Starting phenix.real_space_refine on Tue Sep 24 15:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6e_29764/09_2024/8g6e_29764.cif" } 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. Time to flip 29 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 28.14, per 1000 atoms: 0.54 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 6.0 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... Secondary structure from input PDB file: 178 helices and 72 sheets defined 39.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.577A pdb=" N GLU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 112 Processing helix chain 'A' and resid 116 through 134 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 178 through 194 Processing helix chain 'A' and resid 200 through 221 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.579A pdb=" N TYR B 6 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 7 " --> pdb=" O GLY B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 7' Processing helix chain 'B' and resid 19 through 31 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 79 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.716A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 223 through 233 removed outlier: 4.233A pdb=" N GLU B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 79 through 102 Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.655A pdb=" N ALA C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 200 Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 228 through 243 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 76 through 99 Processing helix chain 'D' and resid 103 through 119 Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.572A pdb=" N VAL D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 218 through 237 Processing helix chain 'E' and resid 21 through 29 Processing helix chain 'E' and resid 81 through 104 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 Processing helix chain 'E' and resid 233 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 19 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 77 through 100 Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.720A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 179 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) Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'G' and resid 53 through 56 Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 125 removed outlier: 3.779A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 180 Processing helix chain 'G' and resid 181 through 182 No H-bonds generated for 'chain 'G' and resid 181 through 182' Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'G' and resid 188 through 204 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 233 through 251 Proline residue: G 239 - end of helix removed outlier: 3.555A pdb=" N LEU G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 71 Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.561A pdb=" N ASN H 143 " --> pdb=" O ILE H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 197 removed outlier: 4.011A pdb=" N ILE H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR H 192 " --> pdb=" O TYR H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 221 Processing helix chain 'I' and resid 48 through 71 Processing helix chain 'I' and resid 75 through 90 Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 147 through 166 Processing helix chain 'J' and resid 3 through 9 removed outlier: 4.239A pdb=" N ASN J 8 " --> pdb=" O ILE J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 81 Processing helix chain 'J' and resid 85 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 155 through 167 Processing helix chain 'J' and resid 172 through 189 Processing helix chain 'K' and resid 50 through 72 Processing helix chain 'K' and resid 77 through 94 removed outlier: 4.185A pdb=" N ARG K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 147 removed outlier: 5.192A pdb=" N ALA K 141 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 171 Processing helix chain 'L' and resid 48 through 71 Processing helix chain 'L' and resid 75 through 89 Processing helix chain 'L' and resid 131 through 142 Processing helix chain 'L' and resid 148 through 167 Processing helix chain 'L' and resid 193 through 201 removed outlier: 3.600A pdb=" N TYR L 198 " --> pdb=" O PHE L 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 108 Processing helix chain 'M' and resid 112 through 126 Processing helix chain 'M' and resid 169 through 182 Proline residue: M 175 - end of helix Processing helix chain 'M' and resid 194 through 213 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 79 Processing helix chain 'N' and resid 81 through 85 Processing helix chain 'N' and resid 87 through 106 Processing helix chain 'N' and resid 125 through 129 removed outlier: 3.695A pdb=" N ASN N 129 " --> pdb=" O ASN N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 157 No H-bonds generated for 'chain 'N' and resid 155 through 157' Processing helix chain 'N' and resid 179 through 182 Processing helix chain 'N' and resid 183 through 193 removed outlier: 3.586A pdb=" N LEU N 188 " --> pdb=" O PHE N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 217 Processing helix chain 'N' and resid 254 through 258 Processing helix chain 'O' and resid 22 through 35 removed outlier: 3.573A pdb=" N GLU O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR O 35 " --> pdb=" O ALA O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 112 Processing helix chain 'O' and resid 116 through 134 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 178 through 194 Processing helix chain 'O' and resid 200 through 221 Processing helix chain 'O' and resid 225 through 227 No H-bonds generated for 'chain 'O' and resid 225 through 227' Processing helix chain 'O' and resid 245 through 258 Processing helix chain 'P' and resid 3 through 7 removed outlier: 3.718A pdb=" N TYR P 6 " --> pdb=" O ASP P 3 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 31 Processing helix chain 'P' and resid 58 through 62 Processing helix chain 'P' and resid 79 through 102 Processing helix chain 'P' and resid 106 through 121 removed outlier: 3.708A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 Processing helix chain 'P' and resid 183 through 199 Processing helix chain 'P' and resid 223 through 233 removed outlier: 4.250A pdb=" N GLU P 233 " --> pdb=" O ASP P 229 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 18 through 30 Processing helix chain 'Q' and resid 79 through 102 Processing helix chain 'Q' and resid 106 through 124 Processing helix chain 'Q' and resid 167 through 179 removed outlier: 3.653A pdb=" N ALA Q 171 " --> pdb=" O ASN Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 200 Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'Q' and resid 228 through 243 Processing helix chain 'R' and resid 16 through 28 Processing helix chain 'R' and resid 76 through 99 Processing helix chain 'R' and resid 103 through 119 Processing helix chain 'R' and resid 164 through 174 removed outlier: 3.615A pdb=" N VAL R 168 " --> pdb=" O ASN R 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 195 Processing helix chain 'R' and resid 200 through 202 No H-bonds generated for 'chain 'R' and resid 200 through 202' Processing helix chain 'R' and resid 218 through 237 Processing helix chain 'S' and resid 21 through 29 Processing helix chain 'S' and resid 81 through 104 Processing helix chain 'S' and resid 108 through 122 Processing helix chain 'S' and resid 123 through 125 No H-bonds generated for 'chain 'S' and resid 123 through 125' Processing helix chain 'S' and resid 175 through 187 Processing helix chain 'S' and resid 192 through 208 Processing helix chain 'S' and resid 233 through 243 Processing helix chain 'T' and resid 19 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 77 through 100 Processing helix chain 'T' and resid 104 through 119 removed outlier: 3.735A pdb=" N ASN T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 179 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) Processing helix chain 'T' and resid 182 through 196 Processing helix chain 'T' and resid 224 through 241 Processing helix chain 'U' and resid 21 through 34 Processing helix chain 'U' and resid 53 through 56 Processing helix chain 'U' and resid 83 through 106 Processing helix chain 'U' and resid 110 through 124 Processing helix chain 'U' and resid 125 through 127 No H-bonds generated for 'chain 'U' and resid 125 through 127' Processing helix chain 'U' and resid 171 through 180 Processing helix chain 'U' and resid 181 through 182 No H-bonds generated for 'chain 'U' and resid 181 through 182' Processing helix chain 'U' and resid 183 through 187 Processing helix chain 'U' and resid 188 through 204 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 211 through 215 Processing helix chain 'U' and resid 233 through 251 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 48 through 71 Processing helix chain 'V' and resid 93 through 98 Processing helix chain 'V' and resid 128 through 143 removed outlier: 3.561A pdb=" N ASN V 143 " --> pdb=" O ILE V 139 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 197 removed outlier: 4.016A pdb=" N ILE V 189 " --> pdb=" O GLY V 185 " (cutoff:3.500A) 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 202 through 221 Processing helix chain 'W' and resid 48 through 71 Processing helix chain 'W' and resid 75 through 90 Processing helix chain 'W' and resid 130 through 142 Processing helix chain 'W' and resid 147 through 166 Processing helix chain 'X' and resid 3 through 9 removed outlier: 4.238A pdb=" N ASN X 8 " --> pdb=" O ILE X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 81 Processing helix chain 'X' and resid 85 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 155 through 167 Processing helix chain 'X' and resid 172 through 189 Processing helix chain 'Y' and resid 50 through 72 Processing helix chain 'Y' and resid 77 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 135 through 147 removed outlier: 5.332A pdb=" N ALA Y 141 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 171 Processing helix chain 'Z' and resid 48 through 71 Processing helix chain 'Z' and resid 75 through 89 Processing helix chain 'Z' and resid 131 through 142 Processing helix chain 'Z' and resid 148 through 167 Processing helix chain 'Z' and resid 193 through 201 removed outlier: 3.592A pdb=" N TYR Z 198 " --> pdb=" O PHE Z 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 108 Processing helix chain 'a' and resid 112 through 126 Processing helix chain 'a' and resid 169 through 182 Proline residue: a 175 - end of helix Processing helix chain 'a' and resid 194 through 213 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 79 Processing helix chain 'b' and resid 81 through 85 Processing helix chain 'b' and resid 87 through 105 Processing helix chain 'b' and resid 125 through 129 removed outlier: 3.587A pdb=" N ASN b 129 " --> pdb=" O ASN b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 157 No H-bonds generated for 'chain 'b' and resid 155 through 157' Processing helix chain 'b' and resid 179 through 182 Processing helix chain 'b' and resid 183 through 193 removed outlier: 3.605A pdb=" N LEU b 188 " --> pdb=" O PHE b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 198 through 217 Processing helix chain 'b' and resid 254 through 258 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 174 Processing sheet with id=AA2, 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=AA3, 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=AA4, first strand: chain 'B' and resid 65 through 69 