REVERT: P 186 ASP cc_start: 0.6736 (m-30) cc_final: 0.6473 (m-30) REVERT: Q 3 ARG cc_start: 0.7312 (ptp90) cc_final: 0.6960 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6484 (tmtt) REVERT: Q 225 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7779 (tttp) REVERT: R 178 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5858 (mt-10) REVERT: R 179 ASN cc_start: 0.6905 (m-40) cc_final: 0.6667 (m-40) REVERT: S 8 TYR cc_start: 0.4427 (OUTLIER) cc_final: 0.4116 (t80) REVERT: S 65 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5415 (pm20) REVERT: S 78 MET cc_start: 0.8352 (ptp) cc_final: 0.7833 (mtm) REVERT: S 135 MET cc_start: 0.8132 (mmt) cc_final: 0.7809 (mmt) REVERT: T 16 GLU cc_start: 0.7004 (mp0) cc_final: 0.6647 (mp0) REVERT: T 51 LYS cc_start: 0.7329 (ptmt) cc_final: 0.6916 (ptpp) REVERT: T 53 ILE cc_start: 0.6738 (mm) cc_final: 0.6487 (mp) REVERT: T 96 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8164 (mtpp) REVERT: T 230 GLU cc_start: 0.6381 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: T 234 LYS cc_start: 0.6798 (mtpt) cc_final: 0.6314 (tptm) REVERT: U 213 GLN cc_start: 0.7008 (mp10) cc_final: 0.6582 (mt0) REVERT: U 246 GLU cc_start: 0.5844 (pp20) cc_final: 0.5381 (pp20) REVERT: W 216 LYS cc_start: 0.7656 (ptmt) cc_final: 0.7334 (pttt) REVERT: Y 96 ASN cc_start: 0.5877 (t0) cc_final: 0.5587 (p0) REVERT: Y 109 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7160 (mttp) REVERT: Y 110 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7266 (ttmm) REVERT: Z 73 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7169 (mmtt) REVERT: Z 91 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7439 (tttt) REVERT: Z 189 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: Z 206 LYS cc_start: 0.7157 (ptpt) cc_final: 0.6919 (mmtt) REVERT: a 64 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: b 106 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8251 (mm) REVERT: b 122 LYS cc_start: 0.7927 (pttt) cc_final: 0.7687 (pttp) REVERT: b 200 GLU cc_start: 0.7143 (mp0) cc_final: 0.6921 (mp0) REVERT: b 235 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7823 (mt-10) outliers start: 135 outliers final: 72 residues processed: 756 average time/residue: 1.3737 time to fit residues: 1295.6310 Evaluate side-chains 725 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 631 time to evaluate : 4.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 234 GLU Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 73 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 595 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 chunk 450 optimal weight: 9.9990 chunk 349 optimal weight: 20.0000 chunk 519 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 614 optimal weight: 9.9990 chunk 384 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 283 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN A 179 GLN G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 118 HIS J 129 ASN N 125 ASN N 126 ASN O 63 GLN Q 149 HIS V 163 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 129 ASN b 126 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 53030 Z= 0.492 Angle : 0.808 11.533 71626 Z= 0.432 Chirality : 0.055 0.396 7984 Planarity : 0.006 0.080 9138 Dihedral : 10.932 178.118 7314 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.01 % Allowed : 17.40 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 6434 helix: 1.38 (0.10), residues: 2378 sheet: 0.62 (0.13), residues: 1456 loop : -0.31 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Z 55 HIS 0.012 0.002 HIS I 116 PHE 0.029 0.004 PHE J 102 TYR 0.027 0.004 TYR Y 37 ARG 0.011 0.001 ARG M 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 648 time to evaluate : 4.645 Fit side-chains REVERT: A 198 GLN cc_start: 0.4309 (tp40) cc_final: 0.4005 (tp-100) REVERT: