Starting phenix.real_space_refine on Tue Sep 24 00:15:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tcz_10462/09_2024/6tcz_10462.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians S 326 5.16 5 C 30952 2.51 5 N 8496 2.21 5 O 9472 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 394 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49248 Number of models: 1 Model: "" Number of chains: 30 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: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1577 Classifications: {'peptide': 202} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 199} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'N2E': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'N2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.69, per 1000 atoms: 0.46 Number of scatterers: 49248 At special positions: 0 Unit cell: (138.876, 188.292, 133.764, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 326 16.00 F 2 9.00 O 9472 8.00 N 8496 7.00 C 30952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.17 Conformation dependent library (CDL) restraints added in 4.6 seconds 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 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: 178 helices and 70 sheets defined 38.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.868A pdb=" N VAL A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 30' Processing helix chain 'A' and resid 80 through 103 removed outlier: 3.561A pdb=" N ARG A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 123 removed outlier: 3.789A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.524A pdb=" N ALA A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 235 through 247 removed outlier: 4.093A pdb=" N GLU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.965A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 96 " --> pdb=" O CYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.838A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.617A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.641A pdb=" N ALA B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.658A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 231 No H-bonds generated for 'chain 'B' and resid 230 through 231' Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.938A pdb=" N TYR C 5 " --> pdb=" O SER C 2 " (cutoff:3.500A) removed outlier: 3.635A 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 29 Processing helix chain 'C' and resid 85 through 108 removed outlier: 3.719A pdb=" N TYR C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.658A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 190 through 207 Processing helix chain 'C' and resid 230 through 234 Processing helix chain 'C' and resid 250 through 271 removed outlier: 3.596A pdb=" N LEU C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix removed outlier: 3.701A pdb=" N ARG C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 28 removed outlier: 3.615A pdb=" N LYS D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 98 removed outlier: 3.502A pdb=" N LYS D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 119 removed outlier: 3.516A pdb=" N LEU D 107 " --> pdb=" O ASP D 103 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 173 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.848A pdb=" N VAL D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 241 removed outlier: 3.598A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 228 " --> pdb=" O LYS D 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 removed outlier: 3.552A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 160 through 164 Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.858A pdb=" N ALA E 185 " --> pdb=" O MET E 181 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 221 removed outlier: 3.734A pdb=" N LEU E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) 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: 4.041A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 305 Processing helix chain 'E' and resid 331 through 340 Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.857A pdb=" N GLU F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 264 removed outlier: 4.456A pdb=" N VAL F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 252 " --> pdb=" O VAL F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 4.075A pdb=" N ASP F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 341 removed outlier: 4.381A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 361 Processing helix chain 'F' and resid 371 through 375 removed outlier: 4.087A pdb=" N THR F 375 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 399 removed outlier: 4.161A pdb=" N ARG F 395 " --> pdb=" O GLU F 391 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'G' and resid 81 through 102 removed outlier: 3.517A pdb=" N ASN G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER G 99 " --> pdb=" O GLU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'G' and resid 169 through 175 removed outlier: 3.513A pdb=" N GLU G 175 " --> pdb=" O VAL G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 179 removed outlier: 3.566A pdb=" N LEU G 179 " --> pdb=" O LEU G 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 176 through 179' Processing helix chain 'G' and resid 185 through 201 removed outlier: 4.644A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 228 through 232 removed outlier: 3.838A pdb=" N VAL G 232 " --> pdb=" O ALA G 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 removed outlier: 3.834A pdb=" N THR H 106 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 