removed outlier: 6.867A pdb=" N ILE B 72 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 172 Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 71 removed outlier: 6.466A pdb=" N ILE E 74 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 155 " --> pdb=" O PHE E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 157 through 160 removed outlier: 7.388A pdb=" N LEU F 211 " --> pdb=" O GLU F 222 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU F 222 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 213 " --> pdb=" O TRP F 220 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP F 220 " --> pdb=" O VAL F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 63 through 67 removed outlier: 6.448A pdb=" N ILE F 70 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 165 through 168 Processing sheet with id=AB5, first strand: chain 'G' and resid 69 through 71 removed outlier: 3.878A pdb=" N ILE G 151 " --> pdb=" O TYR G 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 113 through 117 Processing sheet with id=AB7, 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=AB8, first strand: chain 'H' and resid 34 through 38 removed outlier: 6.489A pdb=" N LEU H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU H 164 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER H 172 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 124 through 127 Processing sheet with id=AC1, 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=AC2, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.271A pdb=" N ILE I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 212 through 219 removed outlier: 6.687A pdb=" N LYS J 212 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU I 215 " --> pdb=" O LYS J 210 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS J 210 " --> pdb=" O GLU I 215 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE I 217 " --> pdb=" O ILE J 208 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE J 208 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA J 198 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N CYS J 11 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 29 through 31 removed outlier: 6.514A pdb=" N LEU J 29 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.603A pdb=" N VAL J 51 " --> pdb=" O MET J 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER J 56 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 129 through 132 Processing sheet with id=AC7, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.458A pdb=" N SER K 21 " --> pdb=" O LEU K 28 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AC9, first strand: chain 'L' and resid 125 through 128 removed outlier: 6.310A pdb=" N VAL L 174 " --> pdb=" O GLU L 189 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLU L 189 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL L 176 " --> pdb=" O ILE L 187 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.573A pdb=" N ALA L 20 " --> pdb=" O SER L 27 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.446A pdb=" N ILE L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE L 100 " --> pdb=" O THR L 44 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.929A pdb=" N LEU M 57 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 71 through 75 removed outlier: 6.418A pdb=" N CYS M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN M 136 " --> pdb=" O TYR M 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU M 149 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 34 through 37 removed outlier: 3.790A pdb=" N LYS N 36 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA N 29 " --> pdb=" O LYS N 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR N 50 " --> pdb=" O ILE N 46 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 34 through 37 removed outlier: 3.790A pdb=" N LYS N 36 " --> pdb=" O ALA N 29 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA N 29 " --> pdb=" O LYS N 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 175 through 177 Processing sheet with id=AD9, first strand: chain 'N' and resid 175 through 177 Processing sheet with id=AE1, first strand: chain 'O' and resid 171 through 174 Processing sheet with id=AE2, 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=AE3, 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=AE4, first strand: chain 'P' and resid 65 through 69 removed outlier: 6.861A pdb=" N ILE P 72 " --> pdb=" O ILE P 68 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 161 through 164 Processing sheet with id=AE6, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'R' and resid 62 through 64 Processing sheet with id=AE9, first strand: chain 'S' and resid 169 through 172 Processing sheet with id=AF1, first strand: chain 'S' and resid 67 through 71 removed outlier: 6.451A pdb=" N ILE S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU S 155 " --> pdb=" O PHE S 167 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 157 through 160 removed outlier: 7.381A pdb=" N LEU T 211 " --> pdb=" O GLU T 222 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU T 222 " --> pdb=" O LEU T 211 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL T 213 " --> pdb=" O TRP T 220 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP T 220 " --> pdb=" O VAL T 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 63 through 67 removed outlier: 6.448A pdb=" N ILE T 70 " --> pdb=" O ILE T 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 165 through 168 Processing sheet with id=AF5, first strand: chain 'U' and resid 69 through 71 removed outlier: 3.849A pdb=" N ILE U 151 " --> pdb=" O TYR U 163 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 113 through 117 Processing sheet with id=AF7, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.905A pdb=" N THR V 20 " --> pdb=" O SER V 27 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 34 through 38 removed outlier: 6.486A pdb=" N LEU V 41 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU V 164 " --> pdb=" O LYS V 176 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER V 172 " --> pdb=" O ASN V 168 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 124 through 127 Processing sheet with id=AG1, 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=AG2, first strand: chain 'W' and resid 34 through 38 removed outlier: 6.255A pdb=" N ILE W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 212 through 219 removed outlier: 6.703A pdb=" N LYS X 212 " --> pdb=" O LEU W 213 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU W 215 " --> pdb=" O LYS X 210 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS X 210 " --> pdb=" O GLU W 215 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE W 217 " --> pdb=" O ILE X 208 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE X 208 " --> pdb=" O ILE W 217 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA X 198 " --> pdb=" O LEU X 213 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N CYS X 11 " --> pdb=" O ASP X 26 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 29 through 31 removed outlier: 6.527A pdb=" N LEU X 29 " --> pdb=" O VAL X 37 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 44 through 48 removed outlier: 6.597A pdb=" N VAL X 51 " --> pdb=" O MET X 47 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER X 56 " --> pdb=" O ASN X 108 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id=AG7, first strand: chain 'Y' and resid 21 through 23 removed outlier: 6.424A pdb=" N SER Y 21 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 36 through 39 Processing sheet with id=AG9, first strand: chain 'Z' and resid 125 through 128 removed outlier: 6.310A pdb=" N VAL Z 174 " --> pdb=" O GLU Z 189 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLU Z 189 " --> pdb=" O VAL Z 174 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL Z 176 " --> pdb=" O ILE Z 187 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 20 through 22 removed outlier: 6.569A pdb=" N ALA Z 20 " --> pdb=" O SER Z 27 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.438A pdb=" N ILE Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE Z 100 " --> pdb=" O THR Z 44 " (cutoff:3.500A) Processing sheet with id=AH3, 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=AH4, first strand: chain 'a' and resid 57 through 59 removed outlier: 6.935A pdb=" N LEU a 57 " --> pdb=" O TYR a 64 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'a' and resid 71 through 75 removed outlier: 6.427A pdb=" N CYS a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN a 136 " --> pdb=" O TYR a 152 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU a 149 " --> pdb=" O ALA a 161 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 34 through 37 removed outlier: 3.787A pdb=" N LYS b 36 " --> pdb=" O ALA b 29 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA b 29 " --> pdb=" O LYS b 36 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR b 50 " --> pdb=" O ILE b 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'b' and resid 34 through 37 removed outlier: 3.787A pdb=" N LYS b 36 " --> pdb=" O ALA b 29 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA b 29 " --> pdb=" O LYS b 36 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'b' and resid 175 through 177 Processing sheet with id=AH9, first strand: chain 'b' and resid 175 through 177 2960 hydrogen bonds defined for protein. 8485 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: 26.44 Time building geometry restraints manager: 11.90 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=" N ILE Y 25 " pdb=" CA ILE Y 25 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" C43 YRE C 301 " pdb=" N38 YRE C 301 " ideal model delta sigma weight residual 1.446 1.502 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C16 YRE W 301 " pdb=" C17 YRE W 301 " ideal model delta sigma weight residual 1.545 1.600 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" N THR L 201 " pdb=" CA THR L 201 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.26e-02 6.30e+03 6.69e+00 bond pdb=" N THR Z 201 " pdb=" CA THR Z 201 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.28e+00 ... (remaining 53025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 70427 1.79 - 3.59: 1061 3.59 - 5.38: 109 5.38 - 7.17: 24 7.17 - 8.97: 5 Bond angle restraints: 71626 Sorted by residual: angle pdb=" N ASN M 136 " pdb=" CA ASN M 136 " pdb=" C ASN M 136 " ideal model delta sigma weight residual 108.90 115.09 -6.19 1.63e+00 3.76e-01 1.44e+01 angle pdb=" N ASN a 136 " pdb=" CA ASN a 136 " pdb=" C ASN a 136 " ideal model delta sigma weight residual 108.90 114.92 -6.02 1.63e+00 3.76e-01 1.36e+01 angle pdb=" CA ILE Y 25 " pdb=" C ILE Y 25 " pdb=" O ILE Y 25 " ideal model delta sigma weight residual 120.78 116.35 4.43 1.25e+00 6.40e-01 1.26e+01 angle pdb=" C PHE a 135 " pdb=" N ASN a 136 " pdb=" CA ASN a 136 " ideal model delta sigma weight residual 122.99 118.06 4.93 1.41e+00 5.03e-01 1.22e+01 angle pdb=" C PHE M 135 " pdb=" N ASN M 136 " pdb=" CA ASN M 136 " ideal model delta sigma weight residual 122.99 118.11 4.88 1.41e+00 5.03e-01 1.20e+01 ... (remaining 71621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 31024 34.89 - 69.77: 947 69.77 - 104.66: 107 104.66 - 139.54: 10 139.54 - 174.43: 22 Dihedral angle restraints: 32110 sinusoidal: 13036 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=" C16 YRE C 301 " pdb=" C17 YRE C 301 " pdb=" C18 YRE C 301 " pdb=" C19 YRE C 301 " ideal model delta sinusoidal sigma weight residual 56.44 -117.99 174.43 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 32107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 7253 0.079 - 0.158: 723 0.158 - 