Starting phenix.real_space_refine on Tue Sep 24 02:02:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6td5_10463/09_2024/6td5_10463_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians S 326 5.16 5 B 6 2.79 5 C 31062 2.51 5 N 8518 2.21 5 O 9494 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 49408 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "D" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1573 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "a" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1861 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 12, 'TRANS': 232} Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1753 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "c" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2155 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 11, 'TRANS': 260} Chain: "d" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1882 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 4, 'TRANS': 235} Chain: "e" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1802 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 10, 'TRANS': 224} Chain: "f" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "g" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1741 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 7, 'TRANS': 222} Chain: "h" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1709 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "i" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "j" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "k" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "l" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1573 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "m" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "n" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'BO2': 1, 'N2E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'BO2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'BO2': 1, 'N2E': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.07, per 1000 atoms: 0.47 Number of scatterers: 49408 At special positions: 0 Unit cell: (138.46, 184.9, 135.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 326 16.00 F 2 9.00 O 9494 8.00 N 8518 7.00 C 31062 6.00 B 6 5.00 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 4.7 seconds 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11716 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 76 sheets defined 36.1% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.627A pdb=" N ALA A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 103 removed outlier: 3.523A pdb=" N ARG A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.677A pdb=" N LYS A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 119 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.584A pdb=" N MET A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 removed outlier: 3.687A pdb=" N VAL A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.529A pdb=" N THR B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.505A pdb=" N ARG B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.619A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.769A pdb=" N PHE B 171 " --> pdb=" O ASP B 167 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 190 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.800A pdb=" N GLU B 195 " --> pdb=" O LEU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.900A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.703A pdb=" N TYR C 5 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP C 6 " --> pdb=" O HIS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 18 through 30 removed outlier: 3.717A pdb=" N GLN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 108 removed outlier: 3.540A pdb=" N ALA C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 130 removed outlier: 3.512A pdb=" N CYS C 121 " --> pdb=" O CYS C 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 removed outlier: 3.930A pdb=" N ALA C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 3.541A pdb=" N LYS C 204 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 268 Proline residue: C 256 - end of helix removed outlier: 4.059A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 261 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.501A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 25 " --> pdb=" O TYR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 95 removed outlier: 3.633A pdb=" N ARG D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.786A pdb=" N VAL D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.536A pdb=" N VAL D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 241 removed outlier: 3.678A pdb=" N LYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 227 " --> pdb=" O GLN D 223 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 235 " --> pdb=" O LYS D 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.675A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA E 130 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 133 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.587A pdb=" N SER E 163 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET E 164 " --> pdb=" O PRO E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 164' Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.655A pdb=" N ALA E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 194 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 218 Processing helix chain 'E' and resid 271 through 273 No H-bonds generated for 'chain 'E' and resid 271 through 273' Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.917A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 305 removed outlier: 3.544A pdb=" N ALA E 298 " --> pdb=" O GLY E 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 340 removed outlier: 4.030A pdb=" N ALA E 337 " --> pdb=" O THR E 333 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET E 339 " --> pdb=" O ILE E 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.928A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 194 " --> pdb=" O ASN F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 265 removed outlier: 3.808A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.599A pdb=" N ASP F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 338 Processing helix chain 'F' and resid 339 through 344 removed outlier: 5.407A pdb=" N GLU F 342 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F 344 " --> pdb=" O PHE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 361 removed outlier: 3.627A pdb=" N THR F 354 " --> pdb=" O ASP F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 364 No H-bonds generated for 'chain 'F' and resid 362 through 364' Processing helix chain 'F' and resid 394 through 399 Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.622A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 102 removed outlier: 3.857A pdb=" N ALA G 87 " --> pdb=" O PRO G 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.556A pdb=" N GLU G 118 " --> pdb=" O ASN G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 177 removed outlier: 3.713A pdb=" N SER G 174 " --> pdb=" O THR G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.084A pdb=" N VAL G 190 " --> pdb=" O CYS G 186 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.561A pdb=" N LEU H 109 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 143 removed outlier: 3.625A pdb=" N LEU H 136 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE H 137 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 188 removed outlier: 3.638A pdb=" N PHE H 188 " --> pdb=" O GLY H 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 188' Processing helix chain 'H' and resid 189 through 197 removed outlier: 3.660A pdb=" N ALA H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR H 197 " --> pdb=" O PHE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 221 removed outlier: 3.551A pdb=" N ALA H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 removed outlier: 3.811A pdb=" N MET I 87 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU I 98 " --> pdb=" O LEU I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.536A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS I 115 " --> pdb=" O LEU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.537A pdb=" N ALA I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 193 removed outlier: 3.578A pdb=" N ARG I 189 " --> pdb=" O ALA I 185 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 removed outlier: 3.804A pdb=" N ALA J 64 " --> pdb=" O GLN J 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 98 removed outlier: 3.652A pdb=" N SER J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU J 95 " --> pdb=" O ILE J 91 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 4.244A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET J 149 " --> pdb=" O SER J 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU J 151 " --> pdb=" O HIS J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 removed outlier: 3.562A pdb=" N PHE J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 removed outlier: 3.507A pdb=" N ARG K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL K 55 " --> pdb=" O ASN K 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN K 56 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.649A pdb=" N CYS K 89 " --> pdb=" O PHE K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.856A pdb=" N ALA K 152 " --> pdb=" O CYS K 148 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 153 " --> pdb=" O PHE K 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 182 removed outlier: 3.831A pdb=" N VAL K 178 " --> pdb=" O CYS K 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 170 removed outlier: 3.646A pdb=" N ARG L 156 " --> pdb=" O GLN L 152 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG L 163 " --> pdb=" O GLY L 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU L 166 " --> pdb=" O CYS L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 removed outlier: 3.855A pdb=" N LYS L 180 " --> pdb=" O ALA L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 242 removed outlier: 3.659A pdb=" N ALA L 234 " --> pdb=" O GLY L 230 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY L 241 " --> pdb=" O VAL L 237 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 264 removed outlier: 3.554A pdb=" N PHE L 260 " --> pdb=" O ARG L 256 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA L 262 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.509A pdb=" N TYR L 298 " --> pdb=" O LEU L 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 204 removed outlier: 3.599A pdb=" N GLN M 188 " --> pdb=" O ALA M 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.968A pdb=" N TYR M 223 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 279 Proline residue: M 273 - end of helix removed outlier: 3.505A pdb=" N LEU M 278 " --> pdb=" O LEU M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 312 removed outlier: 3.707A pdb=" N ASN M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA M 304 " --> pdb=" O MET M 300 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE M 305 " --> pdb=" O LEU M 301 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU M 310 " --> pdb=" O THR M 306 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG M 311 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 74 removed outlier: 3.502A pdb=" N PHE N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS N 61 " --> pdb=" O GLN N 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS N 74 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 98 removed outlier: 3.679A pdb=" N SER N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS N 95 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 152 removed outlier: 4.396A pdb=" N LEU N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA N 149 " --> pdb=" O LEU N 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU N 150 " --> pdb=" O LEU N 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU N 151 " --> pdb=" O ARG N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 177 removed outlier: 3.633A pdb=" N ILE N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL N 172 " --> pdb=" O ASP N 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 31 removed outlier: 3.627A pdb=" N ALA a 25 " --> pdb=" O GLN a 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS a 27 " --> pdb=" O GLU a 23 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA a 28 " --> pdb=" O TYR a 24 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 103 removed outlier: 3.523A pdb=" N ARG a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 123 removed outlier: 3.679A pdb=" N LYS a 118 " --> pdb=" O ARG a 114 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL a 121 " --> pdb=" O ASP a 117 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 186 Processing helix chain 'a' and resid 194 through 211 removed outlier: 3.584A pdb=" N MET a 200 " --> pdb=" O LYS a 196 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE a 201 " --> pdb=" O GLU a 197 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA a 209 " --> pdb=" O ALA a 205 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 248 removed outlier: 3.687A pdb=" N VAL a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU a 240 " --> pdb=" O ASN a 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA a 245 " --> pdb=" O GLU a 241 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 27 removed outlier: 3.528A pdb=" N THR b 25 " --> pdb=" O GLU b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 100 removed outlier: 3.505A pdb=" N ARG b 82 " --> pdb=" O GLY b 78 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR b 95 " --> pdb=" O ASN b 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS b 96 " --> pdb=" O CYS b 92 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET b 98 " --> pdb=" O GLN b 94 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 120 removed outlier: 3.620A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU b 118 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE b 119 " --> pdb=" O ILE b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 176 removed outlier: 3.769A pdb=" N PHE b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 181 through 190 Processing helix chain 'b' and resid 190 through 195 removed outlier: 3.801A pdb=" N GLU b 195 " --> pdb=" O LEU b 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 229 removed outlier: 3.899A pdb=" N TYR b 227 " --> pdb=" O GLN b 223 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP b 229 " --> pdb=" O ARG b 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 6 removed outlier: 3.703A pdb=" N TYR c 5 " --> pdb=" O SER c 2 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP c 6 " --> pdb=" O HIS c 