B 100 GLN cc_start: 0.7872 (mt0) cc_final: 0.7577 (mt0) REVERT: B 171 MET cc_start: 0.7602 (tpp) cc_final: 0.7390 (tpt) REVERT: B 193 LEU cc_start: 0.7040 (mm) cc_final: 0.6661 (tp) REVERT: B 228 LYS cc_start: 0.5676 (tptm) cc_final: 0.5430 (mtpt) REVERT: C 3 ARG cc_start: 0.7286 (ptp90) cc_final: 0.6890 (ptm-80) REVERT: C 17 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6119 (mtm180) REVERT: C 176 LYS cc_start: 0.7043 (ttmm) cc_final: 0.6805 (ttpp) REVERT: D 67 GLU cc_start: 0.7188 (mp0) cc_final: 0.6919 (mp0) REVERT: D 213 ASP cc_start: 0.6906 (p0) cc_final: 0.6395 (p0) REVERT: E 180 GLU cc_start: 0.6539 (tp30) cc_final: 0.6329 (tt0) REVERT: E 189 LYS cc_start: 0.6123 (mttp) cc_final: 0.5746 (mttm) REVERT: E 236 ASP cc_start: 0.6652 (m-30) cc_final: 0.6284 (m-30) REVERT: F 230 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.6036 (tm-30) REVERT: G 213 GLN cc_start: 0.7067 (mp10) cc_final: 0.6660 (mt0) REVERT: H 75 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7125 (mtt-85) REVERT: H 249 ASN cc_start: 0.6296 (m110) cc_final: 0.5596 (t0) REVERT: I 194 MET cc_start: 0.6626 (ptp) cc_final: 0.6146 (ptp) REVERT: J 169 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7617 (tttp) REVERT: K 96 ASN cc_start: 0.5976 (t0) cc_final: 0.5570 (p0) REVERT: K 110 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7173 (ttmm) REVERT: L 91 LYS cc_start: 0.7797 (ttpt) cc_final: 0.7442 (tttt) REVERT: L 206 LYS cc_start: 0.7249 (ptpt) cc_final: 0.6974 (mmtt) REVERT: M 64 TYR cc_start: 0.9239 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: M 146 LYS cc_start: 0.7308 (mtpt) cc_final: 0.7076 (tttt) REVERT: N 122 LYS cc_start: 0.7893 (pttt) cc_final: 0.7672 (pttp) REVERT: P 100 GLN cc_start: 0.7823 (mt0) cc_final: 0.7479 (mt0) REVERT: P 169 ASN cc_start: 0.7181 (m-40) cc_final: 0.6712 (m-40) REVERT: P 209 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: P 228 LYS cc_start: 0.6046 (OUTLIER) cc_final: 0.5477 (mmmt) REVERT: Q 3 ARG cc_start: 0.7276 (ptp90) cc_final: 0.6895 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6586 (tmtt) REVERT: Q 225 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7702 (tttp) REVERT: R 178 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5825 (mt-10) REVERT: R 179 ASN cc_start: 0.6951 (m-40) cc_final: 0.6702 (m-40) REVERT: R 213 ASP cc_start: 0.6901 (p0) cc_final: 0.6389 (p0) REVERT: S 8 TYR cc_start: 0.4447 (OUTLIER) cc_final: 0.4218 (t80) REVERT: S 65 GLU cc_start: 0.5744 (OUTLIER) cc_final: 0.5401 (pm20) REVERT: S 78 MET cc_start: 0.8353 (ptp) cc_final: 0.7889 (mtm) REVERT: S 135 MET cc_start: 0.8159 (mmt) cc_final: 0.7858 (mmt) REVERT: T 53 ILE cc_start: 0.6792 (mm) cc_final: 0.6578 (mp) REVERT: T 96 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: T 230 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.6056 (tm-30) REVERT: T 234 LYS cc_start: 0.6823 (mtpt) cc_final: 0.6344 (tptm) REVERT: U 213 GLN cc_start: 0.7052 (mp10) cc_final: 0.6604 (mt0) REVERT: U 246 GLU cc_start: 0.5917 (pp20) cc_final: 0.5347 (pp20) REVERT: V 249 ASN cc_start: 0.6327 (m110) cc_final: 0.5632 (t0) REVERT: Y 96 ASN cc_start: 0.5925 (t0) cc_final: 0.5602 (p0) REVERT: Y 109 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7253 (mttp) REVERT: Y 110 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7118 (ttmm) REVERT: Z 91 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7605 (tttt) REVERT: Z 189 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: Z 206 LYS cc_start: 0.7212 (ptpt) cc_final: 0.6941 (mmtt) REVERT: a 64 TYR cc_start: 0.9238 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: a 146 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6806 (mttt) REVERT: b 106 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8294 (mm) REVERT: b 122 LYS cc_start: 0.7920 (pttt) cc_final: 0.7677 (pttp) REVERT: b 200 GLU cc_start: 0.7257 (mp0) cc_final: 0.7047 (mp0) REVERT: b 235 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7861 (mt-10) outliers start: 172 outliers final: 104 residues processed: 780 average time/residue: 1.3509 time to fit residues: 1308.1336 Evaluate side-chains 750 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 624 time to evaluate : 4.