0.237: 2 0.237 - 0.316: 2 0.316 - 0.395: 4 Chirality restraints: 7984 Sorted by residual: chirality pdb=" C16 YRE Q 301 " pdb=" C15 YRE Q 301 " pdb=" C17 YRE Q 301 " pdb=" N29 YRE Q 301 " both_signs ideal model delta sigma weight residual False 2.13 2.53 -0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C16 YRE C 301 " pdb=" C15 YRE C 301 " pdb=" C17 YRE C 301 " pdb=" N29 YRE C 301 " both_signs ideal model delta sigma weight residual False 2.13 2.51 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C16 YRE Z 301 " pdb=" C15 YRE Z 301 " pdb=" C17 YRE Z 301 " pdb=" N29 YRE Z 301 " both_signs ideal model delta sigma weight residual False 2.13 2.51 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (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: 40183 3.13 - 3.72: 84686 3.72 - 4.31: 126851 4.31 - 4.90: 208152 Nonbonded interactions: 460123 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 3.040 nonbonded pdb=" OG1 THR J 60 " pdb=" OG SER K 122 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR N 123 " pdb=" OD2 ASP N 158 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR b 123 " pdb=" OD2 ASP b 158 " model vdw 2.261 3.040 ... (remaining 460118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.550 Check model and map are aligned: 0.320 Set scattering table: 0.380 Process input model: 108.030 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.530 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.790 ------------------------------------------------------------------------------- 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 : 0.004 0.056 53030 Z= 0.287 Angle : 0.598 8.966 71626 Z= 0.327 Chirality : 0.045 0.395 7984 Planarity : 0.004 0.045 9138 Dihedral : 17.672 174.428 19914 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 : 4.626 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: 1.4861 time to fit residues: 1595.3448 Evaluate side-chains 703 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 678 time to evaluate : 4.590 ------------------------------------------------------------------------------- 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: 7.9990 chunk 268 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 500 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 chunk 304 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 579 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 C 149 HIS D 169 GLN E 227 GLN G 112 HIS H 190 GLN H 208 ASN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 71 ASN J 108 ASN J 129 ASN N 125 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN O 59 GLN Q 149 HIS R 169 GLN S 227 GLN T 227 GLN V 104 ASN V 190 GLN V 208 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN X 80 GLN X 108 ASN X 129 ASN b 112 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 53030 Z= 0.244 Angle : 0.593 7.363 71626 Z= 0.329 Chirality : 0.046 0.176 7984 Planarity : 0.004 0.048 9138 Dihedral : 11.405 167.922 7514 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.56 % Allowed : 15.32 % Favored : 82.13 % 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: 1.24 (0.10), residues: 6434 helix: 2.02 (0.10), residues: 2382 sheet: 0.67 (0.13), residues: 1484 loop : -0.16 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 55 HIS 0.006 0.001 HIS Q 149 PHE 0.019 0.002 PHE F 160 TYR 0.020 0.002 TYR L 161 ARG 0.006 0.001 ARG I 67 *********************** 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 851 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 705 time to evaluate : 4.596 Fit side-chains REVERT: A 86 MET cc_start: 0.8419 (mmt) cc_final: 0.8161 (mmt) REVERT: A 198 GLN cc_start: 0.4304 (tp40) cc_final: 0.3995 (tp-100) REVERT: B 100 GLN cc_start: 0.7684 (mt0) cc_final: 0.7395 (mt0) REVERT: B 209 GLU cc_start: 0.7472 (tt0) cc_final: 0.7086 (mm-30) REVERT: C 233 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6317 (mm-30) REVERT: D 67 GLU cc_start: 0.7177 (mp0) cc_final: 0.6890 (mp0) REVERT: D 179 ASN cc_start: 0.6807 (m-40) cc_final: 0.6600 (m-40) REVERT: E 62 ASP cc_start: 0.5872 (m-30) cc_final: 0.5638 (m-30) REVERT: E 180 GLU cc_start: 0.6460 (tp30) cc_final: 0.6186 (tt0) REVERT: E 189 LYS cc_start: 0.6122 (mttp) cc_final: 0.5870 (ttmm) REVERT: E 191 MET cc_start: 0.6842 (mtp) cc_final: 0.6538 (ttp) REVERT: F 16 GLU cc_start: 0.7017 (mp0) cc_final: 0.6716 (mp0) REVERT: F 53 ILE cc_start: 0.6784 (mm) cc_final: 0.6556 (mp) REVERT: F 176 HIS cc_start: 0.7031 (p-80) cc_final: 0.6707 (p90) REVERT: F 230 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: F 234 LYS cc_start: 0.6835 (mtpt) cc_final: 0.6352 (tptm) REVERT: G 213 GLN cc_start: 0.7094 (mp10) cc_final: 0.6679 (mt0) REVERT: I 216 LYS cc_start: 0.7600 (ptmt) cc_final: 0.7275 (pttt) REVERT: K 11 ASN cc_start: 0.7610 (OUTLIER) cc_final: 0.7316 (m-40) REVERT: K 20 TYR cc_start: 0.8165 (m-80) cc_final: 0.7963 (m-10) REVERT: K 96 ASN cc_start: 0.5932 (t0) cc_final: 0.5559 (p0) REVERT: K 109 LYS cc_start: 0.7470 (OUTLIER) cc_final: 0.7158 (mttp) REVERT: L 91 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7414 (tttt) REVERT: L 206 LYS cc_start: 0.7125 (ptpt) cc_final: 0.6679 (mtmt) REVERT: M 146 LYS cc_start: 0.7165 (mtpt) cc_final: 0.6915 (tttt) REVERT: N 122 LYS cc_start: 0.7897 (pttt) cc_final: 0.7630 (pttp) REVERT: N 200 GLU cc_start: 0.7135 (mp0) cc_final: 0.6924 (mp0) REVERT: O 8 MET cc_start: 0.4542 (ptm) cc_final: 0.3866 (mmt) REVERT: P 100 GLN cc_start: 0.7678 (mt0) cc_final: 0.7367 (mt0) REVERT: P 169 ASN cc_start: 0.7134 (m-40) cc_final: 0.6787 (m-40) REVERT: P 186 ASP cc_start: 0.6803 (m-30) cc_final: 0.6534 (m-30) REVERT: Q 54 LYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6518 (tmtt) REVERT: Q 225 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7780 (tttp) REVERT: R 4 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7106 (m-30) REVERT: R 178 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5834 (mt-10) REVERT: R 179 ASN cc_start: 0.6954 (m-40) cc_final: 0.6693 (m-40) REVERT: R 213 ASP cc_start: 0.6842 (p0) cc_final: 0.6330 (p0) REVERT: S 8 TYR cc_start: 0.4524 (OUTLIER) cc_final: 0.4187 (t80) REVERT: S 62 ASP cc_start: 0.5879 (m-30) cc_final: 0.5644 (m-30) REVERT: S 65 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: S 78 MET cc_start: 0.8342 (ptp) cc_final: 0.7846 (mtm) REVERT: S 135 MET cc_start: 0.8134 (mmt) cc_final: 0.7797 (mmt) REVERT: S 180 GLU cc_start: 0.6414 (tp30) cc_final: 0.6176 (tt0) REVERT: S 236 ASP cc_start: 0.6756 (m-30) cc_final: 0.6422 (m-30) REVERT: T 53 ILE cc_start: 0.6800 (mm) cc_final: 0.6548 (mp) REVERT: T 96 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: T 176 HIS cc_start: 0.7040 (p-80) cc_final: 0.6660 (p90) REVERT: T 230 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.6003 (tm-30) REVERT: T 234 LYS cc_start: 0.6785 (mtpt) cc_final: 0.6291 (tptm) REVERT: U 63 LYS cc_start: 0.6847 (tttp) cc_final: 0.6608 (ttmm) REVERT: U 213 GLN cc_start: 0.7071 (mp10) cc_final: 0.6646 (mt0) REVERT: U 238 THR cc_start: 0.7967 (m) cc_final: 0.7683 (m) REVERT: U 246 GLU cc_start: 0.5865 (pp20) cc_final: 0.5344 (pp20) REVERT: W 73 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: W 194 MET cc_start: 0.6568 (ptp) cc_final: 0.6108 (ptp) REVERT: W 216 LYS cc_start: 0.7591 (ptmt) cc_final: 0.7281 (pttt) REVERT: Y 11 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7332 (m110) REVERT: Y 20 TYR cc_start: 0.8179 (m-80) cc_final: 0.7957 (m-10) REVERT: Y 96 ASN cc_start: 0.5823 (t0) cc_final: 0.5536 (p0) REVERT: Y 110 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7223 (ttmm) REVERT: Y 161 LYS cc_start: 0.8015 (tppp) cc_final: 0.7678 (tptm) REVERT: Z 91 LYS cc_start: 0.7774 (ttpt) cc_final: 0.7455 (tttt) REVERT: Z 189 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: Z 206 LYS cc_start: 0.7103 (ptpt) cc_final: 0.6863 (mmtt) REVERT: b 122 LYS cc_start: 0.7875 (pttt) cc_final: 0.7613 (pttp) REVERT: b 200 GLU cc_start: 0.7142 (mp0) cc_final: 0.6932 (mp0) outliers start: 146 outliers final: 58 residues processed: 812 average time/residue: 1.3702 time to fit residues: 1394.6508 Evaluate side-chains 722 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 649 time to evaluate : 4.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 185 GLU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 206 LYS 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 89 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 160 PHE Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain G residue 234 GLU 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 208 ILE Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 109 LYS Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain M residue 228 MET 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 185 GLU 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 178 GLU Chi-restraints excluded: chain R residue 228 LEU 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 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 U residue 234 GLU 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 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 83 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 321 optimal weight: 0.0870 chunk 179 optimal weight: 7.9990 chunk 482 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 580 optimal weight: 9.9990 chunk 627 optimal weight: 6.9990 chunk 516 optimal weight: 10.0000 chunk 575 optimal weight: 30.0000 chunk 197 optimal weight: 0.9980 chunk 465 optimal weight: 3.9990 overall best weight: 3.6164 ------------------------------------------------------------------------------- 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 B 42 ASN D 169 GLN E 227 GLN F 60 GLN G 206 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN J 80 GLN J 129 ASN M 136 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 P 42 ASN Q 149 HIS R 169 GLN V 104 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN X 80 GLN X 129 ASN a 136 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: 0.8293 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 53030 Z= 0.252 Angle : 0.593 7.711 71626 Z= 0.328 Chirality : 0.046 0.155 7984 Planarity : 0.004 0.051 9138 Dihedral : 11.185 173.264 7493 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.03 % Allowed : 15.65 % Favored : 81.32 % 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: 1.27 (0.10), residues: 6434 helix: 2.03 (0.10), residues: 2372 sheet: 0.78 (0.13), residues: 1450 loop : -0.18 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 55 HIS 0.007 0.001 HIS Q 149 PHE 0.019 0.002 PHE F 160 TYR 0.018 0.002 TYR L 161 ARG 0.007 0.001 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 852 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 679 time to evaluate : 4.566 Fit side-chains revert: symmetry clash REVERT: A 86 MET cc_start: 0.8449 (mmt) cc_final: 0.8248 (mmt) REVERT: A 198 GLN cc_start: 0.4255 (tp40) cc_final: 0.3952 (tp-100) REVERT: B 100 GLN cc_start: 0.7668 (mt0) cc_final: 0.7380 (mt0) REVERT: B 209 GLU cc_start: 0.7484 (tt0) cc_final: 0.7088 (mm-30) REVERT: B 228 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5419 (mmmt) REVERT: C 176 LYS cc_start: 0.7018 (ttmm) cc_final: 0.6699 (ttpp) REVERT: C 233 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6295 (mm-30) REVERT: D 67 GLU cc_start: 0.7188 (mp0) cc_final: 0.6915 (mp0) REVERT: D 107 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8586 (mm) REVERT: E 180 GLU cc_start: 0.6473 (tp30) cc_final: 0.6190 (tt0) REVERT: E 189 LYS cc_start: 0.6172 (mttp) cc_final: 0.5914 (ttmm) REVERT: E 191 MET cc_start: 0.6933 (mtp) cc_final: 0.6576 (ttp) REVERT: F 230 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5990 (tm-30) REVERT: F 234 LYS cc_start: 