144 removed outlier: 4.158A pdb=" N ALA H 133 " --> pdb=" O ASN H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 188 removed outlier: 3.852A 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: 4.185A pdb=" N ALA H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR H 197 " --> pdb=" O PHE H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 221 removed outlier: 4.209A pdb=" N ARG H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 248 removed outlier: 3.741A pdb=" N ARG H 247 " --> pdb=" O PRO H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.717A pdb=" N VAL H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 removed outlier: 3.514A pdb=" N THR I 85 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.501A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.080A pdb=" N GLN I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 169 " --> pdb=" O ALA I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 removed outlier: 3.956A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 98 removed outlier: 4.167A pdb=" N ALA J 98 " --> pdb=" O MET J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.576A pdb=" N ALA J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 177 removed outlier: 4.129A pdb=" N GLU J 165 " --> pdb=" O GLU J 161 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 71 Processing helix chain 'K' and resid 78 through 94 removed outlier: 3.988A pdb=" N ILE K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 147 through 170 removed outlier: 3.503A pdb=" N ARG L 163 " --> pdb=" O GLY L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 removed outlier: 3.939A pdb=" N LEU L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR L 189 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 240 removed outlier: 4.261A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 266 removed outlier: 3.599A pdb=" N HIS L 261 " --> pdb=" O ARG L 257 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG L 265 " --> pdb=" O HIS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 299 removed outlier: 3.596A pdb=" N TYR L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG L 297 " --> pdb=" O LYS L 293 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 204 removed outlier: 3.782A pdb=" N GLN M 191 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.813A 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 Processing helix chain 'M' and resid 293 through 309 Processing helix chain 'N' and resid 52 through 74 removed outlier: 3.868A pdb=" N PHE N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU N 68 " --> pdb=" O GLU N 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS N 74 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 98 removed outlier: 3.624A pdb=" N ASP N 98 " --> pdb=" O GLN N 94 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 140 removed outlier: 3.726A pdb=" N ALA N 139 " --> pdb=" O GLY N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 152 removed outlier: 4.479A pdb=" N LEU N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 177 removed outlier: 3.904A pdb=" N ILE N 165 " --> pdb=" O GLU N 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL N 172 " --> pdb=" O ASP N 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 208 through 212 removed outlier: 3.514A pdb=" N TYR N 211 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 25 Processing helix chain 'a' and resid 25 through 30 removed outlier: 3.869A pdb=" N VAL a 29 " --> pdb=" O ALA a 25 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR a 30 " --> pdb=" O PHE a 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 25 through 30' Processing helix chain 'a' and resid 80 through 103 removed outlier: 3.561A pdb=" N ARG a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 123 removed outlier: 3.789A pdb=" N ARG a 122 " --> pdb=" O LYS a 118 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR a 123 " --> pdb=" O ALA a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 186 removed outlier: 3.524A pdb=" N ALA a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 193 Processing helix chain 'a' and resid 194 through 211 Processing helix chain 'a' and resid 215 through 217 No H-bonds generated for 'chain 'a' and resid 215 through 217' Processing helix chain 'a' and resid 235 through 247 removed outlier: 4.093A pdb=" N GLU a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 27 Processing helix chain 'b' and resid 77 through 100 removed outlier: 3.966A pdb=" N VAL b 83 " --> pdb=" O PRO b 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU b 84 " --> pdb=" O ASP b 80 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS b 90 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS b 96 " --> pdb=" O CYS b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 120 removed outlier: 3.839A pdb=" N ILE b 115 " --> pdb=" O LYS b 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR b 116 " --> pdb=" O ILE b 112 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN b 117 " --> pdb=" O SER b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 176 removed outlier: 3.617A pdb=" N ALA b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS b 174 " --> pdb=" O ALA b 170 " (cutoff:3.500A) Processing helix chain 'b' and resid 181 through 195 removed outlier: 3.641A pdb=" N ALA b 185 " --> pdb=" O GLU b 181 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 229 removed outlier: 3.659A pdb=" N TYR b 227 " --> pdb=" O GLN b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 230 through 231 No H-bonds generated for 'chain 'b' and resid 230 through 231' Processing helix chain 