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 225 SER Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 209 LYS Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 169 LYS Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain O residue 63 GLN Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 233 ILE Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain P residue 228 LYS Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 230 ASP Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 9 ASP Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 134 ILE Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 74 MET Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 225 SER Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 181 ASP Chi-restraints excluded: chain W residue 186 ILE Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain a residue 146 LYS Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 380 optimal weight: 5.9990 chunk 245 optimal weight: 3.9990 chunk 367 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 390 optimal weight: 0.9990 chunk 418 optimal weight: 9.9990 chunk 304 optimal weight: 0.5980 chunk 57 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN G 206 HIS G 242 ASN H 163 GLN I 9 GLN I 71 ASN I 73 GLN J 118 HIS J 129 ASN N 126 ASN O 63 GLN T 176 HIS ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 126 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 53030 Z= 0.157 Angle : 0.531 9.961 71626 Z= 0.287 Chirality : 0.044 0.367 7984 Planarity : 0.003 0.050 9138 Dihedral : 10.302 178.155 7314 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.66 % Allowed : 18.86 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.10), residues: 6434 helix: 2.10 (0.10), residues: 2378 sheet: 0.81 (0.13), residues: 1490 loop : -0.16 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 55 HIS 0.024 0.001 HIS Q 149 PHE 0.014 0.001 PHE M 129 TYR 0.025 0.001 TYR A 255 ARG 0.007 0.000 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 649 time to evaluate : 4.525 Fit side-chains REVERT: A 198 GLN cc_start: 0.4155 (tp40) cc_final: 0.3908 (tp-100) REVERT: B 42 ASN cc_start: 0.7900 (p0) cc_final: 0.7513 (p0) REVERT: B 100 GLN cc_start: 0.7650 (mt0) cc_final: 0.7374 (mm110) REVERT: C 3 ARG cc_start: 0.7289 (ptp90) cc_final: 0.6900 (ptm-80) REVERT: C 17 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6055 (mtm180) REVERT: C 176 LYS cc_start: 0.6946 (ttmm) cc_final: 0.6706 (ttpp) REVERT: D 67 GLU cc_start: 0.7097 (mp0) cc_final: 0.6829 (mp0) REVERT: E 180 GLU cc_start: 0.6476 (tp30) cc_final: 0.6261 (tt0) REVERT: E 189 LYS cc_start: 0.6151 (mttp) cc_final: 0.5780 (mttm) REVERT: E 236 ASP cc_start: 0.6525 (m-30) cc_final: 0.6195 (m-30) REVERT: F 230 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: G 213 GLN cc_start: 0.7027 (mp10) cc_final: 0.6626 (mt0) REVERT: H 75 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7021 (mtt-85) REVERT: H 249 ASN cc_start: 0.6315 (m110) cc_final: 0.5601 (t0) REVERT: I 194 MET cc_start: 0.6581 (ptp) cc_final: 0.6138 (ptp) REVERT: K 96 ASN cc_start: 0.5801 (t0) cc_final: 0.5415 (p0) REVERT: L 91 LYS cc_start: 0.7702 (ttpt) cc_final: 0.7406 (tttt) REVERT: L 206 LYS cc_start: 0.7140 (ptpt) cc_final: 0.6895 (mmtt) REVERT: M 64 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: M 146 LYS cc_start: 0.7118 (mtpt) cc_final: 0.6847 (tttt) REVERT: N 122 LYS cc_start: 0.7901 (pttt) cc_final: 0.7653 (pttp) REVERT: O 8 MET cc_start: 0.4646 (ptm) cc_final: 0.3952 (mmt) REVERT: P 1 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4094 (ptt) REVERT: P 100 GLN cc_start: 0.7613 (mt0) cc_final: 0.7318 (mm110) REVERT: P 186 ASP cc_start: 0.6721 (m-30) cc_final: 0.6452 (m-30) REVERT: P 209 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: Q 3 ARG cc_start: 0.7307 (ptp90) cc_final: 0.6957 (ptm-80) REVERT: R 171 PHE cc_start: 0.7792 (t80) cc_final: 0.7510 (t80) REVERT: R 178 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5808 (mt-10) REVERT: R 179 ASN cc_start: 0.6913 (m-40) cc_final: 0.6666 (m-40) REVERT: S 8 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.4229 (t80) REVERT: S 78 MET cc_start: 0.8338 (ptp) cc_final: 0.7836 (mtm) REVERT: S 135 MET cc_start: 0.8119 (mmt) cc_final: 0.7816 (mmt) REVERT: T 53 ILE cc_start: 0.6725 (mm) cc_final: 0.6483 (mp) REVERT: T 96 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (mtpp) REVERT: T 230 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6085 (tm-30) REVERT: T 234 LYS cc_start: 0.6801 (mtpt) cc_final: 0.6298 (tptm) REVERT: U 213 GLN cc_start: 0.7029 (mp10) cc_final: 0.6612 (mt0) REVERT: V 249 ASN cc_start: 0.6357 (m110) cc_final: 0.5641 (t0) REVERT: Y 96 ASN cc_start: 0.5815 (t0) cc_final: 0.5517 (p0) REVERT: Y 109 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7166 (mttp) REVERT: Z 91 LYS cc_start: 0.7736 (ttpt) cc_final: 0.7419 (tttt) REVERT: Z 189 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7319 (mm-30) REVERT: Z 206 LYS cc_start: 0.7126 (ptpt) cc_final: 0.6855 (pttp) REVERT: b 106 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (mm) REVERT: b 122 LYS cc_start: 0.7919 (pttt) cc_final: 0.7680 (pttp) REVERT: b 191 ASP cc_start: 0.7214 (t0) cc_final: 0.6973 (t0) REVERT: b 200 GLU cc_start: 0.7157 (mp0) cc_final: 0.6930 (mp0) REVERT: b 235 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7815 (mt-10) outliers start: 95 outliers final: 53 residues processed: 721 average time/residue: 1.2850 time to fit residues: 1148.1642 Evaluate side-chains 697 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 630 time to evaluate : 3.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 109 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 559 optimal weight: 20.0000 chunk 589 optimal weight: 3.9990 chunk 537 optimal weight: 10.0000 chunk 573 optimal weight: 0.0670 chunk 588 optimal weight: 8.9990 chunk 344 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 chunk 449 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 517 optimal weight: 10.0000 chunk 541 optimal weight: 2.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 153 ASN A 179 GLN G 206 HIS G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 118 HIS J 129 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 242 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 129 ASN b 126 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 53030 Z= 0.277 Angle : 0.626 10.286 71626 Z= 0.337 Chirality : 0.047 0.397 7984 Planarity : 0.004 0.065 9138 Dihedral : 10.513 178.531 7314 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.94 % Allowed : 18.75 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 6434 helix: 1.91 (0.10), residues: 2380 sheet: 0.77 (0.13), residues: 1460 loop : -0.19 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 55 HIS 0.006 0.001 HIS I 116 PHE 0.019 0.002 PHE J 102 TYR 0.032 0.002 TYR A 255 ARG 0.007 0.001 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 633 time to evaluate : 3.949 Fit side-chains REVERT: A 198 GLN cc_start: 0.4162 (tp40) cc_final: 0.3865 (tp-100) REVERT: A 201 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7008 (mm) REVERT: B 100 GLN cc_start: 0.7713 (mt0) cc_final: 0.7447 (mt0) REVERT: B 209 GLU cc_start: 0.7467 (tt0) cc_final: 0.6873 (tp30) REVERT: C 3 ARG cc_start: 0.7314 (ptp90) cc_final: 0.6947 (ptm-80) REVERT: C 17 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6042 (mtm180) REVERT: C 176 LYS cc_start: 0.7015 (ttmm) cc_final: 0.6773 (ttpp) REVERT: D 67 GLU cc_start: 0.7164 (mp0) cc_final: 0.6921 (mp0) REVERT: E 180 GLU cc_start: 0.6475 (tp30) cc_final: 0.6254 (tt0) REVERT: E 189 LYS cc_start: 0.6130 (mttp) cc_final: 0.5761 (mttm) REVERT: F 230 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: G 213 GLN cc_start: 0.7029 (mp10) cc_final: 0.6626 (mt0) REVERT: H 75 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7097 (mtt-85) REVERT: H 249 ASN cc_start: 0.6330 (m110) cc_final: 0.5614 (t0) REVERT: I 194 MET cc_start: 0.6652 (ptp) cc_final: 0.6155 (ptp) REVERT: K 96 ASN cc_start: 0.5875 (t0) cc_final: 0.5456 (p0) REVERT: K 110 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7171 (ttmm) REVERT: L 91 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7439 (tttt) REVERT: L 206 LYS cc_start: 0.7179 (ptpt) cc_final: 0.6923 (mmtt) REVERT: M 64 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: M 146 LYS cc_start: 0.7224 (mtpt) cc_final: 0.6962 (tttt) REVERT: N 122 LYS cc_start: 0.7912 (pttt) cc_final: 0.7676 (pttp) REVERT: O 8 MET cc_start: 0.4680 (ptm) cc_final: 0.3969 (mmt) REVERT: O 201 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7022 (mm) REVERT: P 1 MET cc_start: 0.4997 (OUTLIER) cc_final: 0.4104 (ptt) REVERT: P 100 GLN cc_start: 0.7712 (mt0) cc_final: 0.7392 (mt0) REVERT: P 186 ASP cc_start: 0.6743 (m-30) cc_final: 0.6473 (m-30) REVERT: P 209 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6726 (mm-30) REVERT: Q 3 ARG cc_start: 0.7277 (ptp90) cc_final: 0.6885 (ptm-80) REVERT: Q 54 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6493 (tmtt) REVERT: R 178 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5842 (mt-10) REVERT: R 179 ASN cc_start: 0.6925 (m-40) cc_final: 0.6678 (m-40) REVERT: S 8 TYR cc_start: 0.4498 (OUTLIER) cc_final: 0.4227 (t80) REVERT: S 78 MET cc_start: 0.8354 (ptp) cc_final: 0.7830 (mtm) REVERT: S 135 MET cc_start: 0.8150 (mmt) cc_final: 0.7822 (mmt) REVERT: T 16 GLU cc_start: 0.7072 (mp0) cc_final: 0.6703 (mp0) REVERT: T 53 ILE cc_start: 0.6730 (mm) cc_final: 0.6485 (mp) REVERT: T 96 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8171 (mtpp) REVERT: T 230 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6123 (tm-30) REVERT: T 234 LYS cc_start: 0.6792 (mtpt) cc_final: 0.6310 (tptm) REVERT: U 213 GLN cc_start: 0.7047 (mp10) cc_final: 0.6629 (mt0) REVERT: V 249 ASN cc_start: 0.6368 (m110) cc_final: 0.5655 (t0) REVERT: Y 96 ASN cc_start: 0.5828 (t0) cc_final: 0.5552 (p0) REVERT: Y 110 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7192 (ttmm) REVERT: Z 91 LYS cc_start: 0.7890 (ttpt) cc_final: 0.7562 (tttt) REVERT: Z 189 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: Z 206 LYS cc_start: 0.7169 (ptpt) cc_final: 0.6908 (mmtt) REVERT: a 64 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8400 (m-80) REVERT: b 106 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8329 (mm) REVERT: b 122 LYS cc_start: 0.7912 (pttt) cc_final: 0.7680 (pttp) REVERT: b 200 GLU cc_start: 0.7141 (mp0) cc_final: 0.6931 (mp0) REVERT: b 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (mt-10) outliers start: 111 outliers final: 63 residues processed: 720 average time/residue: 1.2688 time to fit residues: 1134.1726 Evaluate side-chains 715 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 633 time to evaluate : 3.