0.6823 (mtpt) cc_final: 0.6355 (tptm) REVERT: G 213 GLN cc_start: 0.7083 (mp10) cc_final: 0.6665 (mt0) REVERT: H 75 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7142 (mtt-85) REVERT: I 216 LYS cc_start: 0.7595 (ptmt) cc_final: 0.7282 (pttt) REVERT: K 11 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7363 (m-40) REVERT: K 96 ASN cc_start: 0.5953 (t0) cc_final: 0.5532 (p0) REVERT: K 109 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7194 (mttp) REVERT: L 91 LYS cc_start: 0.7743 (ttpt) cc_final: 0.7431 (tttt) REVERT: L 206 LYS cc_start: 0.7177 (ptpt) cc_final: 0.6933 (mmtt) REVERT: M 64 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: M 146 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6939 (tttt) REVERT: N 122 LYS cc_start: 0.7899 (pttt) cc_final: 0.7644 (pttp) REVERT: N 200 GLU cc_start: 0.7143 (mp0) cc_final: 0.6932 (mp0) REVERT: O 8 MET cc_start: 0.4520 (ptm) cc_final: 0.3757 (mmp) REVERT: P 100 GLN cc_start: 0.7683 (mt0) cc_final: 0.7393 (mt0) REVERT: P 169 ASN cc_start: 0.7129 (m-40) cc_final: 0.6779 (m-40) REVERT: P 171 MET cc_start: 0.7527 (mmm) cc_final: 0.7146 (mmm) REVERT: P 186 ASP cc_start: 0.6809 (m-30) cc_final: 0.6535 (m-30) REVERT: Q 54 LYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6502 (tmtt) REVERT: Q 218 LYS cc_start: 0.5609 (OUTLIER) cc_final: 0.5178 (ptmm) REVERT: Q 225 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7788 (tttp) REVERT: R 4 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: R 107 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8584 (mm) REVERT: R 178 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.5814 (mt-10) REVERT: R 179 ASN cc_start: 0.6959 (m-40) cc_final: 0.6696 (m-40) REVERT: R 213 ASP cc_start: 0.6885 (p0) cc_final: 0.6367 (p0) REVERT: S 8 TYR cc_start: 0.4627 (OUTLIER) cc_final: 0.4306 (t80) REVERT: S 65 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5417 (pm20) REVERT: S 135 MET cc_start: 0.8149 (mmt) cc_final: 0.7799 (mmt) REVERT: S 180 GLU cc_start: 0.6465 (tp30) cc_final: 0.6207 (tt0) REVERT: T 16 GLU cc_start: 0.6986 (mp0) cc_final: 0.6631 (mp0) REVERT: T 53 ILE cc_start: 0.6772 (mm) cc_final: 0.6542 (mp) REVERT: T 96 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8143 (mtpp) REVERT: T 230 GLU cc_start: 0.6284 (OUTLIER) cc_final: 0.6046 (tm-30) REVERT: T 234 LYS cc_start: 0.6780 (mtpt) cc_final: 0.6279 (tptm) REVERT: U 213 GLN cc_start: 0.7077 (mp10) cc_final: 0.6639 (mt0) REVERT: U 246 GLU cc_start: 0.5883 (pp20) cc_final: 0.5355 (pp20) REVERT: W 216 LYS cc_start: 0.7647 (ptmt) cc_final: 0.7332 (pttt) REVERT: Y 20 TYR cc_start: 0.8204 (m-80) cc_final: 0.7967 (m-10) REVERT: Y 96 ASN cc_start: 0.5799 (t0) cc_final: 0.5523 (p0) REVERT: Y 109 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7191 (mttp) REVERT: Y 110 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7203 (ttmm) REVERT: Z 91 LYS cc_start: 0.7796 (ttpt) cc_final: 0.7473 (tttt) REVERT: Z 189 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: Z 206 LYS cc_start: 0.7159 (ptpt) cc_final: 0.6915 (mmtt) REVERT: a 64 TYR cc_start: 0.9180 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: b 122 LYS cc_start: 0.7893 (pttt) cc_final: 0.7655 (pttp) REVERT: b 200 GLU cc_start: 0.7194 (mp0) cc_final: 0.6974 (mp0) REVERT: b 235 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7798 (mt-10) outliers start: 173 outliers final: 83 residues processed: 806 average time/residue: 1.3634 time to fit residues: 1375.0726 Evaluate side-chains 736 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 631 time to evaluate : 4.544 ------------------------------------------------------------------------------- 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 52 SER Chi-restraints excluded: chain B residue 95 ILE 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 228 LYS 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 107 ILE 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 89 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 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 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE 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 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 130 SER 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 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 172 SER Chi-restraints excluded: chain P residue 185 GLU 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 170 THR Chi-restraints excluded: chain Q residue 176 LYS Chi-restraints excluded: chain Q residue 183 MET Chi-restraints excluded: chain Q residue 218 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 107 ILE Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 152 ILE Chi-restraints excluded: chain R residue 178 GLU Chi-restraints excluded: chain R residue 228 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 65 GLU Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 102 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 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 234 GLU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 115 LYS 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 11 ASN 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 130 SER 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 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: 7.9990 chunk 389 optimal weight: 7.9990 chunk 582 optimal weight: 8.9990 chunk 616 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 552 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 B 42 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 HIS G 206 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN J 129 ASN ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN N 125 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN O 63 GLN O 153 ASN P 42 ASN T 174 ASN T 176 HIS ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 54 HIS A W 73 GLN X 80 GLN X 129 ASN ** Z 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 136 ASN b 125 ASN b 126 ASN b 192 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 53030 Z= 0.345 Angle : 0.673 9.115 71626 Z= 0.370 Chirality : 0.049 0.177 7984 Planarity : 0.005 0.067 9138 Dihedral : 11.346 176.952 7493 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.17 % Allowed : 16.37 % Favored : 80.46 % 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: 1.05 (0.10), residues: 6434 helix: 1.77 (0.10), residues: 2380 sheet: 0.70 (0.13), residues: 1440 loop : -0.24 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 55 HIS 0.007 0.002 HIS I 116 PHE 0.022 0.003 PHE X 102 TYR 0.022 0.003 TYR K 37 ARG 0.007 0.001 ARG W 67 *********************** 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 832 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 651 time to evaluate : 4.644 Fit side-chains revert: symmetry clash REVERT: A 198 GLN cc_start: 0.4280 (tp40) cc_final: 0.3973 (tp-100) REVERT: B 100 GLN cc_start: 0.7802 (mt0) cc_final: 0.7500 (mt0) REVERT: B 177 ARG cc_start: 0.6922 (ptm160) cc_final: 0.6719 (ptp-110) REVERT: B 209 GLU cc_start: 0.7485 (tt0) cc_final: 0.7220 (mt-10) REVERT: B 228 LYS cc_start: 0.6031 (OUTLIER) cc_final: 0.5403 (mmmt) REVERT: C 176 LYS cc_start: 0.7011 (ttmm) cc_final: 0.6718 (ttpp) REVERT: D 67 GLU cc_start: 0.7190 (mp0) cc_final: 0.6925 (mp0) REVERT: E 180 GLU cc_start: 0.6505 (tp30) cc_final: 0.6272 (tt0) REVERT: E 189 LYS cc_start: 0.6209 (mttp) cc_final: 0.5933 (ttmm) REVERT: F 147 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6933 (mpt-90) REVERT: F 230 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: F 234 LYS cc_start: 0.6852 (mtpt) cc_final: 0.6390 (tptm) REVERT: G 213 GLN cc_start: 0.7076 (mp10) cc_final: 0.6669 (mt0) REVERT: H 75 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7146 (mtt-85) REVERT: I 216 LYS cc_start: 0.7671 (ptmt) cc_final: 0.7338 (pttt) REVERT: K 96 ASN cc_start: 0.6004 (t0) cc_final: 0.5563 (p0) REVERT: K 175 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: L 91 LYS cc_start: 0.7766 (ttpt) cc_final: 0.7472 (tttt) REVERT: L 206 LYS cc_start: 0.7206 (ptpt) cc_final: 0.6952 (mmtt) REVERT: M 64 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: M 146 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6987 (tttt) REVERT: N 122 LYS cc_start: 0.7881 (pttt) cc_final: 0.7647 (pttp) REVERT: N 200 GLU cc_start: 0.7218 (mp0) cc_final: 0.7005 (mp0) REVERT: O 8 MET cc_start: 0.4580 (ptm) cc_final: 0.3880 (mmt) REVERT: P 100 GLN cc_start: 0.7750 (mt0) cc_final: 0.7440 (mt0) REVERT: P 169 ASN cc_start: 0.7127 (m-40) cc_final: 0.6787 (m-40) REVERT: Q 17 ARG cc_start: 0.6879 (mtp180) cc_final: 0.6612 (mtp180) REVERT: Q 54 LYS cc_start: 0.6907 (OUTLIER) cc_final: 0.6517 (tmtt) REVERT: Q 218 LYS cc_start: 0.5613 (OUTLIER) cc_final: 0.5201 (ptmm) REVERT: Q 225 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7634 (tttp) REVERT: R 4 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: R 178 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5797 (mt-10) REVERT: R 179 ASN cc_start: 0.6939 (m-40) cc_final: 0.6667 (m-40) REVERT: R 213 ASP cc_start: 0.6884 (p0) cc_final: 0.6368 (p0) REVERT: S 8 TYR cc_start: 0.4678 (OUTLIER) cc_final: 0.4325 (t80) REVERT: S 65 GLU cc_start: 0.5690 (OUTLIER) cc_final: 0.5335 (pm20) REVERT: S 135 MET cc_start: 0.8163 (mmt) cc_final: 0.7848 (mmt) REVERT: T 53 ILE cc_start: 0.6810 (mm) cc_final: 0.6593 (mp) REVERT: T 96 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (mtpp) REVERT: T 230 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6064 (tm-30) REVERT: T 234 LYS cc_start: 0.6770 (mtpt) cc_final: 0.6282 (tptm) REVERT: U 213 GLN cc_start: 0.7100 (mp10) cc_final: 0.6662 (mt0) REVERT: U 246 GLU cc_start: 0.5929 (pp20) cc_final: 0.5336 (pp20) REVERT: W 216 LYS cc_start: 0.7684 (ptmt) cc_final: 0.7356 (pttt) REVERT: Y 20 TYR cc_start: 0.8218 (m-80) cc_final: 0.7973 (m-10) REVERT: Y 109 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7221 (mttp) REVERT: Y 110 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7156 (ttmm) REVERT: Z 91 LYS cc_start: 0.7840 (ttpt) cc_final: 0.7530 (tttt) REVERT: Z 189 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: Z 206 LYS cc_start: 0.7174 (ptpt) cc_final: 0.6904 (mmtt) REVERT: a 64 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: b 122 LYS cc_start: 0.7911 (pttt) cc_final: 0.7675 (pttp) REVERT: b 200 GLU cc_start: 0.7225 (mp0) cc_final: 0.7001 (mp0) REVERT: b 235 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7872 (mt-10) outliers start: 181 outliers final: 99 residues processed: 786 average time/residue: 1.3896 time to fit residues: 1365.0715 Evaluate side-chains 746 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 627 time to evaluate : 4.602 ------------------------------------------------------------------------------- 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 198 SER Chi-restraints excluded: chain B residue 228 LYS 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 4 ASP 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 35 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 8 THR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 103 SER 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 J residue 169 LYS Chi-restraints excluded: chain K residue 11 ASN Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 175 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER 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 M residue 234 THR 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 172 SER Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 37 LEU 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 218 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 