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 2 through 6' Processing helix chain 'c' and resid 18 through 30 removed outlier: 3.718A pdb=" N GLN c 30 " --> pdb=" O GLU c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 108 removed outlier: 3.540A pdb=" N ALA c 89 " --> pdb=" O VAL c 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR c 90 " --> pdb=" O THR c 86 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN c 104 " --> pdb=" O ALA c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 130 removed outlier: 3.511A pdb=" N CYS c 121 " --> pdb=" O CYS c 117 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR c 128 " --> pdb=" O LYS c 124 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN c 129 " --> pdb=" O GLN c 125 " (cutoff:3.500A) Processing helix chain 'c' and resid 173 through 184 removed outlier: 3.930A pdb=" N ALA c 179 " --> pdb=" O GLN c 175 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) Processing helix chain 'c' and resid 190 through 206 removed outlier: 3.541A pdb=" N LYS c 204 " --> pdb=" O ARG c 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR c 205 " --> pdb=" O VAL c 201 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET c 206 " --> pdb=" O LEU c 202 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 268 Proline residue: c 256 - end of helix removed outlier: 4.059A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA c 261 " --> pdb=" O HIS c 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN c 263 " --> pdb=" O GLU c 259 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 removed outlier: 3.501A pdb=" N GLU d 24 " --> pdb=" O GLU d 20 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA d 25 " --> pdb=" O TYR d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 95 removed outlier: 3.633A pdb=" N ARG d 81 " --> pdb=" O SER d 77 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN d 92 " --> pdb=" O GLN d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 118 Processing helix chain 'd' and resid 164 through 172 removed outlier: 3.786A pdb=" N VAL d 168 " --> pdb=" O HIS d 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE d 169 " --> pdb=" O ASP d 165 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 194 removed outlier: 3.535A pdb=" N VAL d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 218 through 241 removed outlier: 3.678A pdb=" N LYS d 224 " --> pdb=" O GLU d 220 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE d 225 " --> pdb=" O GLU d 221 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL d 227 " --> pdb=" O GLN d 223 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU d 235 " --> pdb=" O LYS d 231 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 133 removed outlier: 3.675A pdb=" N GLU e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA e 130 " --> pdb=" O TYR e 126 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE e 131 " --> pdb=" O ALA e 127 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS e 132 " --> pdb=" O VAL e 128 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU e 133 " --> pdb=" O GLU e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 164 removed outlier: 3.587A pdb=" N SER e 163 " --> pdb=" O VAL e 160 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET e 164 " --> pdb=" O PRO e 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 160 through 164' Processing helix chain 'e' and resid 181 through 204 removed outlier: 3.654A pdb=" N ALA e 185 " --> pdb=" O MET e 181 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU e 188 " --> pdb=" O ASP e 184 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL e 194 " --> pdb=" O GLU e 190 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG e 200 " --> pdb=" O SER e 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 208 through 218 Processing helix chain 'e' and resid 271 through 273 No H-bonds generated for 'chain 'e' and resid 271 through 273' Processing helix chain 'e' and resid 274 through 283 removed outlier: 3.916A pdb=" N SER e 279 " --> pdb=" O GLU e 275 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL e 280 " --> pdb=" O ALA e 276 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU e 283 " --> pdb=" O SER e 279 " (cutoff:3.500A) Processing helix chain 'e' and resid 290 through 305 removed outlier: 3.545A pdb=" N ALA e 298 " --> pdb=" O GLY e 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP e 300 " --> pdb=" O THR e 296 " (cutoff:3.500A) Processing helix chain 'e' and resid 331 through 340 removed outlier: 4.030A pdb=" N ALA e 337 " --> pdb=" O THR e 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE e 338 " --> pdb=" O GLU e 334 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET e 339 " --> pdb=" O ILE e 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 194 removed outlier: 3.928A pdb=" N GLU f 191 " --> pdb=" O GLU f 187 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA f 192 " --> pdb=" O TYR f 188 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL f 193 " --> pdb=" O ALA f 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN f 194 " --> pdb=" O ASN f 190 " (cutoff:3.500A) Processing helix chain 'f' and resid 242 through 265 removed outlier: 3.807A pdb=" N VAL f 248 " --> pdb=" O ALA f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 269 through 283 removed outlier: 3.598A pdb=" N ASP f 275 " --> pdb=" O ASN f 271 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY f 278 " --> pdb=" O ALA f 274 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU f 279 " --> pdb=" O ASP f 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG f 283 " --> pdb=" O GLU f 279 " (cutoff:3.500A) Processing helix chain 'f' and resid 330 through 338 Processing helix chain 'f' and resid 339 through 344 removed outlier: 5.409A pdb=" N GLU f 342 " --> pdb=" O ARG f 339 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE f 344 " --> pdb=" O PHE f 341 " (cutoff:3.500A) Processing helix chain 'f' and resid 348 through 361 removed outlier: 3.628A pdb=" N THR f 354 " --> pdb=" O ASP f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 362 through 364 No H-bonds generated for 'chain 'f' and resid 362 through 364' Processing helix chain 'f' and resid 394 through 399 Processing helix chain 'g' and resid 21 through 33 removed outlier: 3.622A pdb=" N LYS g 29 " --> pdb=" O GLU g 25 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA g 30 " --> pdb=" O TYR g 26 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL g 31 " --> pdb=" O ALA g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 102 removed outlier: 3.858A pdb=" N ALA g 87 " --> pdb=" O PRO g 83 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE g 88 " --> pdb=" O ASP g 84 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN g 94 " --> pdb=" O SER g 90 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER g 99 " --> pdb=" O GLU g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 122 removed outlier: 3.555A pdb=" N GLU g 118 " --> pdb=" O ASN g 114 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 177 removed outlier: 3.715A pdb=" N SER g 174 " --> pdb=" O THR g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 201 removed outlier: 4.084A pdb=" N VAL g 190 " --> pdb=" O CYS g 186 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU g 199 " --> pdb=" O SER g 195 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 125 removed outlier: 3.561A pdb=" N LEU h 109 " --> pdb=" O ASP h 105 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN h 115 " --> pdb=" O GLU h 111 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 143 removed outlier: 3.625A pdb=" N LEU h 136 " --> pdb=" O THR h 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE h 137 " --> pdb=" O ALA h 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN h 138 " --> pdb=" O ALA h 134 " (cutoff:3.500A) Processing helix chain 'h' and resid 185 through 188 removed outlier: 3.639A pdb=" N PHE h 188 " --> pdb=" O GLY h 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 185 through 188' Processing helix chain 'h' and resid 189 through 197 removed outlier: 3.660A pdb=" N ALA h 195 " --> pdb=" O SER h 191 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR h 197 " --> pdb=" O PHE h 193 " (cutoff:3.500A) Processing helix chain 'h' and resid 202 through 221 removed outlier: 3.551A pdb=" N ALA h 208 " --> pdb=" O SER h 204 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 100 removed outlier: 3.810A pdb=" N MET i 87 " --> pdb=" O ALA i 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 118 removed outlier: 3.535A pdb=" N ALA i 108 " --> pdb=" O ARG i 104 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS i 115 " --> pdb=" O LEU i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 171 removed outlier: 3.537A pdb=" N ALA i 165 " --> pdb=" O ILE i 161 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA i 169 " --> pdb=" O ALA i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 176 through 193 removed outlier: 3.577A pdb=" N ARG i 189 " --> pdb=" O ALA i 185 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS i 190 " --> pdb=" O SER i 186 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY i 191 " --> pdb=" O ALA i 187 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 78 removed outlier: 3.804A pdb=" N ALA j 64 " --> pdb=" O GLN j 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET j 73 " --> pdb=" O PHE j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 98 removed outlier: 3.652A pdb=" N SER j 93 " --> pdb=" O ALA j 89 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU j 95 " --> pdb=" O ILE j 91 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA j 98 " --> pdb=" O MET j 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 142 through 152 removed outlier: 4.245A pdb=" N GLY j 148 " --> pdb=" O GLU j 144 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET j 149 " --> pdb=" O SER j 145 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU j 151 " --> pdb=" O HIS j 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 176 removed outlier: 3.563A pdb=" N PHE j 164 " --> pdb=" O PRO j 160 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU j 165 " --> pdb=" O GLU j 161 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE j 166 " --> pdb=" O GLU j 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 71 removed outlier: 3.508A pdb=" N ARG k 54 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL k 55 " --> pdb=" O ASN k 51 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN k 56 " --> pdb=" O GLY k 52 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR k 60 " --> pdb=" O ASN k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 92 removed outlier: 3.650A pdb=" N CYS k 89 " --> pdb=" O PHE k 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 158 removed outlier: 3.856A pdb=" N ALA k 152 " --> pdb=" O CYS k 148 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU k 153 " --> pdb=" O PHE k 149 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG k 156 " --> pdb=" O ALA k 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 182 removed outlier: 3.831A pdb=" N VAL k 178 " --> pdb=" O CYS k 174 " (cutoff:3.500A) Processing helix chain 'l' and resid 147 through 170 removed outlier: 3.538A pdb=" N TRP l 154 " --> pdb=" O ASP l 150 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG l 156 " --> pdb=" O GLN l 152 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG l 163 " --> pdb=" O GLY l 159 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU l 166 " --> pdb=" O CYS l 162 " (cutoff:3.500A) Processing helix chain 'l' and resid 174 through 189 removed outlier: 3.841A pdb=" N LYS l 180 " --> pdb=" O ALA l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 230 through 242 removed outlier: 3.673A pdb=" N ALA l 234 " --> pdb=" O GLY l 230 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU l 238 " --> pdb=" O ALA l 234 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR l 240 " --> pdb=" O GLY l 236 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY l 241 " --> pdb=" O VAL l 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 247 through 264 removed outlier: 3.507A pdb=" N PHE l 260 " --> pdb=" O ARG l 256 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA l 262 " --> pdb=" O SER l 258 " (cutoff:3.500A) Processing helix chain 'l' and resid 294 through 299 removed outlier: 3.521A pdb=" N TYR l 298 " --> pdb=" O LEU l 294 " (cutoff:3.500A) Processing helix chain 'm' and resid 182 through 204 removed outlier: 3.598A pdb=" N GLN m 188 " --> pdb=" O ALA m 184 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL m 197 " --> pdb=" O LEU m 193 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS m 198 " --> pdb=" O LYS m 194 " (cutoff:3.500A) Processing helix chain 'm' and resid 210 through 225 removed outlier: 3.968A pdb=" N TYR m 223 " --> pdb=" O SER m 219 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG m 225 " --> pdb=" O MET m 221 " (cutoff:3.500A) Processing helix chain 'm' and resid 267 through 279 Proline residue: m 273 - end of helix removed outlier: 3.504A pdb=" N LEU m 278 " --> pdb=" O LEU m 274 " (cutoff:3.500A) Processing helix chain 'm' and resid 293 through 312 removed outlier: 3.708A pdb=" N ASN m 303 " --> pdb=" O ALA m 299 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA m 304 " --> pdb=" O MET m 300 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE m 305 " --> pdb=" O LEU m 301 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU m 310 " --> pdb=" O THR m 306 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG m 311 " --> pdb=" O GLY m 307 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 74 removed outlier: 3.502A pdb=" N PHE n 56 " --> pdb=" O SER n 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS n 61 " --> pdb=" O GLN n 57 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE n 67 " --> pdb=" O VAL n 63 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 98 removed outlier: 3.680A pdb=" N SER n 86 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS n 95 " --> pdb=" O SER n 91 " (cutoff:3.500A) Processing helix chain 'n' and resid 141 through 152 removed outlier: 4.397A pdb=" N LEU n 145 " --> pdb=" O ILE n 141 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA n 149 " --> pdb=" O LEU n 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU n 150 " --> pdb=" O LEU n 146 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU n 151 " --> pdb=" O ARG n 147 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 177 removed outlier: 3.632A pdb=" N ILE n 165 " --> pdb=" O GLU n 161 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU n 166 " --> pdb=" O ALA n 162 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL n 172 " --> pdb=" O ASP n 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.524A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.677A pdb=" N ILE