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 228 MET Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 571 optimal weight: 9.9990 chunk 376 optimal weight: 9.9990 chunk 605 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 287 optimal weight: 10.0000 chunk 421 optimal weight: 9.9990 chunk 635 optimal weight: 9.9990 chunk 585 optimal weight: 1.9990 chunk 506 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 390 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN A 179 GLN F 165 HIS G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 118 HIS J 129 ASN N 126 ASN O 53 GLN O 63 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 129 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 53030 Z= 0.401 Angle : 0.740 11.045 71626 Z= 0.397 Chirality : 0.052 0.396 7984 Planarity : 0.005 0.076 9138 Dihedral : 10.818 178.513 7314 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.75 % Allowed : 18.86 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.10), residues: 6434 helix: 1.52 (0.10), residues: 2372 sheet: 0.61 (0.13), residues: 1458 loop : -0.29 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP L 55 HIS 0.009 0.002 HIS I 116 PHE 0.025 0.003 PHE J 102 TYR 0.034 0.003 TYR a 64 ARG 0.009 0.001 ARG D 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12868 Ramachandran restraints generated. 6434 Oldfield, 0 Emsley, 6434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 639 time to evaluate : 3.959 Fit side-chains REVERT: A 198 GLN cc_start: 0.4224 (tp40) cc_final: 0.3922 (tp-100) REVERT: A 201 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7064 (mm) REVERT: B 100 GLN cc_start: 0.7808 (mt0) cc_final: 0.7533 (mt0) REVERT: B 171 MET cc_start: 0.7604 (tpp) cc_final: 0.7392 (tpt) REVERT: B 209 GLU cc_start: 0.7477 (tt0) cc_final: 0.6907 (tp30) REVERT: B 228 LYS cc_start: 0.5888 (tptm) cc_final: 0.5626 (mmmt) REVERT: C 3 ARG cc_start: 0.7286 (ptp90) cc_final: 0.6896 (ptm-80) REVERT: C 17 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6069 (mtm180) REVERT: C 176 LYS cc_start: 0.7001 (ttmm) cc_final: 0.6764 (ttpp) REVERT: D 67 GLU cc_start: 0.7155 (mp0) cc_final: 0.6891 (mp0) REVERT: D 213 ASP cc_start: 0.6899 (p0) cc_final: 0.6389 (p0) REVERT: E 180 GLU cc_start: 0.6485 (tp30) cc_final: 0.6272 (tt0) REVERT: F 230 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6039 (tm-30) REVERT: G 213 GLN cc_start: 0.7061 (mp10) cc_final: 0.6647 (mt0) REVERT: H 75 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7122 (mtt-85) REVERT: H 249 ASN cc_start: 0.6292 (m110) cc_final: 0.5588 (t0) REVERT: I 194 MET cc_start: 0.6616 (ptp) cc_final: 0.6140 (ptp) REVERT: K 96 ASN cc_start: 0.5936 (t0) cc_final: 0.5509 (p0) REVERT: K 110 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7167 (ttmm) REVERT: L 91 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7447 (tttt) REVERT: L 206 LYS cc_start: 0.7213 (ptpt) cc_final: 0.6954 (mmtt) REVERT: M 64 TYR cc_start: 0.9236 (OUTLIER) cc_final: 0.8421 (m-80) REVERT: M 146 LYS cc_start: 0.7224 (mtpt) cc_final: 0.7000 (tttt) REVERT: N 122 LYS cc_start: 0.7894 (pttt) cc_final: 0.7669 (pttp) REVERT: O 8 MET cc_start: 0.4792 (ptm) cc_final: 0.3995 (mmt) REVERT: O 201 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7075 (mm) REVERT: P 100 GLN cc_start: 0.7789 (mt0) cc_final: 0.7458 (mt0) REVERT: P 169 ASN cc_start: 0.7160 (m-40) cc_final: 0.6712 (m-40) REVERT: P 209 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: Q 3 ARG cc_start: 0.7272 (ptp90) cc_final: 0.6894 (ptm-80) REVERT: R 178 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: R 179 ASN cc_start: 0.6960 (m-40) cc_final: 0.6713 (m-40) REVERT: R 213 ASP cc_start: 0.6933 (p0) cc_final: 0.6412 (p0) REVERT: S 8 TYR cc_start: 0.4481 (OUTLIER) cc_final: 0.4276 (t80) REVERT: S 78 MET cc_start: 0.8356 (ptp) cc_final: 0.7890 (mtm) REVERT: S 135 MET cc_start: 0.8152 (mmt) cc_final: 0.7797 (mmt) REVERT: T 53 ILE cc_start: 0.6736 (mm) cc_final: 0.6522 (mp) REVERT: T 96 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: T 147 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6975 (mpt-90) REVERT: T 230 