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 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 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 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 234 GLU Chi-restraints excluded: chain W residue 73 GLN 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 115 LYS 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 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 28 SER Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER 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 235 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 638 random chunks: chunk 513 optimal weight: 0.8980 chunk 350 optimal weight: 0.0270 chunk 8 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 chunk 526 optimal weight: 2.9990 chunk 426 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 314 optimal weight: 0.9990 chunk 553 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- 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 42 ASN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 GLN F 176 HIS ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 80 GLN J 118 HIS J 129 ASN N 125 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN O 153 ASN P 42 ASN T 176 HIS ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 54 HIS A W 73 GLN X 80 GLN X 129 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: 0.8277 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 53030 Z= 0.198 Angle : 0.550 6.888 71626 Z= 0.305 Chirality : 0.044 0.154 7984 Planarity : 0.004 0.053 9138 Dihedral : 10.823 179.414 7492 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.56 % Allowed : 17.35 % Favored : 80.09 % 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: 1.38 (0.10), residues: 6434 helix: 2.15 (0.10), residues: 2376 sheet: 0.81 (0.13), residues: 1468 loop : -0.14 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.005 0.001 HIS Z 197 PHE 0.017 0.002 PHE M 129 TYR 0.018 0.002 TYR I 90 ARG 0.007 0.000 ARG W 67 *********************** 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 823 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 677 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLN cc_start: 0.4236 (tp40) cc_final: 0.3935 (tp-100) REVERT: B 100 GLN cc_start: 0.7656 (mt0) cc_final: 0.7381 (mt0) REVERT: B 177 ARG cc_start: 0.6928 (ptm160) cc_final: 0.6723 (ptp-110) REVERT: B 186 ASP cc_start: 0.6769 (m-30) cc_final: 0.6493 (m-30) REVERT: B 209 GLU cc_start: 0.7501 (tt0) cc_final: 0.6899 (tp30) REVERT: C 17 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6149 (mtm180) REVERT: C 176 LYS cc_start: 0.6963 (ttmm) cc_final: 0.6651 (ttpp) REVERT: D 67 GLU cc_start: 0.7145 (mp0) cc_final: 0.6874 (mp0) REVERT: E 180 GLU cc_start: 0.6509 (tp30) cc_final: 0.6217 (tt0) REVERT: E 189 LYS cc_start: 0.6270 (mttp) cc_final: 0.5995 (ttmm) REVERT: E 191 MET cc_start: 0.6744 (mtp) cc_final: 0.6490 (ttp) REVERT: F 230 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6105 (tm-30) REVERT: F 234 LYS cc_start: 0.6818 (mtpt) cc_final: 0.6353 (tptm) REVERT: G 213 GLN cc_start: 0.6998 (mp10) cc_final: 0.6682 (mt0) REVERT: G 238 THR cc_start: 0.8058 (m) cc_final: 0.7789 (m) REVERT: H 75 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7150 (mtt-85) REVERT: I 216 LYS cc_start: 0.7595 (ptmt) cc_final: 0.7269 (pttt) REVERT: K 11 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7387 (m-40) REVERT: K 96 ASN cc_start: 0.5909 (t0) cc_final: 0.5446 (p0) REVERT: K 110 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7151 (ttmm) REVERT: L 91 LYS cc_start: 0.7703 (ttpt) cc_final: 0.7404 (tttt) REVERT: L 206 LYS cc_start: 0.7166 (ptpt) cc_final: 0.6923 (mmtt) REVERT: M 64 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: M 146 LYS cc_start: 0.7161 (mtpt) cc_final: 0.6874 (tttt) REVERT: N 122 LYS cc_start: 0.7914 (pttt) cc_final: 0.7654 (pttp) REVERT: N 200 GLU cc_start: 0.7129 (mp0) cc_final: 0.6898 (mp0) REVERT: O 8 MET cc_start: 0.4574 (ptm) cc_final: 0.3907 (mmt) REVERT: O 201 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6870 (mm) REVERT: P 1 MET cc_start: 0.5081 (pmt) cc_final: 0.4340 (ptt) REVERT: P 100 GLN cc_start: 0.7613 (mt0) cc_final: 0.7313 (mm110) REVERT: P 169 ASN cc_start: 0.7110 (m-40) cc_final: 0.6765 (m-40) REVERT: P 186 ASP cc_start: 0.6805 (m-30) cc_final: 0.6537 (m-30) REVERT: Q 54 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6489 (tmtt) REVERT: Q 225 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7752 (tttp) REVERT: R 4 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7103 (m-30) REVERT: R 178 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5796 (mt-10) REVERT: R 179 ASN cc_start: 0.6926 (m-40) cc_final: 0.6661 (m-40) REVERT: S 8 TYR cc_start: 0.4750 (OUTLIER) cc_final: 0.4435 (t80) REVERT: S 65 GLU cc_start: 0.5672 (OUTLIER) cc_final: 0.5316 (pm20) REVERT: S 78 MET cc_start: 0.8357 (ptp) cc_final: 0.7846 (mtm) REVERT: S 135 MET cc_start: 0.8144 (mmt) cc_final: 0.7864 (mmt) REVERT: T 16 GLU cc_start: 0.7053 (mp0) cc_final: 0.6694 (mp0) REVERT: T 53 ILE cc_start: 0.6748 (mm) cc_final: 0.6499 (mp) REVERT: T 230 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6075 (tm-30) REVERT: T 234 LYS cc_start: 0.6760 (mtpt) cc_final: 0.6261 (tptm) REVERT: U 213 GLN cc_start: 0.7066 (mp10) cc_final: 0.6667 (mt0) REVERT: U 238 THR cc_start: 0.8048 (m) cc_final: 0.7771 (m) REVERT: U 246 GLU cc_start: 0.5854 (pp20) cc_final: 0.5347 (pp20) REVERT: V 249 ASN cc_start: 0.6373 (m110) cc_final: 0.5643 (t0) REVERT: W 216 LYS cc_start: 0.7629 (ptmt) cc_final: 0.7314 (pttt) REVERT: Y 96 ASN cc_start: 0.5808 (t0) cc_final: 0.5544 (p0) REVERT: Y 109 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7134 (mttp) REVERT: Y 110 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7260 (ttmm) REVERT: Y 161 LYS cc_start: 0.8005 (tppp) cc_final: 0.7749 (tptm) REVERT: Z 91 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7444 (tttt) REVERT: Z 206 LYS cc_start: 0.7124 (ptpt) cc_final: 0.6851 (pttp) REVERT: a 64 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.8191 (m-80) REVERT: b 122 LYS cc_start: 0.7924 (pttt) cc_final: 0.7682 (pttp) REVERT: b 200 GLU cc_start: 0.7171 (mp0) cc_final: 0.6954 (mp0) REVERT: b 235 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7792 (mt-10) outliers start: 146 outliers final: 70 residues processed: 776 average time/residue: 1.3589 time to fit residues: 1322.3483 Evaluate side-chains 719 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 631 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER 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 37 LEU 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 228 LEU Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG 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 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 72 THR Chi-restraints excluded: chain I residue 73 GLN Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 103 SER 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 110 LYS Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain M residue 64 TYR Chi-restraints excluded: chain M residue 83 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain O residue 201 ILE 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 198 SER Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE 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 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 102 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 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 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 115 LYS 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 130 SER Chi-restraints excluded: chain a residue 64 TYR Chi-restraints excluded: chain a residue 83 SER 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: 10.0000 chunk 555 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 617 optimal weight: 7.9990 chunk 512 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 42 ASN E 227 GLN ** H 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 9 GLN I 73 GLN J 80 GLN J 118 HIS J 129 ASN N 125 ASN N 126 ASN ** N 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 63 GLN O 153 ASN P 42 ASN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 54 HIS A W 73 GLN X 80 GLN X 129 ASN Y 177 ASN b 125 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 53030 Z= 0.353 Angle : 0.676 9.367 71626 Z= 0.371 Chirality : 0.049 0.178 7984 Planarity : 0.005 0.072 9138 Dihedral : 10.949 178.834 7488 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.24 % Allowed : 17.00 % Favored : 79.76 % 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: 1.81 (0.10), residues: 2378 sheet: 0.69 (0.13), residues: 1460 loop : -0.21 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Z 55 HIS 0.008 0.002 HIS I 116 PHE 0.022 0.003 PHE a 129 TYR 0.024 0.003 TYR O 255 ARG 0.007 0.001 ARG W 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 835 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 650 time to evaluate : 4.613 Fit side-chains REVERT: A 198 GLN cc_start: 0.4238 (tp40) cc_final: 0.3933 (tp-100) REVERT: B 100 GLN cc_start: 0.7783 (mt0) cc_final: 0.7488 (mt0) REVERT: B 228 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.5481 (mmmt) REVERT: C 17 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6154 (mtm180) REVERT: C 26 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: C 176 LYS cc_start: 0.6996 (ttmm) cc_final: 0.6695 (ttpp) REVERT: D 67 GLU cc_start: 0.7170 (mp0) cc_final: 0.6922 (mp0) REVERT: E 180 GLU cc_start: 0.6577 (tp30) cc_final: 0.6334 (tt0) REVERT: E 189 LYS cc_start: 0.6161 (mttp) cc_final: 0.5776 (mttm) REVERT: F 147 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6923 (mpt-90) REVERT: F 230 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: F 234 LYS cc_start: 0.6861 (mtpt) cc_final: 0.6377 (tptm) REVERT: G 213 GLN cc_start: 0.7074 (mp10) cc_final: 0.6674 (mt0) REVERT: H 75 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7150 (mtt-85) REVERT: H 249 ASN cc_start: 0.6330 (m110) cc_final: 0.5605 (t0) REVERT: I 216 LYS cc_start: 0.7672 (ptmt) cc_final: 0.7344 (pttt) REVERT: K 96 ASN cc_start: 0.6004 (t0) cc_final: 0.5562 (p0) REVERT: K 110 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7184 (ttmm) REVERT: L 29 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: L 53 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8519 (tp) REVERT: L 91 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7468 (tttt) REVERT: L 206 LYS cc_start: 0.7188 (ptpt) cc_final: 0.6925 (mmtt) REVERT: M 64 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: M 146 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6979 (tttt) REVERT: N 122 LYS cc_start: 0.7908 (pttt) cc_final: 0.7673 (pttp) REVERT: N 200 GLU cc_start: 0.7222 (mp0) cc_final: 0.7012 (mp0) REVERT: O 8 MET cc_start: 0.4626 (ptm) cc_final: 0.3909 (mmt) REVERT: P 1 MET cc_start: 0.5121 (pmt) cc_final: 0.4205 (ptt) REVERT: P 100 GLN cc_start: 0.7745 (mt0) cc_final: 0.7438 (mt0) REVERT: P 169 ASN cc_start: 0.7096 (m-40) cc_final: 0.6814 (m-40) REVERT: P 209 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: Q 17 ARG cc_start: 0.6861 (mtp180) cc_final: 0.6626 (mtp180) REVERT: Q 54 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6516 (tmtt) REVERT: R 4 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: R 178 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5763 (mt-10) REVERT: R 179 ASN cc_start: 0.6910 (m-40) cc_final: 0.6654 (m-40) REVERT: S 8 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.4350 (t80) REVERT: S 65 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5338 (pm20) REVERT: S 135 MET cc_start: 0.8164 (mmt) cc_final: 0.7858 (mmt) REVERT: T 53 ILE cc_start: 0.6812 (mm) cc_final: 0.6605 (mp) REVERT: T 96 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8167 (mtpp) REVERT: T 147 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6930 (mpt-90) REVERT: T 230 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: T 234 LYS cc_start: 0.6796 (mtpt) cc_final: 0.6314 (tptm) REVERT: U 213 GLN cc_start: 0.7068 (mp10) cc_final: 0.6639 (mt0) REVERT: U 246 GLU cc_start: 0.5872 (pp20) cc_final: 0.5347 (pp20) REVERT: V 249 ASN cc_start: 0.6305 (m110) cc_final: 0.5588 (t0) REVERT: W 216 LYS cc_start: 0.7691 (ptmt) cc_final: 0.7368 (pttt) REVERT: Y 110 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7229 (ttmm) REVERT: Y 161 LYS cc_start: 0.7959 (tppp) cc_final: 0.7720 (tptm) REVERT: Z 29 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: Z 91 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7602 (tttt) REVERT: Z 189 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: Z 206 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6917 (mmtt) REVERT: a 64 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: b 122 LYS cc_start: 0.7916 (pttt) cc_final: 0.7683 (pttp) REVERT: b 200 GLU cc_start: 0.7213 (mp0) cc_final: 0.6992 (mp0) REVERT: b 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7849 (mt-10) outliers start: 185 outliers final: 91 residues processed: 788 average time/residue: 1.3919 time to fit residues: 1371.0015 Evaluate side-chains 744 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 629 time to evaluate : 4.615 ------------------------------------------------------------------------------- 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 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 228 LYS Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 73 PHE 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 35 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain J residue 103 SER 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 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 28 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER 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 N residue 106 ILE Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 110 SER 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 172 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 37 LEU 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 147 THR 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 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 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 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 234 GLU Chi-restraints excluded: chain V residue 91 GLU Chi-restraints excluded: chain W residue 73 GLN 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 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 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 29 GLN 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 234 THR Chi-restraints excluded: chain b residue 77 SER 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: 4.9990 chunk 69 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 450 optimal weight: 9.9990 chunk 349 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 614 optimal weight: 8.9990 chunk 384 optimal weight: 5.9990 chunk 374 optimal weight: 8.9990 chunk 283 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 E 227 GLN ** 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 O 153 ASN O 179 GLN P 42 ASN S 227 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 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: 0.8307 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 53030 Z= 0.352 Angle : 0.678 9.209 71626 Z= 0.373 Chirality : 0.049 0.178 7984 Planarity : 0.005 0.070 9138 Dihedral : 10.928 179.510 7488 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.20 % Allowed : 17.03 % Favored : 79.76 % 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: 0.99 (0.10), residues: 6434 helix: 1.71 (0.10), residues: 2378 sheet: 0.66 (0.13), residues: 1454 loop : -0.26 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 55 HIS 0.007 0.002 HIS I 116 PHE 0.022 0.003 PHE J 102 TYR 0.022 0.003 TYR Y 37 ARG 0.008 0.001 ARG W 67 *********************** 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 824 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 641 time to evaluate : 4.666 Fit side-chains REVERT: A 198 GLN cc_start: 0.4249 (tp40) cc_final: 0.3945 (tp-100) REVERT: B 100 GLN cc_start: 0.7772 (mt0) cc_final: 0.7485 (mt0) REVERT: B 228 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5459 (mmmt) REVERT: C 17 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6157 (mtm180) REVERT: C 26 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: C 176 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6699 (ttpp) REVERT: C 233 GLU cc_start: 0.6841 (tp30) cc_final: 0.6616 (mt-10) REVERT: D 67 GLU cc_start: 0.7142 (mp0) cc_final: 0.6891 (mp0) REVERT: D 107 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8585 (mm) REVERT: E 180 GLU cc_start: 0.6542 (tp30) cc_final: 0.6302 (tt0) REVERT: E 189 LYS cc_start: 0.6106 (mttp) cc_final: 0.5735 (mttm) REVERT: F 147 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.6911 (mpt-90) REVERT: F 230 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: F 234 LYS cc_start: 0.6813 (mtpt) cc_final: 0.6357 (tptm) REVERT: G 213 GLN cc_start: 0.7076 (mp10) cc_final: 0.6674 (mt0) REVERT: H 75 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7149 (mtt-85) REVERT: H 249 ASN cc_start: 0.6286 (m110) cc_final: 0.5578 (t0) REVERT: I 216 LYS cc_start: 0.7684 (ptmt) cc_final: 0.7354 (pttt) REVERT: J 169 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7593 (tttp) REVERT: K 96 ASN cc_start: 0.5976 (t0) cc_final: 0.5551 (p0) REVERT: K 110 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7182 (ttmm) REVERT: K 175 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8242 (mt0) REVERT: K 187 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.7055 (pttm) REVERT: L 29 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8323 (mm110) REVERT: L 53 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8523 (tp) REVERT: L 91 LYS cc_start: 0.7782 (ttpt) cc_final: 0.7484 (tttt) REVERT: L 206 LYS cc_start: 0.7195 (ptpt) cc_final: 0.6935 (mmtt) REVERT: M 64 TYR cc_start: 0.9197 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: M 146 LYS cc_start: 0.7236 (mtpt) cc_final: 0.6980 (tttt) REVERT: N 122 LYS cc_start: 0.7907 (pttt) cc_final: 0.7673 (pttp) REVERT: N 200 GLU cc_start: 0.7224 (mp0) cc_final: 0.7014 (mp0) REVERT: O 8 MET cc_start: 0.4636 (ptm) cc_final: 0.3924 (mmt) REVERT: O 228 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7201 (pt0) REVERT: P 1 MET cc_start: 0.5144 (pmt) cc_final: 0.4268 (ptt) REVERT: P 100 GLN cc_start: 0.7739 (mt0) cc_final: 0.7426 (mt0) REVERT: P 169 ASN cc_start: 0.7091 (m-40) cc_final: 0.6800 (m-40) REVERT: P 209 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: Q 17 ARG cc_start: 0.6897 (mtp180) cc_final: 0.6621 (mtp180) REVERT: Q 54 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6530 (tmtt) REVERT: Q 225 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7632 (tttp) REVERT: R 4 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: R 107 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8579 (mm) REVERT: R 178 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5798 (mt-10) REVERT: R 179 ASN cc_start: 0.6911 (m-40) cc_final: 0.6662 (m-40) REVERT: S 8 TYR cc_start: 0.4600 (OUTLIER) cc_final: 0.4318 (t80) REVERT: S 65 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5335 (pm20) REVERT: S 135 MET cc_start: 0.8157 (mmt) cc_final: 0.7855 (mmt) REVERT: T 53 ILE cc_start: 0.6815 (mm) cc_final: 0.6611 (mp) REVERT: T 96 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8169 (mtpp) REVERT: T 147 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6915 (mpt-90) REVERT: T 230 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.6110 (tm-30) REVERT: T 234 LYS cc_start: 0.6782 (mtpt) cc_final: 0.6282 (tptm) REVERT: U 213 GLN cc_start: 0.7065 (mp10) cc_final: 0.6638 (mt0) REVERT: U 246 GLU cc_start: 0.5934 (pp20) cc_final: 0.5335 (pp20) REVERT: V 249 ASN cc_start: 0.6301 (m110) cc_final: 0.5591 (t0) REVERT: W 216 LYS cc_start: 0.7702 (ptmt) cc_final: 0.7380 (pttt) REVERT: X 169 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7580 (tttp) REVERT: Y 96 ASN cc_start: 0.5856 (t0) cc_final: 0.5582 (p0) REVERT: Y 110 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7236 (ttmm) REVERT: Z 29 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8321 (mm110) REVERT: Z 91 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7614 (tttt) REVERT: Z 189 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: Z 206 LYS cc_start: 0.7192 (ptpt) cc_final: 0.6906 (pttp) REVERT: a 64 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: b 122 LYS cc_start: 0.7915 (pttt) cc_final: 0.7681 (pttp) REVERT: b 200 GLU cc_start: 0.7214 (mp0) cc_final: 0.6997 (mp0) REVERT: b 235 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (mt-10) outliers start: 183 outliers final: 101 residues processed: 783 average time/residue: 1.4288 time to fit residues: 1395.7826 Evaluate side-chains 758 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 625 time to evaluate : 4.616 ------------------------------------------------------------------------------- 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 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 228 LYS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 107 ILE 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 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 218 GLU Chi-restraints excluded: chain J residue 103 SER 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 J residue 169 LYS Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 7 LEU 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 K residue 175 GLN Chi-restraints excluded: chain K residue 187 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER 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 228 GLU 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 172 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 54 LYS Chi-restraints excluded: chain Q residue 73 PHE 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 107 ILE Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 147 THR 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 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 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 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 234 GLU Chi-restraints excluded: chain V residue 91 GLU Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 218 GLU 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 169 LYS 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 110 LYS Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER 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 234 THR Chi-restraints excluded: chain b residue 77 SER 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: 7.9990 chunk 367 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 390 optimal weight: 9.9990 chunk 418 optimal weight: 7.9990 chunk 304 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 483 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 42 ASN E 227 GLN I 9 GLN I 73 GLN I 106 ASN J 118 HIS J 129 ASN N 126 ASN O 53 GLN O 63 GLN O 153 ASN O 179 GLN P 42 ASN S 227 GLN W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 126 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 53030 Z= 0.399 Angle : 0.715 9.438 71626 Z= 0.393 Chirality : 0.051 0.187 7984 Planarity : 0.005 0.073 9138 Dihedral : 11.053 