A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 3.522A pdb=" N VAL B 42 " --> pdb=" O VAL B 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 65 removed outlier: 3.650A pdb=" N GLY B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 146 " --> pdb=" O TRP B 154 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.705A pdb=" N SER B 131 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.796A pdb=" N ARG C 222 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 144 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.608A pdb=" N VAL D 42 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.802A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142 Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 169 removed outlier: 4.285A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.549A pdb=" N ILE F 377 " --> pdb=" O PHE F 389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 228 through 230 Processing sheet with id=AB6, first strand: chain 'F' and resid 240 through 241 Processing sheet with id=AB7, first strand: chain 'G' and resid 162 through 165 removed outlier: 3.675A pdb=" N VAL G 163 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.550A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.510A pdb=" N GLU H 239 " --> pdb=" O THR H 232 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.579A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 88 through 90 removed outlier: 3.503A pdb=" N ILE H 153 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 153 through 156 removed outlier: 3.996A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL I 202 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY I 217 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'I' and resid 63 through 65 Processing sheet with id=AC6, first strand: chain 'I' and resid 240 through 247 removed outlier: 3.770A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER J 10 " --> pdb=" O ASP J 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.739A pdb=" N LEU J 28 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS J 33 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 42 through 44 Processing sheet with id=AC9, first strand: chain 'K' and resid 140 through 143 Processing sheet with id=AD1, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.717A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 36 through 38 removed outlier: 4.507A pdb=" N CYS K 105 " --> pdb=" O MET K 129 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.658A pdb=" N VAL L 273 " --> pdb=" O ARG L 288 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG L 288 " --> pdb=" O VAL L 273 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL L 275 " --> pdb=" O ILE L 286 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 119 through 120 removed outlier: 6.947A pdb=" N ALA L 119 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 133 through 137 removed outlier: 3.587A pdb=" N ILE L 136 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU L 140 " --> pdb=" O ILE L 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL L 200 " --> pdb=" O TYR L 211 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY L 202 " --> pdb=" O SER L 209 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 209 " --> pdb=" O GLY L 202 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU L 210 " --> pdb=" O GLN L 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN L 222 " --> pdb=" O LEU L 210 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.295A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY M 149 " --> pdb=" O SER M 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 168 through 170 removed outlier: 3.603A pdb=" N VAL M 236 " --> pdb=" O TYR M 248 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY M 238 " --> pdb=" O VAL M 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 180 through 181 Processing sheet with id=AD9, first strand: chain 'N' and resid 132 through 135 Processing sheet with id=AE1, first strand: chain 'N' and resid 24 through 26 removed outlier: 7.073A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS N 31 " --> pdb=" O LEU N 24 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.510A pdb=" N SER N 45 " --> pdb=" O LEU N 41 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.524A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 66 through 70 removed outlier: 6.678A pdb=" N ILE a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.522A pdb=" N VAL b 42 " --> pdb=" O VAL b 211 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 63 through 65 removed outlier: 3.650A pdb=" N GLY b 141 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN b 146 " --> pdb=" O TRP b 154 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b' and resid 75 through 76 removed outlier: 3.705A pdb=" N SER b 131 " --> pdb=" O SER b 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 167 through 170 removed outlier: 3.797A pdb=" N ARG c 222 " --> pdb=" O ARG c 245 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'c' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE c 78 " --> pdb=" O ILE c 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 71 through 75 removed outlier: 6.530A pdb=" N ILE c 78 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY c 144 " --> pdb=" O GLN c 152 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 158 through 161 removed outlier: 3.609A pdb=" N VAL d 42 " --> pdb=" O VAL d 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 63 through 64 removed outlier: 3.801A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 140 through 142 Processing sheet with id=AF5, first strand: chain 'e' and resid 167 through 169 removed outlier: 4.286A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 323 through 326 removed outlier: 3.548A pdb=" N ILE f 377 " --> pdb=" O PHE f 389 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 228 through 230 Processing sheet with id=AF8, first strand: chain 'f' and resid 240 through 241 Processing sheet with id=AF9, first strand: chain 'g' and resid 162 through 165 removed outlier: 3.676A pdb=" N VAL g 163 " --> pdb=" O ALA g 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.550A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 179 through 182 removed outlier: 3.509A pdb=" N GLU h 239 " --> pdb=" O THR h 232 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 74 through 76 removed outlier: 6.579A pdb=" N SER h 76 " --> pdb=" O VAL h 80 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL h 80 " --> pdb=" O SER h 76 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 88 through 90 removed outlier: 3.503A pdb=" N ILE h 153 " --> pdb=" O CYS h 98 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 153 through 156 removed outlier: 3.995A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL i 202 " --> pdb=" O GLY i 217 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY i 217 " --> pdb=" O VAL i 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'i' and resid 49 through 50 Processing sheet with id=AG7, first strand: chain 'i' and resid 63 through 65 Processing sheet with id=AG8, first strand: chain 'i' and resid 240 through 247 removed outlier: 3.612A pdb=" N LYS i 242 " --> pdb=" O LEU j 199 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS j 194 " --> pdb=" O THR j 191 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER j 10 " --> pdb=" O ASP j 25 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.738A pdb=" N LEU j 28 " --> pdb=" O ILE j 35 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS j 33 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 42 through 44 Processing sheet with id=AH2, first strand: chain 'k' and resid 140 through 143 Processing sheet with id=AH3, first strand: chain 'k' and resid 22 through 24 removed outlier: 6.717A pdb=" N ASN k 22 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'k' and resid 36 through 38 removed outlier: 4.506A pdb=" N CYS k 105 " --> pdb=" O MET k 129 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.650A pdb=" N VAL l 273 " --> pdb=" O ARG l 288 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG l 288 " --> pdb=" O VAL l 273 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL l 275 " --> pdb=" O ILE l 286 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'l' and resid 119 through 121 removed outlier: 6.967A pdb=" N ALA l 119 " --> pdb=" O ALA l 126 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR l 124 " --> pdb=" O THR l 121 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'l' and resid 133 through 137 removed outlier: 3.609A pdb=" N ILE l 136 " --> pdb=" O LEU l 140 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU l 140 " --> pdb=" O ILE l 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL l 200 " --> pdb=" O TYR l 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY l 202 " --> pdb=" O SER l 209 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY l 207 " --> pdb=" O ASP l 204 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU l 210 " --> pdb=" O GLN l 222 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN l 222 " --> pdb=" O LEU l 210 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'm' and resid 261 through 265 removed outlier: 5.295A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY m 149 " --> pdb=" O SER m 320 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'm' and resid 168 through 170 removed outlier: 3.604A pdb=" N VAL m 236 " --> pdb=" O TYR m 248 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY m 238 " --> pdb=" O VAL m 246 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'm' and resid 180 through 181 Processing sheet with id=AI2, first strand: chain 'n' and resid 132 through 135 Processing sheet with id=AI3, first strand: chain 'n' and resid 24 through 26 removed outlier: 7.072A pdb=" N LEU n 24 " --> pdb=" O LYS n 31 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS n 31 " --> pdb=" O LEU n 24 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'n' and resid 39 through 41 removed outlier: 3.509A pdb=" N SER n 45 " --> pdb=" O LEU n 41 " (cutoff:3.500A) 2228 hydrogen bonds defined for protein. 6357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.54 Time building geometry restraints manager: 10.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15542 1.34 - 1.46: 8574 1.46 - 1.58: 25720 1.58 - 1.70: 6 1.70 - 1.82: 512 Bond restraints: 50354 Sorted by residual: bond pdb=" B26 BO2 i 301 " pdb=" O27 BO2 i 301 " ideal model delta sigma weight residual 1.362 1.545 -0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" B26 BO2 I 301 " pdb=" O27 BO2 I 301 " ideal model delta sigma weight residual 1.362 1.545 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" B26 BO2 H 301 " pdb=" O28 BO2 H 301 " ideal model delta sigma weight residual 1.356 1.535 -0.179 2.00e-02 2.50e+03 8.04e+01 bond pdb=" B26 BO2 h 301 " pdb=" O28 BO2 h 301 " ideal model delta sigma weight residual 1.356 1.535 -0.179 2.00e-02 2.50e+03 8.00e+01 bond pdb=" B26 BO2 I 301 " pdb=" O28 BO2 I 301 " ideal model delta sigma weight residual 1.356 1.533 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 50349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 67671 3.75 - 7.50: 358 7.50 - 11.25: 62 11.25 - 15.00: 12 15.00 - 18.75: 13 Bond angle restraints: 68116 Sorted by residual: angle pdb=" C21 BO2 I 301 " pdb=" B26 BO2 I 301 " pdb=" O27 BO2 I 301 " ideal model delta sigma weight residual 121.29 102.54 18.75 3.00e+00 1.11e-01 3.91e+01 angle pdb=" C21 BO2 i 301 " pdb=" B26 BO2 i 301 " pdb=" O27 BO2 i 301 " ideal model delta sigma weight residual 121.29 102.57 18.72 3.00e+00 1.11e-01 3.89e+01 angle pdb=" C GLY i 199 " pdb=" N THR i 200 " pdb=" CA THR i 200 " ideal model delta sigma weight residual 121.54 133.40 -11.86 1.91e+00 2.74e-01 3.85e+01 angle pdb=" C GLY I 199 " pdb=" N THR I 200 " pdb=" CA THR I 200 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 angle pdb=" O27 BO2 i 301 " pdb=" B26 BO2 i 301 " pdb=" O28 BO2 i 301 " ideal model delta sigma weight residual 119.22 101.86 17.36 3.00e+00 1.11e-01 3.35e+01 ... (remaining 68111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 29099 17.70 - 35.40: 890 35.40 - 53.10: 183 53.10 - 70.80: 29 70.80 - 88.50: 33 Dihedral angle restraints: 30234 sinusoidal: 11888 harmonic: 18346 Sorted by residual: dihedral pdb=" CA LYS D 47 " pdb=" C LYS D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta harmonic sigma weight residual 180.00 -149.00 -31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS d 47 " pdb=" C LYS d 47 " pdb=" N LYS d 48 " pdb=" CA LYS d 48 " ideal model delta harmonic sigma weight residual -180.00 -149.01 -30.99 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA GLY J 101 " pdb=" C GLY J 101 " pdb=" N PRO J 102 " pdb=" CA PRO J 102 " ideal model delta harmonic sigma weight residual -180.00 -149.48 -30.52 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 30231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5549 0.052 - 0.104: 1533 0.104 - 0.156: 423 0.156 - 0.208: 34 0.208 - 0.260: 21 Chirality restraints: 7560 Sorted by residual: chirality pdb=" CB VAL k 138 " pdb=" CA VAL k 138 " pdb=" CG1 VAL k 138 " pdb=" CG2 VAL k 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB ILE J 23 " pdb=" CA ILE J 23 " pdb=" CG1 ILE J 23 " pdb=" CG2 ILE J 23 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL K 138 " pdb=" CA VAL K 138 " pdb=" CG1 VAL K 138 " pdb=" CG2 VAL K 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 7557 not shown) Planarity restraints: 8826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 BO2 L 401 " -0.165 2.00e-02 2.50e+03 2.31e-01 6.65e+02 pdb=" C18 BO2 L 401 " 0.072 2.00e-02 2.50e+03 pdb=" C21 BO2 L 401 " -0.269 2.00e-02 2.50e+03 pdb=" N20 BO2 L 401 " 0.400 2.00e-02 2.50e+03 pdb=" O19 BO2 L 401 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 i 301 " 0.179 2.00e-02 2.50e+03 2.10e-01 5.51e+02 pdb=" C18 BO2 i 301 " -0.075 2.00e-02 2.50e+03 pdb=" C21 BO2 i 301 " 0.255 2.00e-02 2.50e+03 pdb=" N20 BO2 i 301 " -0.342 2.00e-02 2.50e+03 pdb=" O19 BO2 i 301 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 BO2 I 301 " -0.179 2.00e-02 2.50e+03 2.10e-01 5.50e+02 pdb=" C18 BO2 I 301 " 0.075 2.00e-02 2.50e+03 pdb=" C21 BO2 I 301 " -0.255 2.00e-02 2.50e+03 pdb=" N20 BO2 I 301 " 0.342 2.00e-02 2.50e+03 pdb=" O19 BO2 I 301 " 0.016 2.00e-02 2.50e+03 ... (remaining 8823 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 858 2.67 - 3.23: 42641 3.23 - 3.78: 74950 3.78 - 4.34: 107646 4.34 - 4.90: 178397 Nonbonded interactions: 404492 Sorted by model distance: nonbonded pdb=" ND2 ASN f 266 " pdb=" OE2 GLU n 83 " model vdw 2.109 3.120 nonbonded pdb=" OE2 GLU d 46 " pdb=" NH2 ARG d 163 " model vdw 2.135 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NH2 ARG D 163 " model vdw 2.136 3.120 nonbonded pdb=" ND2 ASN F 266 " pdb=" OE2 GLU N 83 " model vdw 2.176 3.120 nonbonded pdb=" OE2 GLU D 90 " pdb=" NH2 ARG D 93 " model vdw 2.185 3.120 ... (remaining 404487 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'n' } 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=1.00 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.420 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 86.620 Find NCS groups from input model: 3.420 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.183 50354 Z= 0.368 Angle : 0.952 18.752 68116 Z= 0.534 Chirality : 0.053 0.260 7560 Planarity : 0.008 0.231 8826 Dihedral : 10.272 88.495 18518 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % 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: -4.67 (0.08), residues: 6304 helix: -4.40 (0.05), residues: 2218 sheet: -1.76 (0.13), residues: 1492 loop : -2.46 (0.10), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 185 HIS 0.014 0.002 HIS f 234 PHE 0.022 0.002 PHE J 20 TYR 0.035 0.003 TYR h 96 ARG 0.008 0.001 ARG d 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1840 time to evaluate : 4.