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6097 (tm-30) REVERT: T 234 LYS cc_start: 0.6773 (mtpt) cc_final: 0.6433 (tmtt) REVERT: U 213 GLN cc_start: 0.7045 (mp10) cc_final: 0.6638 (mt0) REVERT: V 249 ASN cc_start: 0.6335 (m110) cc_final: 0.5635 (t0) REVERT: W 194 MET cc_start: 0.6565 (pmm) cc_final: 0.6195 (ptp) REVERT: Y 96 ASN cc_start: 0.5888 (t0) cc_final: 0.5579 (p0) REVERT: Y 110 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7205 (ttmm) REVERT: Z 91 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7599 (tttt) REVERT: Z 189 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: Z 206 LYS cc_start: 0.7207 (ptpt) cc_final: 0.6920 (pttp) REVERT: a 64 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: b 106 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8351 (mm) REVERT: b 122 LYS cc_start: 0.7913 (pttt) cc_final: 0.7669 (pttp) REVERT: b 200 GLU cc_start: 0.7254 (mp0) cc_final: 0.7030 (mp0) REVERT: b 235 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7839 (mt-10) outliers start: 100 outliers final: 68 residues processed: 716 average time/residue: 1.2316 time to fit residues: 1091.9130 Evaluate side-chains 715 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 629 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 234 GLU Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 110 LYS Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain O residue 201 ILE Chi-restraints excluded: chain O residue 242 THR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 73 PHE Chi-restraints excluded: chain Q residue 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain S residue 8 TYR Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 128 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 GLU Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 5 LEU Chi-restraints excluded: chain T residue 96 LYS Chi-restraints excluded: chain T residue 147 ARG Chi-restraints excluded: chain T residue 160 PHE Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain U residue 58 ASN Chi-restraints excluded: chain U residue 209 LYS Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 148 ASP Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 26 ILE Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 83 SER Chi-restraints excluded: chain b residue 106 ILE Chi-restraints excluded: chain b residue 235 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 310 optimal weight: 4.9990 chunk 402 optimal weight: 10.0000 chunk 539 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 140 optimal weight: 0.0000 chunk 506 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 520 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 63 GLN A 153 ASN G 242 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN I 106 ASN J 118 HIS J 129 ASN N 126 ASN O 63 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 129 ASN b 126 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.135180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111482 restraints weight = 79973.805| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.35 r_work: 0.3115 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 53030 Z= 0.305 Angle : 0.656 10.566 71626 Z= 0.353 Chirality : 0.048 0.391 7984 Planarity : 0.005 0.065 9138 Dihedral : 10.691 178.840 7314 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.75 % Allowed : 18.94 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.10), residues: 6434 helix: 1.65 (0.10), residues: 2372 sheet: 0.66 (0.13), residues: 1458 loop : -0.27 (0.12), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 55 HIS 0.006 0.001 HIS H 134 PHE 0.020 0.002 PHE X 102 TYR 0.032 0.002 TYR A 255 ARG 0.008 0.001 ARG W 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20004.12 seconds wall clock time: 350 minutes 57.51 seconds (21057.51 seconds total)