179.517 7488 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.10 % Allowed : 17.07 % Favored : 79.83 % 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: 0.87 (0.10), residues: 6434 helix: 1.57 (0.10), residues: 2378 sheet: 0.63 (0.13), residues: 1450 loop : -0.31 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 55 HIS 0.008 0.002 HIS I 116 PHE 0.024 0.003 PHE J 102 TYR 0.024 0.003 TYR K 37 ARG 0.008 0.001 ARG W 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 816 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 639 time to evaluate : 4.656 Fit side-chains REVERT: A 198 GLN cc_start: 0.4324 (tp40) cc_final: 0.4021 (tp-100) REVERT: B 100 GLN cc_start: 0.7823 (mt0) cc_final: 0.7517 (mt0) REVERT: C 17 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6160 (mtm180) REVERT: C 26 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: C 176 LYS cc_start: 0.6993 (ttmm) cc_final: 0.6709 (ttpp) REVERT: D 67 GLU cc_start: 0.7170 (mp0) cc_final: 0.6905 (mp0) REVERT: D 107 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8587 (mm) REVERT: E 180 GLU cc_start: 0.6523 (tp30) cc_final: 0.6289 (tt0) REVERT: E 189 LYS cc_start: 0.6121 (mttp) cc_final: 0.5759 (mttm) REVERT: F 147 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.6927 (mpt-90) REVERT: F 230 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.6077 (tm-30) REVERT: F 234 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6361 (tptm) REVERT: G 213 GLN cc_start: 0.7073 (mp10) cc_final: 0.6680 (mt0) REVERT: H 75 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7191 (mtt-85) REVERT: H 249 ASN cc_start: 0.6265 (m110) cc_final: 0.5556 (t0) REVERT: I 216 LYS cc_start: 0.7686 (ptmt) cc_final: 0.7358 (pttt) REVERT: J 115 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7853 (tttm) REVERT: K 96 ASN cc_start: 0.5979 (t0) cc_final: 0.5547 (p0) REVERT: K 110 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7174 (ttmm) REVERT: K 175 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: K 187 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7080 (pttm) REVERT: L 29 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8332 (mm110) REVERT: L 91 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7485 (tttt) REVERT: L 206 LYS cc_start: 0.7210 (ptpt) cc_final: 0.6935 (pttp) REVERT: M 64 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: M 146 LYS cc_start: 0.7231 (mtpt) cc_final: 0.6981 (tttt) REVERT: N 122 LYS cc_start: 0.7885 (pttt) cc_final: 0.7654 (pttp) REVERT: N 200 GLU cc_start: 0.7228 (mp0) cc_final: 0.7017 (mp0) REVERT: O 8 MET cc_start: 0.4623 (ptm) cc_final: 0.3898 (mmt) REVERT: P 100 GLN cc_start: 0.7783 (mt0) cc_final: 0.7434 (mt0) REVERT: P 169 ASN cc_start: 0.7101 (m-40) cc_final: 0.6851 (m-40) REVERT: P 176 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6320 (ttmm) REVERT: P 209 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: Q 54 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6556 (tmtt) REVERT: Q 225 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7673 (tttp) REVERT: R 4 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7114 (m-30) REVERT: R 107 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8580 (mm) REVERT: R 178 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5817 (mt-10) REVERT: R 179 ASN cc_start: 0.6917 (m-40) cc_final: 0.6667 (m-40) REVERT: S 8 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.4291 (t80) REVERT: S 65 GLU cc_start: 0.5687 (OUTLIER) cc_final: 0.5348 (pm20) REVERT: S 135 MET cc_start: 0.8158 (mmt) cc_final: 0.7857 (mmt) REVERT: T 53 ILE cc_start: 0.6827 (mm) cc_final: 0.6622 (mp) REVERT: T 96 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (mtpp) REVERT: T 147 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6943 (mpt-90) REVERT: T 230 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6135 (tm-30) REVERT: T 234 LYS cc_start: 0.6817 (mtpt) cc_final: 0.6325 (tptm) REVERT: U 213 GLN cc_start: 0.7064 (mp10) cc_final: 0.6636 (mt0) REVERT: U 246 GLU cc_start: 0.5934 (pp20) cc_final: 0.5331 (pp20) REVERT: V 249 ASN cc_start: 0.6299 (m110) cc_final: 0.5591 (t0) REVERT: W 216 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7383 (pttt) REVERT: Y 96 ASN cc_start: 0.5917 (t0) cc_final: 0.5595 (p0) REVERT: Y 110 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7235 (ttmm) REVERT: Z 29 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8331 (mm110) REVERT: Z 91 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7557 (tttt) REVERT: Z 189 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: Z 206 LYS cc_start: 0.7194 (ptpt) cc_final: 0.6912 (pttp) REVERT: a 64 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: b 122 LYS cc_start: 0.7914 (pttt) cc_final: 0.7684 (pttp) REVERT: b 200 GLU cc_start: 0.7225 (mp0) cc_final: 0.7007 (mp0) REVERT: b 235 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7859 (mt-10) outliers start: 177 outliers final: 109 residues processed: 778 average time/residue: 1.4438 time to fit residues: 1407.4989 Evaluate side-chains 768 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 630 time to evaluate : 4.579 ------------------------------------------------------------------------------- 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 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 231 LEU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 186 ILE Chi-restraints excluded: chain I residue 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 218 GLU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 115 LYS 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 7 LEU 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 K residue 175 GLN Chi-restraints excluded: chain K residue 187 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER 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 95 ILE Chi-restraints excluded: chain P residue 116 SER Chi-restraints excluded: chain P residue 172 SER Chi-restraints excluded: chain P residue 176 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 37 LEU 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 221 GLU Chi-restraints excluded: chain Q residue 223 TYR Chi-restraints excluded: chain Q residue 225 LYS Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 133 ILE Chi-restraints excluded: chain R residue 140 LYS Chi-restraints excluded: chain R residue 147 THR 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 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 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 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 U residue 234 GLU Chi-restraints excluded: chain V residue 91 GLU Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain W residue 218 GLU 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 7 LEU Chi-restraints excluded: chain Y residue 11 ASN Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 28 SER Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 58 SER 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 234 THR Chi-restraints excluded: chain b residue 77 SER 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: 10.0000 chunk 589 optimal weight: 3.9990 chunk 537 optimal weight: 5.9990 chunk 573 optimal weight: 7.9990 chunk 588 optimal weight: 1.9990 chunk 344 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 449 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 517 optimal weight: 9.9990 chunk 541 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 42 ASN C 149 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 53 GLN O 63 GLN O 153 ASN P 42 ASN S 227 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 53030 Z= 0.278 Angle : 0.622 7.896 71626 Z= 0.344 Chirality : 0.047 0.170 7984 Planarity : 0.004 0.066 9138 Dihedral : 10.823 178.751 7488 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.57 % Allowed : 17.86 % Favored : 79.57 % 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: 1.09 (0.10), residues: 6434 helix: 1.82 (0.10), residues: 2378 sheet: 0.69 (0.13), residues: 1460 loop : -0.24 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Z 55 HIS 0.006 0.001 HIS V 134 PHE 0.019 0.002 PHE a 129 TYR 0.019 0.002 TYR Z 161 ARG 0.008 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 789 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 642 time to evaluate : 4.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLN cc_start: 0.4218 (tp40) cc_final: 0.3913 (tp-100) REVERT: B 100 GLN cc_start: 0.7747 (mt0) cc_final: 0.7457 (mt0) REVERT: B 186 ASP cc_start: 0.6705 (m-30) cc_final: 0.6438 (m-30) REVERT: C 17 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6140 (mtm180) REVERT: C 26 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: C 176 LYS cc_start: 0.6986 (ttmm) cc_final: 0.6686 (ttpp) REVERT: D 67 GLU cc_start: 0.7174 (mp0) cc_final: 0.6913 (mp0) REVERT: D 107 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8572 (mm) REVERT: E 180 GLU cc_start: 0.6545 (tp30) cc_final: 0.6306 (tt0) REVERT: E 189 LYS cc_start: 0.6155 (mttp) cc_final: 0.5796 (mttm) REVERT: F 230 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: F 234 LYS cc_start: 0.6818 (mtpt) cc_final: 0.6363 (tptm) REVERT: G 213 GLN cc_start: 0.7066 (mp10) cc_final: 0.6677 (mt0) REVERT: H 75 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7144 (mtt-85) REVERT: H 249 ASN cc_start: 0.6276 (m110) cc_final: 0.5568 (t0) REVERT: I 216 LYS cc_start: 0.7657 (ptmt) cc_final: 0.7324 (pttt) REVERT: K 96 ASN cc_start: 0.5982 (t0) cc_final: 0.5555 (p0) REVERT: K 110 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7179 (ttmm) REVERT: K 175 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8239 (mt0) REVERT: L 29 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (mm110) REVERT: L 91 LYS cc_start: 0.7724 (ttpt) cc_final: 0.7430 (tttt) REVERT: L 206 LYS cc_start: 0.7190 (ptpt) cc_final: 0.6914 (pttp) REVERT: M 64 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8346 (m-80) REVERT: M 146 LYS cc_start: 0.7219 (mtpt) cc_final: 0.6959 (tttt) REVERT: N 122 LYS cc_start: 0.7919 (pttt) cc_final: 0.7679 (pttp) REVERT: N 200 GLU cc_start: 0.7225 (mp0) cc_final: 0.7011 (mp0) REVERT: O 8 MET cc_start: 0.4615 (ptm) cc_final: 0.3923 (mmt) REVERT: P 1 MET cc_start: 0.5012 (pmt) cc_final: 0.4137 (ptt) REVERT: P 100 GLN cc_start: 0.7713 (mt0) cc_final: 0.7407 (mt0) REVERT: P 169 ASN cc_start: 0.7062 (m-40) cc_final: 0.6785 (m-40) REVERT: P 186 ASP cc_start: 0.6774 (m-30) cc_final: 0.6510 (m-30) REVERT: Q 17 ARG cc_start: 0.6921 (mtp180) cc_final: 0.6647 (mtp180) REVERT: Q 54 LYS cc_start: 0.6902 (OUTLIER) cc_final: 0.6514 (tmtt) REVERT: Q 225 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7621 (tttp) REVERT: R 4 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: R 178 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5785 (mt-10) REVERT: R 179 ASN cc_start: 0.6916 (m-40) cc_final: 0.6666 (m-40) REVERT: S 8 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.4311 (t80) REVERT: S 65 GLU cc_start: 0.5741 (OUTLIER) cc_final: 0.5416 (pm20) REVERT: S 135 MET cc_start: 0.8155 (mmt) cc_final: 0.7798 (mmt) REVERT: T 53 ILE cc_start: 0.6810 (mm) cc_final: 0.6606 (mp) REVERT: T 96 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8151 (mtpp) REVERT: T 230 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.6096 (tm-30) REVERT: T 234 LYS cc_start: 0.6756 (mtpt) cc_final: 0.6264 (tptm) REVERT: U 213 GLN cc_start: 0.7051 (mp10) cc_final: 0.6649 (mt0) REVERT: U 246 GLU cc_start: 0.5940 (pp20) cc_final: 0.5342 (pp20) REVERT: V 249 ASN cc_start: 0.6309 (m110) cc_final: 0.5606 (t0) REVERT: W 216 LYS cc_start: 0.7644 (ptmt) cc_final: 0.7328 (pttt) REVERT: Y 96 ASN cc_start: 0.5824 (t0) cc_final: 0.5568 (p0) REVERT: Y 110 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7222 (ttmm) REVERT: Z 29 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8316 (mm110) REVERT: Z 91 LYS cc_start: 0.7884 (ttpt) cc_final: 0.7560 (tttt) REVERT: Z 189 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7475 (mm-30) REVERT: Z 206 LYS cc_start: 0.7182 (ptpt) cc_final: 0.6900 (pttp) REVERT: a 64 TYR cc_start: 0.9184 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: b 122 LYS cc_start: 0.7908 (pttt) cc_final: 0.7672 (pttp) REVERT: b 200 GLU cc_start: 0.7212 (mp0) cc_final: 0.6990 (mp0) REVERT: b 235 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7838 (mt-10) outliers start: 147 outliers final: 92 residues processed: 756 average time/residue: 1.4009 time to fit residues: 1323.8653 Evaluate side-chains 735 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 621 time to evaluate : 4.