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7590 (tptt) REVERT: A 215 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7430 (mmtm) REVERT: C 29 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7215 (mm-40) REVERT: C 50 MET cc_start: 0.6406 (pmt) cc_final: 0.6004 (ttm) REVERT: C 57 ASP cc_start: 0.7907 (t0) cc_final: 0.7501 (t0) REVERT: C 206 MET cc_start: 0.6860 (ptt) cc_final: 0.6569 (ptt) REVERT: C 262 ASP cc_start: 0.7884 (p0) cc_final: 0.7170 (p0) REVERT: D 4 ASP cc_start: 0.7357 (p0) cc_final: 0.6594 (p0) REVERT: D 102 MET cc_start: 0.6175 (ttt) cc_final: 0.5819 (ptm) REVERT: D 183 ASP cc_start: 0.7374 (m-30) cc_final: 0.6794 (m-30) REVERT: D 223 GLN cc_start: 0.6878 (mm110) cc_final: 0.6610 (tp40) REVERT: E 140 ILE cc_start: 0.8833 (mm) cc_final: 0.8600 (mm) REVERT: E 293 GLU cc_start: 0.7735 (tt0) cc_final: 0.7197 (tp30) REVERT: E 301 ILE cc_start: 0.7824 (mt) cc_final: 0.7561 (mt) REVERT: E 314 ASN cc_start: 0.6833 (t0) cc_final: 0.6490 (t0) REVERT: F 214 LYS cc_start: 0.7390 (pttt) cc_final: 0.7115 (pttt) REVERT: F 227 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7303 (mtpt) REVERT: F 396 LYS cc_start: 0.7725 (ptmt) cc_final: 0.7283 (mttp) REVERT: G 18 GLU cc_start: 0.7784 (pm20) cc_final: 0.7516 (pm20) REVERT: G 32 ASP cc_start: 0.8477 (m-30) cc_final: 0.8077 (m-30) REVERT: G 101 ASP cc_start: 0.7409 (m-30) cc_final: 0.7157 (m-30) REVERT: G 105 THR cc_start: 0.8680 (t) cc_final: 0.8411 (p) REVERT: G 118 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7830 (mt-10) REVERT: G 201 HIS cc_start: 0.5810 (t-90) cc_final: 0.5384 (t70) REVERT: H 149 SER cc_start: 0.8227 (t) cc_final: 0.7941 (p) REVERT: H 234 ASP cc_start: 0.8476 (p0) cc_final: 0.8112 (p0) REVERT: I 120 GLN cc_start: 0.7734 (mt0) cc_final: 0.6965 (mm-40) REVERT: I 197 TYR cc_start: 0.8689 (m-80) cc_final: 0.8486 (m-10) REVERT: I 212 THR cc_start: 0.9013 (t) cc_final: 0.8504 (m) REVERT: I 214 LEU cc_start: 0.8362 (tp) cc_final: 0.8147 (tt) REVERT: J 111 SER cc_start: 0.8951 (p) cc_final: 0.8659 (t) REVERT: J 189 ILE cc_start: 0.7855 (pt) cc_final: 0.7618 (mp) REVERT: K 41 THR cc_start: 0.8970 (p) cc_final: 0.8760 (p) REVERT: M 174 TYR cc_start: 0.7873 (m-10) cc_final: 0.7548 (m-80) REVERT: M 207 LYS cc_start: 0.8269 (ttpm) cc_final: 0.7900 (tptm) REVERT: M 293 THR cc_start: 0.7873 (p) cc_final: 0.7619 (m) REVERT: a 42 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7484 (tptt) REVERT: a 55 ASP cc_start: 0.7006 (t0) cc_final: 0.6773 (t0) REVERT: a 215 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7287 (mmtm) REVERT: c 29 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7300 (mm-40) REVERT: c 50 MET cc_start: 0.6398 (pmt) cc_final: 0.5862 (mtt) REVERT: c 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7660 (t0) REVERT: c 172 GLN cc_start: 0.7301 (mt0) cc_final: 0.7043 (mm-40) REVERT: c 262 ASP cc_start: 0.7982 (p0) cc_final: 0.7187 (p0) REVERT: d 4 ASP cc_start: 0.7372 (p0) cc_final: 0.6552 (p0) REVERT: d 33 VAL cc_start: 0.8908 (t) cc_final: 0.8600 (p) REVERT: d 47 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7244 (ttmt) REVERT: d 92 GLN cc_start: 0.5910 (mm110) cc_final: 0.5637 (tm-30) REVERT: d 102 MET cc_start: 0.6023 (ttt) cc_final: 0.5756 (ptm) REVERT: d 139 ASP cc_start: 0.8092 (p0) cc_final: 0.7701 (p0) REVERT: d 181 SER cc_start: 0.7883 (p) cc_final: 0.7348 (t) REVERT: d 183 ASP cc_start: 0.7632 (m-30) cc_final: 0.7205 (m-30) REVERT: e 109 ASP cc_start: 0.6072 (p0) cc_final: 0.5841 (m-30) REVERT: e 162 SER cc_start: 0.7508 (p) cc_final: 0.7121 (t) REVERT: f 214 LYS cc_start: 0.7383 (pttt) cc_final: 0.7168 (pttt) REVERT: f 260 TYR cc_start: 0.8754 (t80) cc_final: 0.8533 (t80) REVERT: f 290 LYS cc_start: 0.6927 (mtpp) cc_final: 0.6704 (mmtm) REVERT: f 396 LYS cc_start: 0.7842 (ptmt) cc_final: 0.7283 (mttp) REVERT: g 32 ASP cc_start: 0.8666 (m-30) cc_final: 0.8393 (m-30) REVERT: g 64 ASN cc_start: 0.8450 (m-40) cc_final: 0.8172 (m110) REVERT: g 101 ASP cc_start: 0.7451 (m-30) cc_final: 0.7183 (m-30) REVERT: g 105 THR cc_start: 0.8658 (t) cc_final: 0.8437 (p) REVERT: g 173 LYS cc_start: 0.7806 (tmtp) cc_final: 0.7486 (tppt) REVERT: g 215 TRP cc_start: 0.8026 (p90) cc_final: 0.7783 (p90) REVERT: h 271 SER cc_start: 0.8499 (t) cc_final: 0.8215 (p) REVERT: i 212 THR cc_start: 0.8982 (t) cc_final: 0.8441 (m) REVERT: i 214 LEU cc_start: 0.8558 (tp) cc_final: 0.8338 (tt) REVERT: j 59 ASP cc_start: 0.8541 (m-30) cc_final: 0.8287 (m-30) REVERT: j 81 ASP cc_start: 0.7204 (m-30) cc_final: 0.6970 (m-30) REVERT: k 40 ASP cc_start: 0.7507 (t0) cc_final: 0.7232 (t0) REVERT: l 229 SER cc_start: 0.8372 (t) cc_final: 0.8135 (p) REVERT: m 174 TYR cc_start: 0.7741 (m-10) cc_final: 0.7505 (m-80) REVERT: m 270 PHE cc_start: 0.8302 (m-80) cc_final: 0.8074 (m-10) REVERT: m 294 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8193 (mtpt) REVERT: n 115 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6402 (mm-30) outliers start: 8 outliers final: 2 residues processed: 1846 average time/residue: 0.6308 time to fit residues: 1829.1395 Evaluate side-chains 1081 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1079 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain j residue 190 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 8.9990 chunk 471 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 318 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 564 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 125 GLN A 228 ASN B 207 GLN B 223 GLN C 65 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 GLN E 268 GLN ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 ASN F 281 HIS G 201 HIS H 264 GLN H 266 GLN J 147 HIS K 22 ASN K 43 GLN K 125 GLN L 128 GLN L 152 GLN L 184 ASN L 222 GLN L 277 HIS L 279 HIS M 303 ASN N 185 GLN a 21 GLN a 125 GLN a 228 ASN c 53 HIS c 65 ASN d 92 GLN d 120 GLN ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 187 HIS ** e 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 168 ASN f 225 GLN f 281 HIS h 107 GLN h 264 GLN h 266 GLN ** i 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 147 HIS k 42 HIS k 43 GLN k 125 GLN l 108 ASN l 128 GLN l 152 GLN l 184 ASN l 277 HIS l 279 HIS m 190 GLN ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 185 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 50354 Z= 0.323 Angle : 0.680 12.892 68116 Z= 0.358 Chirality : 0.047 0.338 7560 Planarity : 0.006 0.064 8826 Dihedral : 7.242 88.516 7116 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.30 % Allowed : 9.71 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.09), residues: 6304 helix: -2.04 (0.09), residues: 2272 sheet: -1.33 (0.13), residues: 1506 loop : -2.00 (0.11), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 185 HIS 0.007 0.001 HIS F 355 PHE 0.017 0.002 PHE l 105 TYR 0.050 0.002 TYR H 218 ARG 0.007 0.001 ARG g 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1135 time to evaluate : 4.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 SER cc_start: 0.8658 (m) cc_final: 0.8444 (p) REVERT: A 42 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7647 (tptt) REVERT: B 184 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: B 187 HIS cc_start: 0.7750 (m-70) cc_final: 0.7347 (m170) REVERT: B 200 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5184 (mm-40) REVERT: B 205 ASN cc_start: 0.8157 (t0) cc_final: 0.7787 (t0) REVERT: B 225 ARG cc_start: 0.6651 (ttm110) cc_final: 0.6425 (ttp-110) REVERT: B 231 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4918 (pp) REVERT: C 29 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7503 (tp40) REVERT: C 57 ASP cc_start: 0.7827 (t0) cc_final: 0.7535 (t0) REVERT: C 196 LEU cc_start: 0.7727 (mt) cc_final: 0.7450 (mt) REVERT: C 262 ASP cc_start: 0.7550 (p0) cc_final: 0.7079 (p0) REVERT: D 4 ASP cc_start: 0.7476 (p0) cc_final: 0.6636 (p0) REVERT: D 79 ASP cc_start: 0.8532 (m-30) cc_final: 0.8243 (m-30) REVERT: D 102 MET cc_start: 0.6212 (ttt) cc_final: 0.5839 (ptm) REVERT: E 109 ASP cc_start: 0.5941 (p0) cc_final: 0.5688 (m-30) REVERT: E 293 GLU cc_start: 0.7637 (tt0) cc_final: 0.6985 (tp30) REVERT: E 295 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 314 ASN cc_start: 0.6627 (t0) cc_final: 0.6334 (t0) REVERT: F 186 ILE cc_start: 0.8784 (mm) cc_final: 0.8435 (mm) REVERT: F 290 LYS cc_start: 0.8061 (mmtm) cc_final: 0.6800 (mtmt) REVERT: G 32 ASP cc_start: 0.8548 (m-30) cc_final: 0.8275 (m-30) REVERT: G 64 ASN cc_start: 0.8710 (m-40) cc_final: 0.8389 (m110) REVERT: G 101 ASP cc_start: 0.7473 (m-30) cc_final: 0.7026 (m-30) REVERT: G 105 THR cc_start: 0.8713 (t) cc_final: 0.8405 (p) REVERT: G 198 HIS cc_start: 0.7986 (m-70) cc_final: 0.7680 (m170) REVERT: H 234 ASP cc_start: 0.8242 (p0) cc_final: 0.7972 (p0) REVERT: I 168 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7798 (mm-30) REVERT: I 181 LYS cc_start: 0.8595 (ttmt) cc_final: 0.8293 (mtmm) REVERT: I 212 THR cc_start: 0.8979 (t) cc_final: 0.8612 (m) REVERT: I 214 LEU cc_start: 0.8659 (tp) cc_final: 0.8424 (tt) REVERT: I 242 LYS cc_start: 0.6658 (tttm) cc_final: 0.6195 (tppt) REVERT: J 4 MET cc_start: 0.8198 (mmm) cc_final: 0.7929 (mmm) REVERT: J 189 ILE cc_start: 0.7942 (pt) cc_final: 0.7640 (mp) REVERT: K 129 MET cc_start: 0.7739 (mtp) cc_final: 0.7528 (ttm) REVERT: L 128 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8395 (tp-100) REVERT: L 169 ASN cc_start: 0.8373 (m-40) cc_final: 0.8160 (m-40) REVERT: M 174 TYR cc_start: 0.7842 (m-10) cc_final: 0.7591 (m-80) REVERT: M 195 TYR cc_start: 0.8019 (m-80) cc_final: 0.7566 (m-80) REVERT: M 207 LYS cc_start: 0.8320 (ttpm) cc_final: 0.7793 (tptm) REVERT: M 225 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7984 (ttp-170) REVERT: a 42 LYS cc_start: 0.7980 (ttpp) cc_final: 0.7579 (tptt) REVERT: a 55 ASP cc_start: 0.7117 (t0) cc_final: 0.6837 (t0) REVERT: b 21 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7182 (mm-30) REVERT: b 187 HIS cc_start: 0.7760 (m170) cc_final: 0.7535 (m170) REVERT: b 200 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5225 (mm-40) REVERT: b 217 GLU cc_start: 0.7710 (pp20) cc_final: 0.7475 (pp20) REVERT: b 231 ILE cc_start: 0.4885 (OUTLIER) cc_final: 0.4667 (pp) REVERT: c 29 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7481 (tp40) REVERT: c 57 ASP cc_start: 0.7896 (t0) cc_final: 0.7646 (t0) REVERT: c 76 GLU cc_start: 0.7611 (pm20) cc_final: 0.7408 (pm20) REVERT: c 196 LEU cc_start: 0.7698 (mt) cc_final: 0.7436 (mt) REVERT: c 262 ASP cc_start: 0.7597 (p0) cc_final: 0.7148 (p0) REVERT: d 4 ASP cc_start: 0.7385 (p0) cc_final: 0.6598 (p0) REVERT: d 47 LYS cc_start: 0.7679 (ttpp) cc_final: 0.7359 (ttmt) REVERT: d 92 GLN cc_start: 0.6084 (mm-40) cc_final: 0.5576 (tm-30) REVERT: d 102 MET cc_start: 0.6282 (ttt) cc_final: 0.5918 (ptm) REVERT: d 167 THR cc_start: 0.8954 (m) cc_final: 0.8750 (p) REVERT: e 166 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6791 (mttm) REVERT: e 314 ASN cc_start: 0.7141 (t0) cc_final: 0.6902 (t0) REVERT: e 316 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6814 (mt-10) REVERT: f 186 ILE cc_start: 0.8685 (mm) cc_final: 0.8368 (mm) REVERT: f 260 TYR cc_start: 0.8800 (t80) cc_final: 0.8595 (t80) REVERT: f 290 LYS cc_start: 0.6994 (mtpp) cc_final: 0.6620 (mmtm) REVERT: g 64 ASN cc_start: 0.8682 (m-40) cc_final: 0.8416 (m110) REVERT: g 97 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7258 (mt-10) REVERT: g 101 ASP cc_start: 0.7467 (m-30) cc_final: 0.7067 (m-30) REVERT: g 105 THR cc_start: 0.8737 (t) cc_final: 0.8487 (p) REVERT: g 173 LYS cc_start: 0.7747 (tmtp) cc_final: 0.7290 (ttmm) REVERT: g 188 GLU cc_start: 0.5630 (pt0) cc_final: 0.5367 (pt0) REVERT: h 102 SER cc_start: 0.8794 (t) cc_final: 0.8175 (t) REVERT: h 105 ASP cc_start: 0.8368 (m-30) cc_final: 0.7839 (m-30) REVERT: h 234 ASP cc_start: 0.8290 (p0) cc_final: 0.8012 (p0) REVERT: h 269 SER cc_start: 0.8479 (p) cc_final: 0.8257 (t) REVERT: i 113 LYS cc_start: 0.8624 (ptmm) cc_final: 0.8291 (pttp) REVERT: i 181 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8405 (mtmm) REVERT: i 212 THR cc_start: 0.8993 (t) cc_final: 0.8786 (t) REVERT: j 75 LYS cc_start: 0.8305 (tttt) cc_final: 0.7995 (tptm) REVERT: k 129 MET cc_start: 0.7714 (mtp) cc_final: 0.7491 (ttm) REVERT: l 128 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8457 (tp-100) REVERT: l 161 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7710 (mm-30) REVERT: l 169 ASN cc_start: 0.8379 (m-40) cc_final: 0.8152 (m-40) REVERT: m 174 TYR cc_start: 0.7839 (m-10) cc_final: 0.7562 (m-80) REVERT: m 195 TYR cc_start: 0.8027 (m-80) cc_final: 0.7515 (m-80) REVERT: n 65 ASP cc_start: 0.7790 (m-30) cc_final: 0.7451 (m-30) outliers start: 173 outliers final: 107 residues processed: 1252 average time/residue: 0.5394 time to fit residues: 1094.8752 Evaluate side-chains 1093 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 978 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 63 CYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 229 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 240 ASP Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 169 LYS Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 146 VAL Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 166 LYS Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 82 LEU Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 196 MET Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 8.9990 chunk 175 optimal weight: 0.3980 chunk 470 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 565 optimal weight: 1.9990 chunk 611 optimal weight: 0.5980 chunk 503 optimal weight: 0.8980 chunk 561 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 453 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS D 120 GLN E 268 GLN ** E 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 225 GLN G 114 ASN H 266 GLN J 