'c' and resid 2 through 6 removed outlier: 3.937A pdb=" N TYR c 5 " --> pdb=" O SER c 2 " (cutoff:3.500A) removed outlier: 3.636A 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 29 Processing helix chain 'c' and resid 85 through 108 removed outlier: 3.720A pdb=" N TYR c 90 " --> pdb=" O THR c 86 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA c 91 " --> pdb=" O SER c 87 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN c 104 " --> pdb=" O ALA c 100 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 120 Processing helix chain 'c' and resid 120 through 127 removed outlier: 3.657A pdb=" N LYS c 124 " --> pdb=" O LEU c 120 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR c 127 " --> pdb=" O GLU c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 173 through 182 Processing helix chain 'c' and resid 190 through 207 Processing helix chain 'c' and resid 230 through 234 Processing helix chain 'c' and resid 250 through 271 removed outlier: 3.595A pdb=" N LEU c 254 " --> pdb=" O THR c 250 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS c 255 " --> pdb=" O ARG c 251 " (cutoff:3.500A) Proline residue: c 256 - end of helix removed outlier: 3.700A pdb=" N ARG c 260 " --> pdb=" O PRO c 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA c 271 " --> pdb=" O ALA c 267 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 28 removed outlier: 3.615A pdb=" N LYS d 27 " --> pdb=" O GLN d 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 28 " --> pdb=" O GLU d 24 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 98 removed outlier: 3.502A pdb=" N LYS d 86 " --> pdb=" O VAL d 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 119 removed outlier: 3.516A pdb=" N LEU d 107 " --> pdb=" O ASP d 103 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR d 119 " --> pdb=" O GLN d 115 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 173 Processing helix chain 'd' and resid 181 through 194 removed outlier: 3.848A pdb=" N VAL d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS d 187 " --> pdb=" O ASP d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 218 through 241 removed outlier: 3.598A pdb=" N PHE d 225 " --> pdb=" O GLU d 221 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU d 228 " --> pdb=" O LYS d 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 130 removed outlier: 3.553A pdb=" N GLU e 129 " --> pdb=" O GLU e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 134 Processing helix chain 'e' and resid 160 through 164 Processing helix chain 'e' and resid 181 through 204 removed outlier: 3.858A pdb=" N ALA e 185 " --> pdb=" O MET e 181 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG e 186 " --> pdb=" O VAL e 182 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE e 187 " --> pdb=" O ALA e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 208 through 221 removed outlier: 3.734A pdb=" N LEU e 219 " --> pdb=" O ALA e 215 " (cutoff:3.500A) 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: 4.041A pdb=" N GLU e 283 " --> pdb=" O SER e 279 " (cutoff:3.500A) Processing helix chain 'e' and resid 290 through 305 Processing helix chain 'e' and resid 331 through 340 Processing helix chain 'f' and resid 183 through 194 removed outlier: 3.858A pdb=" N GLU f 191 " --> pdb=" O GLU f 187 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL f 193 " --> pdb=" O ALA f 189 " (cutoff:3.500A) Processing helix chain 'f' and resid 242 through 264 removed outlier: 4.456A pdb=" N VAL f 248 " --> pdb=" O ALA f 244 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR f 252 " --> pdb=" O VAL f 248 " (cutoff:3.500A) Processing helix chain 'f' and resid 269 through 283 removed outlier: 4.075A pdb=" N ASP f 275 " --> pdb=" O ASN f 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 330 through 341 removed outlier: 4.381A pdb=" N ARG f 339 " --> pdb=" O THR f 335 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS f 340 " --> pdb=" O TYR f 336 " (cutoff:3.500A) Processing helix chain 'f' and resid 348 through 361 Processing helix chain 'f' and resid 371 through 375 removed outlier: 4.087A pdb=" N THR f 375 " --> pdb=" O VAL f 372 " (cutoff:3.500A) Processing helix chain 'f' and resid 390 through 399 removed outlier: 4.161A pdb=" N ARG f 395 " --> pdb=" O GLU f 391 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS f 396 " --> pdb=" O GLU f 392 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR f 397 " --> pdb=" O SER f 393 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 32 Processing helix chain 'g' and resid 81 through 102 removed outlier: 3.518A pdb=" N ASN g 98 " --> pdb=" O GLN g 94 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER g 99 " --> pdb=" O GLU g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 122 Processing helix chain 'g' and resid 169 through 175 removed outlier: 3.513A pdb=" N GLU g 175 " --> pdb=" O VAL g 171 " (cutoff:3.500A) Processing helix chain 'g' and resid 176 through 179 removed outlier: 3.566A pdb=" N LEU g 179 " --> pdb=" O LEU g 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 176 through 179' Processing helix chain 'g' and resid 185 through 201 removed outlier: 4.644A pdb=" N GLY g 191 " --> pdb=" O ASP g 187 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA g 194 " --> pdb=" O VAL g 190 " (cutoff:3.500A) Processing helix chain 'g' and resid 219 through 221 No H-bonds generated for 'chain 'g' and resid 219 through 221' Processing helix chain 'g' and resid 228 through 232 removed outlier: 3.838A pdb=" N VAL g 232 " --> pdb=" O ALA g 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 125 removed outlier: 3.833A