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER 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 26 GLU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 209 THR Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 218 GLU 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 J residue 208 ILE Chi-restraints excluded: chain K residue 7 LEU 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 K residue 175 GLN Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER 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 73 THR Chi-restraints excluded: chain O residue 110 SER 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 172 SER Chi-restraints excluded: chain P residue 198 SER 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 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 147 THR 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 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 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 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 234 GLU Chi-restraints excluded: chain W residue 73 GLN Chi-restraints excluded: chain W residue 209 THR Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain W residue 218 GLU 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 11 ASN Chi-restraints excluded: chain Y residue 110 LYS Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 58 SER 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 234 THR 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: 10.0000 chunk 376 optimal weight: 7.9990 chunk 605 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 287 optimal weight: 5.9990 chunk 421 optimal weight: 1.9990 chunk 635 optimal weight: 3.9990 chunk 585 optimal weight: 5.9990 chunk 506 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 390 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 E 227 GLN ** 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 O 153 ASN P 42 ASN S 227 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN W 106 ASN X 80 GLN X 129 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: 0.8298 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 53030 Z= 0.290 Angle : 0.633 8.225 71626 Z= 0.349 Chirality : 0.047 0.187 7984 Planarity : 0.005 0.067 9138 Dihedral : 10.844 178.890 7488 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.33 % Allowed : 18.05 % Favored : 79.62 % 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: 1.09 (0.10), residues: 6434 helix: 1.82 (0.10), residues: 2378 sheet: 0.69 (0.13), residues: 1460 loop : -0.23 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 55 HIS 0.018 0.001 HIS C 149 PHE 0.020 0.002 PHE a 129 TYR 0.020 0.002 TYR K 37 ARG 0.008 0.001 ARG W 67 ********************** 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 762 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 629 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 GLN cc_start: 0.4214 (tp40) cc_final: 0.3909 (tp-100) REVERT: B 100 GLN cc_start: 0.7748 (mt0) cc_final: 0.7458 (mt0) REVERT: B 186 ASP cc_start: 0.6713 (m-30) cc_final: 0.6451 (m-30) REVERT: C 17 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6111 (mtm180) REVERT: C 26 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7238 (mt-10) REVERT: C 176 LYS cc_start: 0.7008 (ttmm) cc_final: 0.6711 (ttpp) REVERT: C 209 LYS cc_start: 0.6899 (mtpp) cc_final: 0.6447 (mmmt) REVERT: D 67 GLU cc_start: 0.7165 (mp0) cc_final: 0.6912 (mp0) REVERT: E 180 GLU cc_start: 0.6548 (tp30) cc_final: 0.6309 (tt0) REVERT: F 230 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.6058 (tm-30) REVERT: F 234 LYS cc_start: 0.6820 (mtpt) cc_final: 0.6369 (tptm) REVERT: G 213 GLN cc_start: 0.7070 (mp10) cc_final: 0.6677 (mt0) REVERT: H 75 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7142 (mtt-85) REVERT: H 249 ASN cc_start: 0.6316 (m110) cc_final: 0.5602 (t0) REVERT: I 216 LYS cc_start: 0.7657 (ptmt) cc_final: 0.7325 (pttt) REVERT: K 96 ASN cc_start: 0.5961 (t0) cc_final: 0.5537 (p0) REVERT: K 110 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7182 (ttmm) REVERT: L 29 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8316 (mm110) REVERT: L 53 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8512 (tp) REVERT: L 91 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7457 (tttt) REVERT: L 206 LYS cc_start: 0.7189 (ptpt) cc_final: 0.6914 (pttp) REVERT: M 64 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8342 (m-80) REVERT: M 146 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6959 (tttt) REVERT: N 122 LYS cc_start: 0.7914 (pttt) cc_final: 0.7675 (pttp) REVERT: N 200 GLU cc_start: 0.7226 (mp0) cc_final: 0.7012 (mp0) REVERT: N 235 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: O 8 MET cc_start: 0.4614 (ptm) cc_final: 0.3917 (mmt) REVERT: P 1 MET cc_start: 0.5065 (pmt) cc_final: 0.4099 (ptt) REVERT: P 100 GLN cc_start: 0.7714 (mt0) cc_final: 0.7410 (mt0) REVERT: P 169 ASN cc_start: 0.7063 (m-40) cc_final: 0.6785 (m-40) REVERT: P 176 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6299 (ttmm) REVERT: P 186 ASP cc_start: 0.6751 (m-30) cc_final: 0.6478 (m-30) REVERT: P 209 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: Q 17 ARG cc_start: 0.6907 (mtp180) cc_final: 0.6626 (mtp180) REVERT: Q 54 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6514 (tmtt) REVERT: Q 225 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7625 (tttp) REVERT: R 4 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: R 178 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5785 (mt-10) REVERT: R 179 ASN cc_start: 0.6916 (m-40) cc_final: 0.6667 (m-40) REVERT: S 8 TYR cc_start: 0.4559 (OUTLIER) cc_final: 0.4304 (t80) REVERT: S 65 GLU cc_start: 0.5709 (OUTLIER) cc_final: 0.5385 (pm20) REVERT: S 135 MET cc_start: 0.8150 (mmt) cc_final: 0.7856 (mmt) REVERT: T 53 ILE cc_start: 0.6815 (mm) cc_final: 0.6610 (mp) REVERT: T 96 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8151 (mtpp) REVERT: T 230 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: T 234 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6279 (tptm) REVERT: U 213 GLN cc_start: 0.7049 (mp10) cc_final: 0.6644 (mt0) REVERT: U 246 GLU cc_start: 0.5939 (pp20) cc_final: 0.5344 (pp20) REVERT: V 249 ASN cc_start: 0.6307 (m110) cc_final: 0.5604 (t0) REVERT: W 216 LYS cc_start: 0.7641 (ptmt) cc_final: 0.7325 (pttt) REVERT: Y 96 ASN cc_start: 0.5852 (t0) cc_final: 0.5581 (p0) REVERT: Y 110 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7247 (ttmm) REVERT: Z 29 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8317 (mm110) REVERT: Z 91 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7562 (tttt) REVERT: Z 189 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: Z 206 LYS cc_start: 0.7185 (ptpt) cc_final: 0.6902 (pttp) REVERT: a 64 TYR cc_start: 0.9185 (OUTLIER) cc_final: 0.8353 (m-80) REVERT: b 122 LYS cc_start: 0.7908 (pttt) cc_final: 0.7674 (pttp) REVERT: b 200 GLU cc_start: 0.7211 (mp0) cc_final: 0.6990 (mp0) REVERT: b 235 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7838 (mt-10) outliers start: 133 outliers final: 95 residues processed: 733 average time/residue: 1.4719 time to fit residues: 1354.2234 Evaluate side-chains 742 residues out of total 5704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 623 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER 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 231 LEU Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 73 PHE Chi-restraints excluded: chain C residue 223 TYR Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 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 8 THR Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 96 LYS Chi-restraints excluded: chain F residue 147 ARG 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 209 THR Chi-restraints excluded: chain I residue 212 ILE 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 J residue 208 ILE Chi-restraints excluded: chain K residue 7 LEU 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 28 SER Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 53 LEU Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 130 SER Chi-restraints excluded: chain M residue 58 SER 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 N residue 235 GLU Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 110 SER 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 176 LYS Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 209 GLU 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 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 140 LYS Chi-restraints excluded: chain R residue 147 THR 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 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 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 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 234 GLU Chi-restraints excluded: chain W residue 73 GLN 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 W residue 218 GLU 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 110 LYS Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 97 CYS Chi-restraints excluded: chain Z residue 130 SER Chi-restraints excluded: chain Z residue 185 ASP Chi-restraints excluded: chain Z residue 189 GLU Chi-restraints excluded: chain a residue 58 SER 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 234 THR 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: 6.9990 chunk 402 optimal weight: 4.9990 chunk 539 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 chunk 466 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 506 optimal weight: 9.9990 chunk 212 optimal weight: 6.9990 chunk 520 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 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 63 GLN A 153 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** O 63 GLN O 153 ASN P 42 ASN S 227 GLN ** V 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 GLN W 73 GLN X 80 GLN X 129 ASN b 126 ASN ** b 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.111321 restraints weight = 80494.186| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.38 r_work: 0.3108 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 53030 Z= 0.327 Angle : 0.661 8.676 71626 Z= 0.364 Chirality : 0.048 0.189 7984 Planarity : 0.005 0.070 9138 Dihedral : 10.909 178.825 7488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.49 % Allowed : 17.87 % Favored : 79.64 % 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: 1.02 (0.10), residues: 6434 helix: 1.75 (0.10), residues: 2378 sheet: 0.66 (0.13), residues: 1460 loop : -0.25 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 55 HIS 0.007 0.001 HIS V 134 PHE 0.031 0.003 PHE B 173 TYR 0.021 0.003 TYR K 37 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: 20335.50 seconds wall clock time: 348 minutes 54.76 seconds (20934.76 seconds total)