68 GLN K 125 GLN L 152 GLN L 222 GLN M 204 ASN M 234 ASN b 19 GLN b 143 HIS c 186 HIS ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 197 GLN ** e 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN g 8 HIS g 114 ASN h 266 GLN j 147 HIS k 84 ASN k 125 GLN l 108 ASN l 152 GLN l 222 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 234 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 50354 Z= 0.153 Angle : 0.548 10.329 68116 Z= 0.290 Chirality : 0.043 0.204 7560 Planarity : 0.004 0.055 8826 Dihedral : 6.698 84.271 7116 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.33 % Allowed : 12.42 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.78 (0.10), residues: 6304 helix: -0.53 (0.11), residues: 2238 sheet: -0.99 (0.13), residues: 1508 loop : -1.76 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.015 0.001 HIS j 147 PHE 0.020 0.001 PHE a 180 TYR 0.021 0.001 TYR h 218 ARG 0.006 0.000 ARG L 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1076 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7621 (tptt) REVERT: A 156 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8880 (t) REVERT: B 184 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7594 (m-30) REVERT: B 200 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5324 (mm-40) REVERT: B 205 ASN cc_start: 0.8109 (t0) cc_final: 0.7797 (t0) REVERT: B 231 ILE cc_start: 0.5210 (OUTLIER) cc_final: 0.4892 (pp) REVERT: C 29 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7489 (tp40) REVERT: C 196 LEU cc_start: 0.7633 (mt) cc_final: 0.7348 (mt) REVERT: C 262 ASP cc_start: 0.7542 (p0) cc_final: 0.7137 (p0) REVERT: D 4 ASP cc_start: 0.7330 (p0) cc_final: 0.6525 (p0) REVERT: D 46 GLU cc_start: 0.6588 (tm-30) cc_final: 0.6254 (tm-30) REVERT: D 187 HIS cc_start: 0.7731 (t-90) cc_final: 0.7525 (t-90) REVERT: E 109 ASP cc_start: 0.6064 (p0) cc_final: 0.5843 (m-30) REVERT: E 293 GLU cc_start: 0.7477 (tt0) cc_final: 0.6891 (tp30) REVERT: E 314 ASN cc_start: 0.6529 (t0) cc_final: 0.6276 (t0) REVERT: E 316 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6758 (mt-10) REVERT: F 186 ILE cc_start: 0.8630 (mm) cc_final: 0.8367 (mm) REVERT: F 290 LYS cc_start: 0.7970 (mmtm) cc_final: 0.6685 (mtmt) REVERT: F 334 ARG cc_start: 0.7417 (ttm170) cc_final: 0.6871 (mtm180) REVERT: G 32 ASP cc_start: 0.8491 (m-30) cc_final: 0.8251 (m-30) REVERT: G 64 ASN cc_start: 0.8646 (m-40) cc_final: 0.8349 (m110) REVERT: G 97 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7052 (mt-10) REVERT: G 101 ASP cc_start: 0.7436 (m-30) cc_final: 0.6997 (m-30) REVERT: G 105 THR cc_start: 0.8645 (t) cc_final: 0.8385 (p) REVERT: H 234 ASP cc_start: 0.8220 (p0) cc_final: 0.7998 (p0) REVERT: I 71 MET cc_start: 0.7919 (mmt) cc_final: 0.7692 (mmt) REVERT: I 118 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7658 (ttp80) REVERT: I 214 LEU cc_start: 0.8688 (tp) cc_final: 0.8408 (tt) REVERT: I 242 LYS cc_start: 0.6552 (tttm) cc_final: 0.6117 (tppt) REVERT: J 53 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8248 (mp) REVERT: J 171 MET cc_start: 0.8565 (tpp) cc_final: 0.8350 (tpt) REVERT: J 189 ILE cc_start: 0.7927 (pt) cc_final: 0.7617 (mp) REVERT: K 129 MET cc_start: 0.7691 (mtp) cc_final: 0.7448 (ttm) REVERT: M 130 GLN cc_start: 0.7085 (tt0) cc_final: 0.6560 (tt0) REVERT: M 143 ASP cc_start: 0.8448 (p0) cc_final: 0.8247 (p0) REVERT: M 174 TYR cc_start: 0.7825 (m-10) cc_final: 0.7516 (m-80) REVERT: M 182 MET cc_start: 0.7844 (ttt) cc_final: 0.7368 (ttt) REVERT: M 195 TYR cc_start: 0.7983 (m-80) cc_final: 0.7673 (m-80) REVERT: N 195 ARG cc_start: 0.7554 (ttm-80) cc_final: 0.7295 (mmt-90) REVERT: a 18 SER cc_start: 0.8666 (m) cc_final: 0.8413 (p) REVERT: a 42 LYS cc_start: 0.7914 (ttpp) cc_final: 0.7556 (tptt) REVERT: a 49 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8711 (t) REVERT: a 55 ASP cc_start: 0.7087 (t0) cc_final: 0.6810 (t0) REVERT: a 97 ASP cc_start: 0.6991 (m-30) cc_final: 0.6747 (m-30) REVERT: a 215 LYS cc_start: 0.7735 (mtpt) cc_final: 0.7288 (mmtm) REVERT: b 200 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5235 (mm-40) REVERT: b 231 ILE cc_start: 0.4929 (OUTLIER) cc_final: 0.4652 (pp) REVERT: c 29 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7459 (tp40) REVERT: c 76 GLU cc_start: 0.7551 (pm20) cc_final: 0.7338 (pm20) REVERT: c 192 GLU cc_start: 0.7727 (tp30) cc_final: 0.7272 (tp30) REVERT: c 196 LEU cc_start: 0.7636 (mt) cc_final: 0.7401 (mt) REVERT: c 237 LYS cc_start: 0.7133 (tppt) cc_final: 0.6764 (tptm) REVERT: c 262 ASP cc_start: 0.7544 (p0) cc_final: 0.7135 (p0) REVERT: d 4 ASP cc_start: 0.7265 (p0) cc_final: 0.6496 (p0) REVERT: d 47 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7332 (ttmt) REVERT: d 92 GLN cc_start: 0.5832 (mm-40) cc_final: 0.5392 (tm-30) REVERT: d 102 MET cc_start: 0.6121 (ttt) cc_final: 0.5827 (ptm) REVERT: d 167 THR cc_start: 0.8937 (m) cc_final: 0.8734 (p) REVERT: e 314 ASN cc_start: 0.6971 (t0) cc_final: 0.6716 (t0) REVERT: e 316 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6830 (mt-10) REVERT: f 186 ILE cc_start: 0.8574 (mm) cc_final: 0.8340 (mm) REVERT: g 64 ASN cc_start: 0.8633 (m-40) cc_final: 0.8364 (m110) REVERT: g 101 ASP cc_start: 0.7396 (m-30) cc_final: 0.7013 (m-30) REVERT: g 105 THR cc_start: 0.8698 (t) cc_final: 0.8443 (p) REVERT: g 115 ARG cc_start: 0.7713 (mmt90) cc_final: 0.7395 (mmp80) REVERT: g 173 LYS cc_start: 0.7754 (tmtp) cc_final: 0.7297 (ttmm) REVERT: h 105 ASP cc_start: 0.8313 (m-30) cc_final: 0.7880 (m-30) REVERT: h 234 ASP cc_start: 0.8273 (p0) cc_final: 0.8060 (p0) REVERT: i 113 LYS cc_start: 0.8507 (ptmm) cc_final: 0.8237 (pttp) REVERT: j 4 MET cc_start: 0.8213 (mmm) cc_final: 0.7600 (mmm) REVERT: j 32 LEU cc_start: 0.7548 (mt) cc_final: 0.6669 (mt) REVERT: j 53 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8231 (mp) REVERT: j 75 LYS cc_start: 0.8275 (tttt) cc_final: 0.8032 (tptm) REVERT: k 129 MET cc_start: 0.7710 (mtp) cc_final: 0.7476 (ttm) REVERT: k 161 ASP cc_start: 0.8827 (p0) cc_final: 0.8588 (p0) REVERT: m 174 TYR cc_start: 0.7797 (m-10) cc_final: 0.7481 (m-80) REVERT: m 182 MET cc_start: 0.7814 (ttt) cc_final: 0.7295 (ttt) REVERT: m 195 TYR cc_start: 0.7987 (m-80) cc_final: 0.7649 (m-80) outliers start: 122 outliers final: 79 residues processed: 1159 average time/residue: 0.5363 time to fit residues: 1010.3332 Evaluate side-chains 1071 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 983 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 132 GLU Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain n residue 35 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 0.2980 chunk 425 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 379 optimal weight: 2.9990 chunk 567 optimal weight: 10.0000 chunk 601 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 538 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 268 GLN G 198 HIS H 266 GLN K 125 GLN L 128 GLN ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 197 GLN f 225 GLN k 125 GLN l 128 GLN ** m 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 50354 Z= 0.235 Angle : 0.564 9.905 68116 Z= 0.297 Chirality : 0.044 0.200 7560 Planarity : 0.004 0.077 8826 Dihedral : 6.657 81.670 7116 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.02 % Allowed : 12.79 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: 6304 helix: 0.09 (0.11), residues: 2254 sheet: -0.82 (0.13), residues: 1500 loop : -1.62 (0.11), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.007 0.001 HIS F 343 PHE 0.018 0.001 PHE a 180 TYR 0.035 0.001 TYR H 218 ARG 0.005 0.001 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 995 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8855 (t) REVERT: B 184 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: B 200 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.5428 (mm-40) REVERT: B 205 ASN cc_start: 0.8071 (t0) cc_final: 0.7729 (t0) REVERT: B 231 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.5036 (pp) REVERT: C 29 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7486 (tp40) REVERT: C 183 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7024 (mttt) REVERT: C 196 LEU cc_start: 0.7680 (mt) cc_final: 0.7407 (mt) REVERT: C 262 ASP cc_start: 0.7488 (p0) cc_final: 0.7162 (p0) REVERT: D 4 ASP cc_start: 0.7522 (p0) cc_final: 0.6664 (p0) REVERT: D 46 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6189 (tm-30) REVERT: D 182 ARG cc_start: 0.7172 (tmm-80) cc_final: 0.6572 (tmt170) REVERT: D 187 HIS cc_start: 0.7699 (t-90) cc_final: 0.7486 (t-90) REVERT: E 109 ASP cc_start: 0.5980 (p0) cc_final: 0.5690 (m-30) REVERT: E 278 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7358 (mm110) REVERT: E 293 GLU cc_start: 0.7456 (tt0) cc_final: 0.6866 (tp30) REVERT: E 314 ASN cc_start: 0.6629 (t0) cc_final: 0.6330 (t0) REVERT: E 316 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6779 (mt-10) REVERT: F 186 ILE cc_start: 0.8635 (mm) cc_final: 0.8384 (mm) REVERT: F 290 LYS cc_start: 0.7993 (mmtm) cc_final: 0.6692 (mtmt) REVERT: G 64 ASN cc_start: 0.8691 (m-40) cc_final: 0.8380 (m110) REVERT: G 101 ASP cc_start: 0.7457 (m-30) cc_final: 0.7149 (m-30) REVERT: G 105 THR cc_start: 0.8689 (t) cc_final: 0.8399 (p) REVERT: G 221 ASP cc_start: 0.7801 (t70) cc_final: 0.7422 (t70) REVERT: H 234 ASP cc_start: 0.8170 (p0) cc_final: 0.7962 (p0) REVERT: I 168 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7744 (mm-30) REVERT: I 214 LEU cc_start: 0.8734 (tp) cc_final: 0.8521 (tt) REVERT: I 242 LYS cc_start: 0.6650 (tttm) cc_final: 0.6186 (tppt) REVERT: J 4 MET cc_start: 0.8206 (mmm) cc_final: 0.7847 (mmm) REVERT: J 32 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6659 (mt) REVERT: J 171 MET cc_start: 0.8578 (tpp) cc_final: 0.8345 (tpt) REVERT: J 189 ILE cc_start: 0.7925 (pt) cc_final: 0.7584 (mp) REVERT: K 129 MET cc_start: 0.7778 (mtp) cc_final: 0.7571 (ttm) REVERT: L 161 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7316 (mm-30) REVERT: M 130 GLN cc_start: 0.7137 (tt0) cc_final: 0.6625 (tt0) REVERT: M 182 MET cc_start: 0.8066 (ttt) cc_final: 0.7513 (ttt) REVERT: M 195 TYR cc_start: 0.8038 (m-80) cc_final: 0.7722 (m-80) REVERT: M 225 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7660 (ttp-170) REVERT: N 65 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7209 (m-30) REVERT: N 195 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7294 (mmt-90) REVERT: a 18 SER cc_start: 0.8713 (m) cc_final: 0.8411 (p) REVERT: a 97 ASP cc_start: 0.6986 (m-30) cc_final: 0.6780 (m-30) REVERT: a 215 LYS cc_start: 0.7745 (mtpt) cc_final: 0.7338 (mmtm) REVERT: b 200 GLN cc_start: 0.6231 (OUTLIER) cc_final: 0.5325 (mm-40) REVERT: b 231 ILE cc_start: 0.5224 (OUTLIER) cc_final: 0.4984 (pp) REVERT: c 29 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7454 (tp40) REVERT: c 183 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.7024 (mttt) REVERT: c 196 LEU cc_start: 0.7691 (mt) cc_final: 0.7432 (mt) REVERT: c 262 ASP cc_start: 0.7520 (p0) cc_final: 0.7011 (p0) REVERT: c 263 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7304 (mm110) REVERT: d 4 ASP cc_start: 0.7364 (p0) cc_final: 0.6491 (p0) REVERT: d 47 LYS cc_start: 0.7659 (ttpp) cc_final: 0.7397 (ttmt) REVERT: d 92 GLN cc_start: 0.5752 (mm-40) cc_final: 0.5321 (tm-30) REVERT: d 102 MET cc_start: 0.6176 (ttt) cc_final: 0.5929 (ptm) REVERT: d 167 THR cc_start: 0.8980 (m) cc_final: 0.8749 (p) REVERT: e 278 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7123 (mm-40) REVERT: e 314 ASN cc_start: 0.6977 (t0) cc_final: 0.6699 (t0) REVERT: e 316 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6905 (mt-10) REVERT: f 186 ILE cc_start: 0.8657 (mm) cc_final: 0.8420 (mm) REVERT: g 64 ASN cc_start: 0.8665 (m-40) cc_final: 0.8398 (m110) REVERT: g 101 ASP cc_start: 0.7386 (m-30) cc_final: 0.7009 (m-30) REVERT: g 105 THR cc_start: 0.8706 (t) cc_final: 0.8435 (p) REVERT: g 175 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8181 (mt-10) REVERT: g 221 ASP cc_start: 0.7875 (t70) cc_final: 0.7476 (t70) REVERT: h 234 ASP cc_start: 0.8229 (p0) cc_final: 0.7993 (p0) REVERT: j 4 MET cc_start: 0.8222 (mmm) cc_final: 0.7588 (mmm) REVERT: j 32 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.6690 (mt) REVERT: k 129 MET cc_start: 0.7734 (mtp) cc_final: 0.7493 (ttm) REVERT: m 174 TYR cc_start: 0.7838 (m-10) cc_final: 0.7537 (m-80) REVERT: m 182 MET cc_start: 0.8086 (ttt) cc_final: 0.7515 (ttt) REVERT: m 195 TYR cc_start: 0.8160 (m-80) cc_final: 0.7764 (m-80) REVERT: m 225 ARG cc_start: 0.8260 (mtp180) cc_final: 0.7552 (ttp-170) outliers start: 158 outliers final: 120 residues processed: 1095 average time/residue: 0.5298 time to fit residues: 941.8441 Evaluate side-chains 1084 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 953 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain e residue 248 GLU Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 31 LYS Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 3.9990 chunk 341 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 447 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 513 optimal weight: 5.9990 chunk 415 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 539 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS E 252 GLN F 225 GLN H 135 ASN H 266 GLN K 125 GLN L 108 ASN L 222 GLN M 234 ASN N 148 GLN N 185 GLN ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN h 135 ASN l 222 GLN ** m 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 148 GLN n 185 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 50354 Z= 0.280 Angle : 0.584 10.247 68116 Z= 0.307 Chirality : 0.045 0.208 7560 Planarity : 0.004 0.056 8826 Dihedral : 6.718 85.617 7116 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.70 % Allowed : 13.34 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.00 (0.10), residues: 6304 helix: 0.42 (0.11), residues: 2242 sheet: -0.75 (0.13), residues: 1508 loop : -1.52 (0.11), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 185 HIS 0.006 0.001 HIS K 76 PHE 0.027 0.002 PHE A 180 TYR 0.038 0.002 TYR h 218 ARG 0.007 0.001 ARG f 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 968 time to evaluate : 4.296 Fit side-chains REVERT: A 49 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8859 (t) REVERT: B 184 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: B 200 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.5321 (mm-40) REVERT: B 205 ASN cc_start: 0.8059 (t0) cc_final: 0.7721 (t0) REVERT: B 231 ILE cc_start: 0.5397 (OUTLIER) cc_final: 0.5171 (pp) REVERT: C 29 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7480 (tp40) REVERT: C 183 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.7020 (mttt) REVERT: C 196 LEU cc_start: 0.7677 (mt) cc_final: 0.7402 (mt) REVERT: C 262 ASP cc_start: 0.7485 (p0) cc_final: 0.7125 (p0) REVERT: C 263 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7404 (mm110) REVERT: D 4 ASP cc_start: 0.7515 (p0) cc_final: 0.6625 (p0) REVERT: D 46 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6065 (tm-30) REVERT: E 278 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7391 (mm110) REVERT: E 293 GLU cc_start: 0.7399 (tt0) cc_final: 0.6803 (tp30) REVERT: E 314 ASN cc_start: 0.6693 (t0) cc_final: 0.6321 (t0) REVERT: E 316 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6739 (mt-10) REVERT: F 186 ILE cc_start: 0.8698 (mm) cc_final: 0.8442 (mm) REVERT: F 290 LYS cc_start: 0.8030 (mmtm) cc_final: 0.6718 (mtmt) REVERT: G 64 ASN cc_start: 0.8718 (m-40) cc_final: 0.8388 (m110) REVERT: G 97 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7221 (mt-10) REVERT: G 101 ASP cc_start: 0.7503 (m-30) cc_final: 0.7175 (m-30) REVERT: G 105 THR cc_start: 0.8688 (t) cc_final: 0.8369 (p) REVERT: G 210 GLU cc_start: 0.6627 (tp30) cc_final: 0.6338 (tp30) REVERT: G 221 ASP cc_start: 0.7889 (t70) cc_final: 0.7493 (t70) REVERT: I 168 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7766 (mm-30) REVERT: J 4 MET cc_start: 0.8275 (mmm) cc_final: 0.7847 (mmm) REVERT: J 12 MET cc_start: 0.7896 (ttp) cc_final: 0.7560 (ttp) REVERT: J 32 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.6769 (mt) REVERT: J 189 ILE cc_start: 0.7924 (pt) cc_final: 0.7542 (mp) REVERT: K 129 MET cc_start: 0.7793 (mtp) cc_final: 0.7576 (ttm) REVERT: L 128 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8762 (tp-100) REVERT: L 161 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7318 (mm-30) REVERT: L 186 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8717 (m) REVERT: M 195 TYR cc_start: 0.8197 (m-80) cc_final: 0.7790 (m-80) REVERT: M 225 ARG cc_start: 0.8271 (mtp180) cc_final: 0.7765 (ttp-170) REVERT: N 40 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8353 (pp) REVERT: N 65 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7248 (m-30) REVERT: N 195 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7312 (mmt-90) REVERT: a 97 ASP cc_start: 0.6988 (m-30) cc_final: 0.6772 (m-30) REVERT: b 200 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5328 (mm-40) REVERT: b 231 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.5086 (pp) REVERT: c 29 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7253 (mt0) REVERT: c 183 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7081 (mttt) REVERT: c 196 LEU cc_start: 0.7686 (mt) cc_final: 0.7424 (mt) REVERT: c 262 ASP cc_start: 0.7521 (p0) cc_final: 0.7187 (p0) REVERT: c 263 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7408 (mm110) REVERT: d 4 ASP cc_start: 0.7368 (p0) cc_final: 0.6514 (p0) REVERT: d 46 GLU cc_start: 0.6383 (tm-30) cc_final: 0.5945 (tm-30) REVERT: d 92 GLN cc_start: 0.5692 (mm-40) cc_final: 0.5244 (tm-30) REVERT: d 213 GLU cc_start: 0.6293 (pt0) cc_final: 0.5969 (tp30) REVERT: e 278 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7231 (mm-40) REVERT: e 314 ASN cc_start: 0.7063 (t0) cc_final: 0.6767 (t0) REVERT: f 186 ILE cc_start: 0.8684 (mm) cc_final: 0.8443 (mm) REVERT: g 64 ASN cc_start: 0.8690 (m-40) cc_final: 0.8387 (m110) REVERT: g 101 ASP cc_start: 0.7448 (m-30) cc_final: 0.7129 (m-30) REVERT: g 105 THR cc_start: 0.8712 (t) cc_final: 0.8386 (p) REVERT: g 175 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8287 (mt-10) REVERT: g 221 ASP cc_start: 0.7881 (t70) cc_final: 0.7455 (t70) REVERT: h 139 LYS cc_start: 0.8083 (tttm) cc_final: 0.7831 (mmtp) REVERT: h 234 ASP cc_start: 0.8229 (p0) cc_final: 0.8007 (p0) REVERT: j 12 MET cc_start: 0.7927 (ttp) cc_final: 0.7601 (ttp) REVERT: j 32 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.6771 (mt) REVERT: j 106 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7940 (mt-10) REVERT: k 161 ASP cc_start: 0.8868 (p0) cc_final: 0.8659 (p0) REVERT: l 128 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8718 (tp-100) REVERT: m 174 TYR cc_start: 0.7879 (m-10) cc_final: 0.7611 (m-80) REVERT: m 195 TYR cc_start: 0.8172 (m-80) cc_final: 0.7786 (m-80) REVERT: m 225 ARG cc_start: 0.8278 (mtp180) cc_final: 0.8072 (mtp180) outliers start: 194 outliers final: 150 residues processed: 1096 average time/residue: 0.5373 time to fit residues: 956.5288 Evaluate side-chains 1080 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 915 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 97 ARG Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain b residue 200 GLN Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 129 VAL Chi-restraints excluded: chain d residue 169 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain e residue 248 GLU Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 82 LEU Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 135 ASN Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 38 ARG Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 95 HIS Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain i residue 241 LEU Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain k residue 112 THR Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 130 GLN Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 325 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 31 LYS Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 0.9980 chunk 541 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 352 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 601 optimal weight: 7.9990 chunk 499 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 268 GLN F 343 HIS G 8 HIS H 266 GLN K 125 GLN M 130 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 252 GLN h 135 ASN h 266 GLN l 152 GLN l 279 HIS m 234 ASN ** m 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50354 Z= 0.205 Angle : 0.541 9.532 68116 Z= 0.285 Chirality : 0.044 0.206 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.594 86.278 7116 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.38 % Allowed : 14.48 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.10), residues: 6304 helix: 0.69 (0.11), residues: 2238 sheet: -0.60 (0.13), residues: 1500 loop : -1.45 (0.11), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 185 HIS 0.007 0.001 HIS K 76 PHE 0.018 0.001 PHE A 180 TYR 0.027 0.001 TYR h 218 ARG 0.007 0.000 ARG G 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 930 time to evaluate : 4.280 Fit side-chains REVERT: A 49 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 184 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: B 200 GLN cc_start: 0.6122 (OUTLIER) cc_final: 0.5309 (mm-40) REVERT: B 205 ASN cc_start: 0.8022 (t0) cc_final: 0.7679 (t0) REVERT: B 231 ILE cc_start: 0.5422 (OUTLIER) cc_final: 0.5196 (pp) REVERT: C 29 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7303 (mt0) REVERT: C 183 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.6985 (mttt) REVERT: C 196 LEU cc_start: 0.7654 (mt) cc_final: 0.7383 (mt) REVERT: C 262 ASP cc_start: 0.7493 (p0) cc_final: 0.7177 (p0) REVERT: C 263 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7435 (mm110) REVERT: D 4 ASP cc_start: 0.7513 (p0) cc_final: 0.6635 (p0) REVERT: D 46 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6186 (tm-30) REVERT: D 182 ARG cc_start: 0.7214 (tmm-80) cc_final: 0.6586 (tmt170) REVERT: E 278 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7332 (mm110) REVERT: E 293 GLU cc_start: 0.7319 (tt0) cc_final: 0.6666 (tp30) REVERT: E 314 ASN cc_start: 0.6679 (t0) cc_final: 0.6281 (t0) REVERT: F 186 ILE cc_start: 0.8686 (mm) cc_final: 0.8469 (mm) REVERT: F 290 LYS cc_start: 0.7980 (mmtm) cc_final: 0.6696 (mtmt) REVERT: G 64 ASN cc_start: 0.8713 (m-40) cc_final: 0.8374 (m110) REVERT: G 97 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7178 (mt-10) REVERT: G 101 ASP cc_start: 0.7475 (m-30) cc_final: 0.7096 (m-30) REVERT: G 105 THR cc_start: 0.8634 (t) cc_final: 0.8354 (p) REVERT: G 221 ASP cc_start: 0.7898 (t70) cc_final: 0.7498 (t70) REVERT: I 118 ARG cc_start: 0.8018 (ttp80) cc_final: 0.7762 (ttp80) REVERT: I 242 LYS cc_start: 0.6707 (tttt) cc_final: 0.6209 (tppt) REVERT: J 12 MET cc_start: 0.7913 (ttp) cc_final: 0.7567 (ttp) REVERT: J 18 GLU cc_start: 0.6846 (pm20) cc_final: 0.6556 (pm20) REVERT: J 32 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6725 (mt) REVERT: J 189 ILE cc_start: 0.7919 (pt) cc_final: 0.7527 (mp) REVERT: K 31 ASP cc_start: 0.7953 (t0) cc_final: 0.7748 (t0) REVERT: K 59 GLU cc_start: 0.6787 (tt0) cc_final: 0.6570 (pt0) REVERT: K 129 MET cc_start: 0.7791 (mtp) cc_final: 0.7570 (ttm) REVERT: L 128 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8742 (tp-100) REVERT: L 161 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7386 (mm-30) REVERT: L 186 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8649 (m) REVERT: M 130 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6495 (mt0) REVERT: M 195 TYR cc_start: 0.8147 (m-80) cc_final: 0.7792 (m-80) REVERT: N 40 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8260 (pp) REVERT: N 65 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: N 195 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7343 (mmt-90) REVERT: a 97 ASP cc_start: 0.6968 (m-30) cc_final: 0.6750 (m-30) REVERT: b 231 ILE cc_start: 0.5378 (OUTLIER) cc_final: 0.5116 (pp) REVERT: c 29 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7253 (mt0) REVERT: c 183 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7097 (mttt) REVERT: c 196 LEU cc_start: 0.7669 (mt) cc_final: 0.7410 (mt) REVERT: c 262 ASP cc_start: 0.7503 (p0) cc_final: 0.7195 (p0) REVERT: c 263 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7478 (mm110) REVERT: d 4 ASP cc_start: 0.7336 (p0) cc_final: 0.6526 (p0) REVERT: d 46 GLU cc_start: 0.6353 (tm-30) cc_final: 0.5694 (tm-30) REVERT: d 92 GLN cc_start: 0.5531 (mm-40) cc_final: 0.5106 (tm-30) REVERT: d 182 ARG cc_start: 0.6934 (tmm160) cc_final: 0.6733 (tmm160) REVERT: d 183 ASP cc_start: 0.6767 (m-30) cc_final: 0.6557 (p0) REVERT: d 213 GLU cc_start: 0.6404 (pt0) cc_final: 0.6026 (tp30) REVERT: e 278 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7210 (mm-40) REVERT: e 314 ASN cc_start: 0.6932 (t0) cc_final: 0.6632 (t0) REVERT: f 186 ILE cc_start: 0.8670 (mm) cc_final: 0.8461 (mm) REVERT: g 64 ASN cc_start: 0.8666 (m-40) cc_final: 0.8366 (m-40) REVERT: g 101 ASP cc_start: 0.7371 (m-30) cc_final: 0.7015 (m-30) REVERT: g 105 THR cc_start: 0.8635 (t) cc_final: 0.8367 (p) REVERT: g 175 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8217 (mt-10) REVERT: g 221 ASP cc_start: 0.7840 (t70) cc_final: 0.7447 (t70) REVERT: h 139 LYS cc_start: 0.8041 (tttm) cc_final: 0.7770 (mmtp) REVERT: h 234 ASP cc_start: 0.8265 (p0) cc_final: 0.8054 (p0) REVERT: j 12 MET cc_start: 0.7919 (ttp) cc_final: 0.7585 (ttp) REVERT: j 18 GLU cc_start: 0.6761 (pm20) cc_final: 0.6488 (pm20) REVERT: j 32 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.6724 (mt) REVERT: j 106 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7958 (mt-10) REVERT: k 161 ASP cc_start: 0.8891 (p0) cc_final: 0.8679 (p0) REVERT: l 128 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8720 (tp-100) REVERT: m 174 TYR cc_start: 0.7865 (m-10) cc_final: 0.7622 (m-80) REVERT: m 195 TYR cc_start: 0.8152 (m-80) cc_final: 0.7766 (m-80) REVERT: m 207 LYS cc_start: 0.7968 (tttp) cc_final: 0.7190 (tptm) REVERT: m 225 ARG cc_start: 0.8211 (mtp180) cc_final: 0.7762 (ttp-170) outliers start: 177 outliers final: 131 residues processed: 1047 average time/residue: 0.5305 time to fit residues: 897.7650 Evaluate side-chains 1052 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 906 time to evaluate : 4.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain M residue 130 GLN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 319 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 95 HIS Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 130 GLN Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 319 VAL Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 31 LYS Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 151 GLU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 342 optimal weight: 0.8980 chunk 439 optimal weight: 1.9990 chunk 340 optimal weight: 8.9990 chunk 506 optimal weight: 6.9990 chunk 336 optimal weight: 0.9990 chunk 599 optimal weight: 2.9990 chunk 375 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 chunk 276 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN E 286 HIS H 135 ASN H 266 GLN K 125 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 GLN h 135 ASN h 266 GLN l 222 GLN m 303 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 50354 Z= 0.166 Angle : 0.526 10.094 68116 Z= 0.276 Chirality : 0.043 0.181 7560 Planarity : 0.004 0.054 8826 Dihedral : 6.458 86.300 7116 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.23 % Allowed : 14.87 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 6304 helix: 0.96 (0.11), residues: 2236 sheet: -0.49 (0.13), residues: 1488 loop : -1.36 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.008 0.001 HIS K 76 PHE 0.017 0.001 PHE A 180 TYR 0.024 0.001 TYR k 128 ARG 0.008 0.000 ARG F 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 953 time to evaluate : 4.268 Fit side-chains REVERT: A 49 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8850 (t) REVERT: A 97 ASP cc_start: 0.7028 (m-30) cc_final: 0.6737 (m-30) REVERT: A 215 LYS cc_start: 0.7712 (mtpt) cc_final: 0.7294 (mmtm) REVERT: B 200 GLN cc_start: 0.6168 (OUTLIER) cc_final: 0.5333 (mm-40) REVERT: B 205 ASN cc_start: 0.7960 (t0) cc_final: 0.7490 (t0) REVERT: C 29 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7333 (mt0) REVERT: C 183 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7012 (mttt) REVERT: C 196 LEU cc_start: 0.7663 (mt) cc_final: 0.7399 (mt) REVERT: C 262 ASP cc_start: 0.7480 (p0) cc_final: 0.7164 (p0) REVERT: C 263 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7449 (mm110) REVERT: D 4 ASP cc_start: 0.7486 (p0) cc_final: 0.6603 (p0) REVERT: D 46 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6288 (tm-30) REVERT: D 182 ARG cc_start: 0.7185 (tmm-80) cc_final: 0.6571 (tmt170) REVERT: E 278 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7440 (mm110) REVERT: E 293 GLU cc_start: 0.7359 (tt0) cc_final: 0.6733 (tp30) REVERT: E 314 ASN cc_start: 0.6631 (t0) cc_final: 0.6263 (t0) REVERT: F 290 LYS cc_start: 0.7947 (mmtm) cc_final: 0.6661 (mtmt) REVERT: G 41 CYS cc_start: 0.7629 (t) cc_final: 0.7265 (t) REVERT: G 64 ASN cc_start: 0.8714 (m-40) cc_final: 0.8429 (m110) REVERT: G 97 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7113 (mt-10) REVERT: G 101 ASP cc_start: 0.7462 (m-30) cc_final: 0.7096 (m-30) REVERT: G 105 THR cc_start: 0.8676 (t) cc_final: 0.8437 (p) REVERT: G 115 ARG cc_start: 0.7612 (mmt90) cc_final: 0.7075 (mtt180) REVERT: G 221 ASP cc_start: 0.7873 (t70) cc_final: 0.7467 (t70) REVERT: I 242 LYS cc_start: 0.6678 (tttt) cc_final: 0.6218 (tppt) REVERT: J 12 MET cc_start: 0.7938 (ttp) cc_final: 0.7619 (ttp) REVERT: J 18 GLU cc_start: 0.6800 (pm20) cc_final: 0.6520 (pm20) REVERT: J 32 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6652 (mt) REVERT: J 171 MET cc_start: 0.8558 (tpp) cc_final: 0.8297 (tpt) REVERT: J 189 ILE cc_start: 0.7838 (pt) cc_final: 0.7483 (mp) REVERT: K 31 ASP cc_start: 0.7890 (t0) cc_final: 0.7667 (t0) REVERT: K 129 MET cc_start: 0.7736 (mtp) cc_final: 0.7522 (ttm) REVERT: L 128 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (tp-100) REVERT: L 161 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7393 (mm-30) REVERT: L 186 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8573 (m) REVERT: M 195 TYR cc_start: 0.8101 (m-80) cc_final: 0.7810 (m-80) REVERT: N 40 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8231 (pp) REVERT: N 65 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: N 195 ARG cc_start: 0.7624 (ttm-80) cc_final: 0.7372 (mmt-90) REVERT: a 18 SER cc_start: 0.8704 (m) cc_final: 0.8467 (p) REVERT: a 93 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6875 (mt-10) REVERT: a 97 ASP cc_start: 0.6929 (m-30) cc_final: 0.6703 (m-30) REVERT: b 21 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7011 (mm-30) REVERT: b 205 ASN cc_start: 0.8147 (t0) cc_final: 0.7656 (t0) REVERT: b 231 ILE cc_start: 0.5404 (OUTLIER) cc_final: 0.5178 (pp) REVERT: c 29 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7335 (mt0) REVERT: c 183 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.7090 (mttt) REVERT: c 196 LEU cc_start: 0.7699 (mt) cc_final: 0.7431 (mt) REVERT: c 237 LYS cc_start: 0.7097 (tppt) cc_final: 0.6587 (tptm) REVERT: c 262 ASP cc_start: 0.7481 (p0) cc_final: 0.7223 (p0) REVERT: c 263 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7504 (mm110) REVERT: d 4 ASP cc_start: 0.7314 (p0) cc_final: 0.6493 (p0) REVERT: d 46 GLU cc_start: 0.6391 (tm-30) cc_final: 0.5826 (tm-30) REVERT: d 92 GLN cc_start: 0.5470 (mm-40) cc_final: 0.5084 (tm-30) REVERT: d 213 GLU cc_start: 0.6458 (pt0) cc_final: 0.6140 (tp30) REVERT: e 278 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7239 (mm110) REVERT: e 314 ASN cc_start: 0.6840 (t0) cc_final: 0.6535 (t0) REVERT: f 186 ILE cc_start: 0.8669 (mm) cc_final: 0.8467 (mm) REVERT: g 41 CYS cc_start: 0.7520 (t) cc_final: 0.7147 (t) REVERT: g 64 ASN cc_start: 0.8663 (m-40) cc_final: 0.8351 (m110) REVERT: g 101 ASP cc_start: 0.7347 (m-30) cc_final: 0.7020 (m-30) REVERT: g 105 THR cc_start: 0.8620 (t) cc_final: 0.8363 (p) REVERT: g 175 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8237 (mt-10) REVERT: g 221 ASP cc_start: 0.7833 (t70) cc_final: 0.7436 (t70) REVERT: h 139 LYS cc_start: 0.8054 (tttm) cc_final: 0.7767 (mmtp) REVERT: i 181 LYS cc_start: 0.8292 (mttp) cc_final: 0.7852 (mttt) REVERT: j 12 MET cc_start: 0.7951 (ttp) cc_final: 0.7592 (ttp) REVERT: j 18 GLU cc_start: 0.6744 (pm20) cc_final: 0.6483 (pm20) REVERT: j 32 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6641 (mt) REVERT: j 106 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7947 (mt-10) REVERT: k 125 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8294 (mm-40) REVERT: k 129 MET cc_start: 0.7751 (mtp) cc_final: 0.7508 (ttm) REVERT: k 161 ASP cc_start: 0.8879 (p0) cc_final: 0.8672 (p0) REVERT: l 128 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8707 (tp-100) REVERT: m 174 TYR cc_start: 0.7851 (m-10) cc_final: 0.7613 (m-80) REVERT: m 195 TYR cc_start: 0.8123 (m-80) cc_final: 0.7791 (m-80) REVERT: m 225 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7947 (ttp-170) REVERT: m 303 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.7249 (m-40) REVERT: n 93 TYR cc_start: 0.8974 (t80) cc_final: 0.8743 (t80) outliers start: 169 outliers final: 123 residues processed: 1059 average time/residue: 0.5336 time to fit residues: 916.8587 Evaluate side-chains 1039 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 903 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 223 GLN Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 190 ASN Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 135 ASN Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 102 GLN Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 303 ASN Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 31 LYS Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 358 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 381 optimal weight: 7.9990 chunk 408 optimal weight: 6.9990 chunk 296 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 471 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN D 120 GLN H 135 ASN H 266 GLN K 125 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 252 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 266 GLN m 130 GLN m 234 ASN m 303 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50354 Z= 0.218 Angle : 0.548 9.489 68116 Z= 0.287 Chirality : 0.044 0.292 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.479 87.227 7116 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.24 % Allowed : 15.08 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 6304 helix: 1.02 (0.11), residues: 2244 sheet: -0.46 (0.13), residues: 1480 loop : -1.35 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.009 0.001 HIS K 76 PHE 0.021 0.001 PHE a 180 TYR 0.030 0.001 TYR h 218 ARG 0.008 0.000 ARG f 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 925 time to evaluate : 4.370 Fit side-chains REVERT: A 49 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8847 (t) REVERT: A 97 ASP cc_start: 0.7046 (m-30) cc_final: 0.6705 (m-30) REVERT: A 215 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7291 (mmtm) REVERT: B 200 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5485 (mm-40) REVERT: B 205 ASN cc_start: 0.7972 (t0) cc_final: 0.7490 (t0) REVERT: B 231 ILE cc_start: 0.5450 (OUTLIER) cc_final: 0.5231 (pp) REVERT: C 29 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7453 (mt0) REVERT: C 196 LEU cc_start: 0.7659 (mt) cc_final: 0.7380 (mt) REVERT: C 262 ASP cc_start: 0.7466 (p0) cc_final: 0.7186 (p0) REVERT: C 263 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7472 (mm110) REVERT: D 4 ASP cc_start: 0.7495 (p0) cc_final: 0.6610 (p0) REVERT: D 46 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6277 (tm-30) REVERT: D 120 GLN cc_start: 0.8279 (tt0) cc_final: 0.8077 (tt0) REVERT: D 182 ARG cc_start: 0.7194 (tmm-80) cc_final: 0.6547 (tmt170) REVERT: E 142 THR cc_start: 0.7838 (OUTLIER) cc_final: 0.7612 (p) REVERT: E 278 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7373 (mm110) REVERT: E 293 GLU cc_start: 0.7354 (tt0) cc_final: 0.6724 (tp30) REVERT: E 314 ASN cc_start: 0.6645 (t0) cc_final: 0.6281 (t0) REVERT: F 290 LYS cc_start: 0.7984 (mmtm) cc_final: 0.6692 (mtmt) REVERT: G 41 CYS cc_start: 0.7606 (t) cc_final: 0.7255 (t) REVERT: G 64 ASN cc_start: 0.8699 (m-40) cc_final: 0.8389 (m110) REVERT: G 97 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7185 (mt-10) REVERT: G 101 ASP cc_start: 0.7445 (m-30) cc_final: 0.7083 (m-30) REVERT: G 105 THR cc_start: 0.8654 (t) cc_final: 0.8408 (p) REVERT: G 115 ARG cc_start: 0.7606 (mmt90) cc_final: 0.7108 (mtt180) REVERT: G 188 GLU cc_start: 0.5720 (pt0) cc_final: 0.5382 (pt0) REVERT: G 221 ASP cc_start: 0.7847 (t70) cc_final: 0.7434 (t70) REVERT: I 133 ASP cc_start: 0.6366 (OUTLIER) cc_final: 0.6145 (t0) REVERT: I 242 LYS cc_start: 0.6696 (tttt) cc_final: 0.6225 (tppt) REVERT: J 18 GLU cc_start: 0.6820 (pm20) cc_final: 0.6537 (pm20) REVERT: J 32 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6648 (mt) REVERT: J 189 ILE cc_start: 0.7839 (pt) cc_final: 0.7460 (mp) REVERT: K 31 ASP cc_start: 0.7903 (t0) cc_final: 0.7691 (t0) REVERT: K 129 MET cc_start: 0.7745 (mtp) cc_final: 0.7525 (ttm) REVERT: L 128 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8790 (tp-100) REVERT: L 161 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7425 (mm-30) REVERT: L 186 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8617 (m) REVERT: M 195 TYR cc_start: 0.8158 (m-80) cc_final: 0.7807 (m-80) REVERT: N 40 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8292 (pp) REVERT: N 65 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7189 (m-30) REVERT: N 195 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7357 (mmt-90) REVERT: a 18 SER cc_start: 0.8722 (m) cc_final: 0.8463 (p) REVERT: a 93 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6879 (mt-10) REVERT: a 97 ASP cc_start: 0.6964 (m-30) cc_final: 0.6733 (m-30) REVERT: a 191 ASP cc_start: 0.7177 (t0) cc_final: 0.6950 (t0) REVERT: b 21 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7033 (mm-30) REVERT: b 205 ASN cc_start: 0.8141 (t0) cc_final: 0.7659 (t0) REVERT: b 231 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5282 (pp) REVERT: c 29 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7360 (mt0) REVERT: c 183 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7087 (mttt) REVERT: c 196 LEU cc_start: 0.7696 (mt) cc_final: 0.7420 (mt) REVERT: c 237 LYS cc_start: 0.7088 (tppt) cc_final: 0.6607 (tptm) REVERT: c 262 ASP cc_start: 0.7471 (p0) cc_final: 0.7219 (p0) REVERT: c 263 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7514 (mm110) REVERT: d 4 ASP cc_start: 0.7345 (p0) cc_final: 0.6520 (p0) REVERT: d 46 GLU cc_start: 0.6351 (tm-30) cc_final: 0.5971 (tm-30) REVERT: d 92 GLN cc_start: 0.5502 (mm-40) cc_final: 0.5123 (tm-30) REVERT: d 182 ARG cc_start: 0.6844 (tmm160) cc_final: 0.6517 (tmm160) REVERT: d 213 GLU cc_start: 0.6452 (pt0) cc_final: 0.6114 (tp30) REVERT: e 278 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7252 (mm110) REVERT: e 314 ASN cc_start: 0.6903 (t0) cc_final: 0.6586 (t0) REVERT: g 41 CYS cc_start: 0.7532 (t) cc_final: 0.7207 (t) REVERT: g 60 GLU cc_start: 0.7170 (tt0) cc_final: 0.6941 (mt-10) REVERT: g 64 ASN cc_start: 0.8660 (m-40) cc_final: 0.8359 (m110) REVERT: g 101 ASP cc_start: 0.7378 (m-30) cc_final: 0.7076 (m-30) REVERT: g 105 THR cc_start: 0.8622 (t) cc_final: 0.8340 (p) REVERT: g 175 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8220 (mt-10) REVERT: g 221 ASP cc_start: 0.7825 (t70) cc_final: 0.7433 (t70) REVERT: h 139 LYS cc_start: 0.8051 (tttm) cc_final: 0.7765 (mmtp) REVERT: i 181 LYS cc_start: 0.8306 (mttp) cc_final: 0.7871 (mttt) REVERT: j 12 MET cc_start: 0.8005 (ttp) cc_final: 0.7678 (ttp) REVERT: j 18 GLU cc_start: 0.6750 (pm20) cc_final: 0.6471 (pm20) REVERT: j 32 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.6654 (mt) REVERT: j 106 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7944 (mt-10) REVERT: k 129 MET cc_start: 0.7759 (mtp) cc_final: 0.7520 (ttm) REVERT: k 161 ASP cc_start: 0.8896 (p0) cc_final: 0.8686 (p0) REVERT: l 128 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8724 (tp-100) REVERT: m 174 TYR cc_start: 0.7842 (m-10) cc_final: 0.7615 (m-80) REVERT: m 195 TYR cc_start: 0.8159 (m-80) cc_final: 0.7819 (m-80) REVERT: m 293 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7804 (m) outliers start: 170 outliers final: 141 residues processed: 1034 average time/residue: 0.5222 time to fit residues: 875.2617 Evaluate side-chains 1042 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 886 time to evaluate : 4.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 187 ASP Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 133 ASP Chi-restraints excluded: chain I residue 158 SER Chi-restraints excluded: chain I residue 210 ASP Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 331 GLN Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 192 ASP Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 137 VAL Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain b residue 231 ILE Chi-restraints excluded: chain c residue 9 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 190 ASN Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 95 HIS Chi-restraints excluded: chain i residue 102 GLN Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 186 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 10.0000 chunk 574 optimal weight: 0.4980 chunk 524 optimal weight: 0.9990 chunk 558 optimal weight: 0.8980 chunk 336 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 438 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 504 optimal weight: 7.9990 chunk 528 optimal weight: 0.9990 chunk 556 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 186 HIS d 223 GLN e 252 GLN h 135 ASN h 266 GLN ** k 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 130 GLN m 303 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 50354 Z= 0.161 Angle : 0.526 8.936 68116 Z= 0.277 Chirality : 0.043 0.252 7560 Planarity : 0.004 0.051 8826 Dihedral : 6.377 87.196 7116 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.92 % Allowed : 15.57 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 6304 helix: 1.21 (0.11), residues: 2238 sheet: -0.41 (0.13), residues: 1492 loop : -1.27 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.007 0.001 HIS K 76 PHE 0.020 0.001 PHE a 180 TYR 0.025 0.001 TYR k 128 ARG 0.008 0.000 ARG f 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 935 time to evaluate : 4.236 Fit side-chains REVERT: A 49 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8844 (t) REVERT: A 52 LEU cc_start: 0.8075 (pp) cc_final: 0.7676 (mt) REVERT: A 97 ASP cc_start: 0.7015 (m-30) cc_final: 0.6653 (m-30) REVERT: A 215 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7280 (mmtm) REVERT: B 205 ASN cc_start: 0.7935 (t0) cc_final: 0.7483 (t0) REVERT: B 231 ILE cc_start: 0.5497 (OUTLIER) cc_final: 0.5291 (pp) REVERT: C 29 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7393 (mt0) REVERT: C 196 LEU cc_start: 0.7648 (mt) cc_final: 0.7355 (mt) REVERT: D 4 ASP cc_start: 0.7451 (p0) cc_final: 0.6588 (p0) REVERT: D 46 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6383 (tm-30) REVERT: D 182 ARG cc_start: 0.7179 (tmm-80) cc_final: 0.6566 (tmt170) REVERT: E 142 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7683 (p) REVERT: E 162 SER cc_start: 0.7965 (p) cc_final: 0.7588 (t) REVERT: E 278 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7348 (mm110) REVERT: E 293 GLU cc_start: 0.7327 (tt0) cc_final: 0.6700 (tp30) REVERT: E 314 ASN cc_start: 0.6578 (t0) cc_final: 0.6232 (t0) REVERT: F 290 LYS cc_start: 0.7951 (mmtm) cc_final: 0.6708 (mtmt) REVERT: G 41 CYS cc_start: 0.7546 (t) cc_final: 0.7178 (t) REVERT: G 64 ASN cc_start: 0.8673 (m-40) cc_final: 0.8394 (m110) REVERT: G 97 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7119 (mt-10) REVERT: G 101 ASP cc_start: 0.7403 (m-30) cc_final: 0.7070 (m-30) REVERT: G 105 THR cc_start: 0.8610 (t) cc_final: 0.8369 (p) REVERT: G 115 ARG cc_start: 0.7512 (mmt90) cc_final: 0.6879 (mtt180) REVERT: G 188 GLU cc_start: 0.5712 (pt0) cc_final: 0.5357 (pt0) REVERT: G 221 ASP cc_start: 0.7826 (t70) cc_final: 0.7399 (t70) REVERT: I 242 LYS cc_start: 0.6736 (tttt) cc_final: 0.6245 (tppt) REVERT: J 12 MET cc_start: 0.7886 (ttp) cc_final: 0.7573 (ttp) REVERT: J 18 GLU cc_start: 0.6802 (pm20) cc_final: 0.6529 (pm20) REVERT: J 32 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.6611 (mt) REVERT: J 189 ILE cc_start: 0.7814 (pt) cc_final: 0.7436 (mp) REVERT: J 203 ARG cc_start: 0.8298 (mtp85) cc_final: 0.8092 (mtp85) REVERT: K 31 ASP cc_start: 0.7861 (t0) cc_final: 0.7658 (t0) REVERT: K 129 MET cc_start: 0.7730 (mtp) cc_final: 0.7503 (ttm) REVERT: L 128 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8735 (tp-100) REVERT: L 186 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8549 (m) REVERT: M 195 TYR cc_start: 0.8099 (m-80) cc_final: 0.7811 (m-80) REVERT: N 40 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8135 (pp) REVERT: N 65 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7139 (m-30) REVERT: N 195 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7365 (mmt-90) REVERT: a 18 SER cc_start: 0.8709 (m) cc_final: 0.8488 (p) REVERT: a 97 ASP cc_start: 0.6947 (m-30) cc_final: 0.6698 (m-30) REVERT: b 21 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7082 (mm-30) REVERT: b 205 ASN cc_start: 0.7970 (t0) cc_final: 0.7577 (t0) REVERT: c 29 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7378 (mt0) REVERT: c 183 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7043 (mttt) REVERT: c 196 LEU cc_start: 0.7696 (mt) cc_final: 0.7418 (mt) REVERT: c 237 LYS cc_start: 0.7103 (tppt) cc_final: 0.6657 (tptm) REVERT: c 262 ASP cc_start: 0.7449 (p0) cc_final: 0.7240 (p0) REVERT: d 4 ASP cc_start: 0.7301 (p0) cc_final: 0.6490 (p0) REVERT: d 46 GLU cc_start: 0.6395 (tm-30) cc_final: 0.5812 (tm-30) REVERT: d 92 GLN cc_start: 0.5464 (mm-40) cc_final: 0.5110 (tm-30) REVERT: d 213 GLU cc_start: 0.6489 (pt0) cc_final: 0.6134 (tp30) REVERT: e 278 GLN cc_start: 0.7602 (mm-40) cc_final: 0.7214 (mm110) REVERT: e 293 GLU cc_start: 0.7182 (tt0) cc_final: 0.6588 (tp30) REVERT: e 314 ASN cc_start: 0.6860 (t0) cc_final: 0.6575 (t0) REVERT: g 41 CYS cc_start: 0.7419 (t) cc_final: 0.7061 (t) REVERT: g 64 ASN cc_start: 0.8627 (m-40) cc_final: 0.8364 (m110) REVERT: g 101 ASP cc_start: 0.7330 (m-30) cc_final: 0.7025 (m-30) REVERT: g 105 THR cc_start: 0.8581 (t) cc_final: 0.8352 (p) REVERT: g 115 ARG cc_start: 0.7539 (mmt90) cc_final: 0.6978 (mtt180) REVERT: g 175 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8235 (mt-10) REVERT: g 221 ASP cc_start: 0.7806 (t70) cc_final: 0.7421 (t70) REVERT: h 139 LYS cc_start: 0.8048 (tttm) cc_final: 0.7736 (mmtp) REVERT: i 181 LYS cc_start: 0.8265 (mttp) cc_final: 0.7834 (mttt) REVERT: j 12 MET cc_start: 0.7981 (ttp) cc_final: 0.7608 (ttp) REVERT: j 18 GLU cc_start: 0.6719 (pm20) cc_final: 0.6452 (pm20) REVERT: j 32 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6529 (mt) REVERT: j 53 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8373 (mp) REVERT: j 106 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7918 (mt-10) REVERT: k 129 MET cc_start: 0.7739 (mtp) cc_final: 0.7504 (ttm) REVERT: k 161 ASP cc_start: 0.8885 (p0) cc_final: 0.8649 (p0) REVERT: l 128 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8705 (tp-100) REVERT: m 174 TYR cc_start: 0.7845 (m-10) cc_final: 0.7604 (m-80) REVERT: m 195 TYR cc_start: 0.8127 (m-80) cc_final: 0.7795 (m-80) REVERT: m 293 THR cc_start: 0.8140 (OUTLIER) cc_final: 0.7796 (m) REVERT: m 303 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7234 (m-40) outliers start: 153 outliers final: 119 residues processed: 1031 average time/residue: 0.5255 time to fit residues: 880.1786 Evaluate side-chains 1029 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 896 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 331 GLN Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 190 ASN Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 102 GLN Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 303 ASN Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 6.9990 chunk 590 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 chunk 619 optimal weight: 0.9990 chunk 570 optimal weight: 0.9980 chunk 493 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 381 optimal weight: 6.9990 chunk 302 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 HIS H 135 ASN H 266 GLN M 130 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 340 HIS h 135 ASN h 266 GLN m 234 ASN m 303 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 50354 Z= 0.236 Angle : 0.566 9.432 68116 Z= 0.298 Chirality : 0.044 0.241 7560 Planarity : 0.004 0.052 8826 Dihedral : 6.480 88.935 7116 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.96 % Allowed : 15.90 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 6304 helix: 1.18 (0.11), residues: 2248 sheet: -0.44 (0.13), residues: 1486 loop : -1.27 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 146 HIS 0.006 0.001 HIS k 76 PHE 0.021 0.001 PHE A 180 TYR 0.033 0.001 TYR h 218 ARG 0.009 0.000 ARG m 337 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12608 Ramachandran restraints generated. 6304 Oldfield, 0 Emsley, 6304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 900 time to evaluate : 4.301 Fit side-chains REVERT: A 97 ASP cc_start: 0.7019 (m-30) cc_final: 0.6694 (m-30) REVERT: A 215 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7280 (mmtm) REVERT: B 205 ASN cc_start: 0.7957 (t0) cc_final: 0.7662 (t0) REVERT: B 231 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5327 (pp) REVERT: C 29 GLN cc_start: 0.7694 (mm-40) cc_final: 0.7481 (mt0) REVERT: C 196 LEU cc_start: 0.7647 (mt) cc_final: 0.7367 (mt) REVERT: C 262 ASP cc_start: 0.7421 (p0) cc_final: 0.7190 (p0) REVERT: D 4 ASP cc_start: 0.7470 (p0) cc_final: 0.6638 (p0) REVERT: D 46 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6314 (tm-30) REVERT: D 182 ARG cc_start: 0.7229 (tmm-80) cc_final: 0.6647 (tmt170) REVERT: E 142 THR cc_start: 0.7908 (OUTLIER) cc_final: 0.7668 (p) REVERT: E 162 SER cc_start: 0.7920 (p) cc_final: 0.7562 (t) REVERT: E 293 GLU cc_start: 0.7368 (tt0) cc_final: 0.6747 (tp30) REVERT: E 314 ASN cc_start: 0.6642 (t0) cc_final: 0.6252 (t0) REVERT: F 290 LYS cc_start: 0.8019 (mmtm) cc_final: 0.6737 (mtmt) REVERT: G 41 CYS cc_start: 0.7591 (t) cc_final: 0.7238 (t) REVERT: G 64 ASN cc_start: 0.8694 (m-40) cc_final: 0.8403 (m110) REVERT: G 97 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7163 (mt-10) REVERT: G 101 ASP cc_start: 0.7471 (m-30) cc_final: 0.7061 (m-30) REVERT: G 105 THR cc_start: 0.8625 (t) cc_final: 0.8364 (p) REVERT: G 115 ARG cc_start: 0.7546 (mmt90) cc_final: 0.6889 (mtt180) REVERT: G 188 GLU cc_start: 0.5760 (pt0) cc_final: 0.5399 (pt0) REVERT: G 221 ASP cc_start: 0.7823 (t70) cc_final: 0.7396 (t70) REVERT: H 139 LYS cc_start: 0.8429 (mmtp) cc_final: 0.8188 (mmmm) REVERT: I 181 LYS cc_start: 0.8351 (mttp) cc_final: 0.7833 (mttt) REVERT: I 215 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8218 (p) REVERT: I 242 LYS cc_start: 0.6810 (tttt) cc_final: 0.6280 (tppt) REVERT: J 18 GLU cc_start: 0.6841 (pm20) cc_final: 0.6563 (pm20) REVERT: J 32 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6640 (mt) REVERT: J 189 ILE cc_start: 0.7849 (pt) cc_final: 0.7442 (mp) REVERT: K 31 ASP cc_start: 0.7916 (t0) cc_final: 0.7700 (t0) REVERT: K 129 MET cc_start: 0.7742 (mtp) cc_final: 0.7525 (ttm) REVERT: L 128 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8770 (tp-100) REVERT: M 195 TYR cc_start: 0.8177 (m-80) cc_final: 0.7803 (m-80) REVERT: N 40 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8319 (pp) REVERT: N 65 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: N 195 ARG cc_start: 0.7582 (ttm-80) cc_final: 0.7348 (mmt-90) REVERT: a 18 SER cc_start: 0.8746 (m) cc_final: 0.8479 (p) REVERT: a 97 ASP cc_start: 0.6966 (m-30) cc_final: 0.6738 (m-30) REVERT: b 21 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7109 (mm-30) REVERT: b 205 ASN cc_start: 0.7978 (t0) cc_final: 0.7577 (t0) REVERT: c 29 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7469 (mt0) REVERT: c 183 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7079 (mttt) REVERT: c 196 LEU cc_start: 0.7702 (mt) cc_final: 0.7429 (mt) REVERT: c 237 LYS cc_start: 0.7134 (tppt) cc_final: 0.6685 (tptm) REVERT: d 4 ASP cc_start: 0.7360 (p0) cc_final: 0.6500 (p0) REVERT: d 46 GLU cc_start: 0.6384 (tm-30) cc_final: 0.5978 (tm-30) REVERT: d 92 GLN cc_start: 0.5583 (mm-40) cc_final: 0.5209 (tm-30) REVERT: d 182 ARG cc_start: 0.6840 (tmm160) cc_final: 0.6541 (tmm160) REVERT: d 213 GLU cc_start: 0.6483 (pt0) cc_final: 0.6091 (tp30) REVERT: e 142 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7528 (p) REVERT: e 278 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7410 (mm-40) REVERT: e 293 GLU cc_start: 0.7216 (tt0) cc_final: 0.6804 (tp30) REVERT: e 314 ASN cc_start: 0.6907 (t0) cc_final: 0.6568 (t0) REVERT: g 41 CYS cc_start: 0.7514 (t) cc_final: 0.7167 (t) REVERT: g 64 ASN cc_start: 0.8635 (m-40) cc_final: 0.8361 (m110) REVERT: g 101 ASP cc_start: 0.7325 (m-30) cc_final: 0.7023 (m-30) REVERT: g 105 THR cc_start: 0.8598 (t) cc_final: 0.8320 (p) REVERT: g 115 ARG cc_start: 0.7556 (mmt90) cc_final: 0.6992 (mtt180) REVERT: g 175 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8231 (mt-10) REVERT: g 221 ASP cc_start: 0.7848 (t70) cc_final: 0.7453 (t70) REVERT: h 139 LYS cc_start: 0.8076 (tttm) cc_final: 0.7728 (mmtp) REVERT: i 156 MET cc_start: 0.7780 (mmm) cc_final: 0.6993 (mtt) REVERT: i 181 LYS cc_start: 0.8303 (mttp) cc_final: 0.7867 (mttt) REVERT: j 12 MET cc_start: 0.8026 (ttp) cc_final: 0.7654 (ttp) REVERT: j 18 GLU cc_start: 0.6745 (pm20) cc_final: 0.6464 (pm20) REVERT: j 32 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6651 (mt) REVERT: j 106 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7983 (mt-10) REVERT: k 129 MET cc_start: 0.7704 (mtp) cc_final: 0.7468 (ttm) REVERT: l 128 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8756 (tp-100) REVERT: m 174 TYR cc_start: 0.7861 (m-10) cc_final: 0.7633 (m-80) REVERT: m 195 TYR cc_start: 0.8231 (m-80) cc_final: 0.7881 (m-80) REVERT: m 293 THR cc_start: 0.8121 (OUTLIER) cc_final: 0.7798 (m) outliers start: 155 outliers final: 134 residues processed: 1005 average time/residue: 0.5220 time to fit residues: 850.2411 Evaluate side-chains 1029 residues out of total 5240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 883 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 220 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 247 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 205 LYS Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain H residue 271 SER Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 215 THR Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 247 SER Chi-restraints excluded: chain L residue 253 ASP Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 331 GLN Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 65 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 215 LYS Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 ASP Chi-restraints excluded: chain b residue 58 SER Chi-restraints excluded: chain b residue 165 SER Chi-restraints excluded: chain b residue 212 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 183 LYS Chi-restraints excluded: chain d residue 8 THR Chi-restraints excluded: chain d residue 35 VAL Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain d residue 209 LEU Chi-restraints excluded: chain e residue 142 THR Chi-restraints excluded: chain e residue 164 MET Chi-restraints excluded: chain e residue 171 ASP Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 178 MET Chi-restraints excluded: chain e residue 234 SER Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 243 VAL Chi-restraints excluded: chain g residue 11 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 134 CYS Chi-restraints excluded: chain g residue 170 THR Chi-restraints excluded: chain g residue 200 VAL Chi-restraints excluded: chain h residue 135 ASN Chi-restraints excluded: chain h residue 164 SER Chi-restraints excluded: chain h residue 175 VAL Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 271 SER Chi-restraints excluded: chain i residue 53 SER Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 66 MET Chi-restraints excluded: chain i residue 95 HIS Chi-restraints excluded: chain i residue 102 GLN Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 158 SER Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 214 LEU Chi-restraints excluded: chain i residue 219 ASP Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 124 THR Chi-restraints excluded: chain j residue 147 HIS Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain k residue 63 CYS Chi-restraints excluded: chain l residue 112 ILE Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 128 GLN Chi-restraints excluded: chain l residue 129 THR Chi-restraints excluded: chain l residue 186 THR Chi-restraints excluded: chain l residue 198 THR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 247 SER Chi-restraints excluded: chain l residue 292 THR Chi-restraints excluded: chain m residue 145 VAL Chi-restraints excluded: chain m residue 234 ASN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 253 VAL Chi-restraints excluded: chain m residue 293 THR Chi-restraints excluded: chain m residue 329 VAL Chi-restraints excluded: chain m residue 331 GLN Chi-restraints excluded: chain n residue 6 SER Chi-restraints excluded: chain n residue 16 VAL Chi-restraints excluded: chain n residue 35 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 103 LEU Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain n residue 215 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 2.9990 chunk 525 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 454 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 137 optimal weight: 0.3980 chunk 494 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 507 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 ASN M 130 GLN ** M 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 135 ASN l 108 ASN ** m 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127362 restraints weight = 58045.906| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.70 r_work: 0.3310 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 50354 Z= 0.230 Angle : 0.645 59.199 68116 Z= 0.358 Chirality : 0.044 0.520 7560 Planarity : 0.004 0.132 8826 Dihedral : 6.480 88.981 7116 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.90 % Allowed : 15.99 % Favored : 81.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 6304 helix: 1.18 (0.11), residues: 2250 sheet: -0.43 (0.13), residues: 1486 loop : -1.27 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 185 HIS 0.005 0.001 HIS k 76 PHE 0.020 0.001 PHE A 180 TYR 0.032 0.001 TYR h 218 ARG 0.008 0.000 ARG m 337 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15141.46 seconds wall clock time: 261 minutes 39.31 seconds (15699.31 seconds total)