pdb=" N THR h 106 " --> pdb=" O SER h 102 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER h 119 " --> pdb=" O ASN h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 144 removed outlier: 4.159A pdb=" N ALA h 133 " --> pdb=" O ASN h 129 " (cutoff:3.500A) Processing helix chain 'h' and resid 185 through 188 removed outlier: 3.851A 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: 4.186A pdb=" N ALA h 195 " --> pdb=" O SER h 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR h 197 " --> pdb=" O PHE h 193 " (cutoff:3.500A) Processing helix chain 'h' and resid 202 through 221 removed outlier: 4.210A pdb=" N ARG h 220 " --> pdb=" O HIS h 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 244 through 248 removed outlier: 3.740A pdb=" N ARG h 247 " --> pdb=" O PRO h 244 " (cutoff:3.500A) Processing helix chain 'h' and resid 255 through 259 removed outlier: 3.718A pdb=" N VAL h 259 " --> pdb=" O PRO h 256 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 100 removed outlier: 3.514A pdb=" N THR i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 119 removed outlier: 3.501A pdb=" N ALA i 108 " --> pdb=" O ARG i 104 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR i 119 " --> pdb=" O HIS i 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 159 through 171 removed outlier: 4.081A pdb=" N GLN i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA i 169 " --> pdb=" O ALA i 165 " (cutoff:3.500A) Processing helix chain 'i' and resid 176 through 195 removed outlier: 3.956A pdb=" N GLY i 191 " --> pdb=" O ALA i 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE i 193 " --> pdb=" O ARG i 189 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 78 Processing helix chain 'j' and resid 83 through 98 removed outlier: 4.167A pdb=" N ALA j 98 " --> pdb=" O MET j 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 142 through 154 removed outlier: 3.575A pdb=" N ALA j 152 " --> pdb=" O GLY j 148 " (cutoff:3.500A) Processing helix chain 'j' and resid 159 through 177 removed outlier: 4.129A pdb=" N GLU j 165 " --> pdb=" O GLU j 161 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG j 177 " --> pdb=" O SER j 173 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 71 Processing helix chain 'k' and resid 78 through 94 removed outlier: 3.989A pdb=" N ILE k 94 " --> pdb=" O LEU k 90 " (cutoff:3.500A) Processing helix chain 'k' and resid 146 through 158 Processing helix chain 'k' and resid 163 through 182 Processing helix chain 'l' and resid 147 through 170 removed outlier: 3.515A pdb=" N ARG l 163 " --> pdb=" O GLY l 159 " (cutoff:3.500A) Processing helix chain 'l' and resid 174 through 189 removed outlier: 3.503A pdb=" N LYS l 180 " --> pdb=" O ALA l 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU l 182 " --> pdb=" O ALA l 178 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR l 189 " --> pdb=" O ILE l 185 " (cutoff:3.500A) Processing helix chain 'l' and resid 230 through 240 removed outlier: 4.237A pdb=" N GLY l 236 " --> pdb=" O ILE l 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL l 237 " --> pdb=" O TYR l 233 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR l 240 " --> pdb=" O GLY l 236 " (cutoff:3.500A) Processing helix chain 'l' and resid 247 through 266 removed outlier: 3.606A pdb=" N HIS l 261 " --> pdb=" O ARG l 257 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA l 262 " --> pdb=" O SER l 258 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG l 265 " --> pdb=" O HIS l 261 " (cutoff:3.500A) Processing helix chain 'l' and resid 291 through 299 removed outlier: 3.563A pdb=" N TYR l 295 " --> pdb=" O GLN l 291 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG l 297 " --> pdb=" O LYS l 293 " (cutoff:3.500A) Processing helix chain 'm' and resid 182 through 204 removed outlier: 3.782A pdb=" N GLN m 191 " --> pdb=" O LEU m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 210 through 225 removed outlier: 3.814A 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 Processing helix chain 'm' and resid 293 through 309 Processing helix chain 'n' and resid 52 through 74 removed outlier: 3.867A pdb=" N PHE n 56 " --> pdb=" O SER n 52 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN n 66 " --> pdb=" O GLN n 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE n 67 " --> pdb=" O VAL n 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU n 68 " --> pdb=" O GLU n 64 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS n 74 " --> pdb=" O GLN n 70 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 98 removed outlier: 3.623A pdb=" N ASP n 98 " --> pdb=" O GLN n 94 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 140 removed outlier: 3.726A pdb=" N ALA n 139 " --> pdb=" O GLY n 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 141 through 152 removed outlier: 4.480A pdb=" N LEU n 145 " --> pdb=" O ILE n 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 158 through 177 removed outlier: 3.905A pdb=" N ILE n 165 " --> pdb=" O GLU n 161 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL n 172 " --> pdb=" O ASP n 168 " (cutoff:3.500A) Processing helix chain 'n' and resid 208 through 212 removed outlier: 3.515A pdb=" N TYR n 211 " --> pdb=" O TYR n 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 5.569A pdb=" N LEU A 35 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL A 221 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.423A 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: 3.518A pdb=" N VAL B 42 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN B 207 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER B 131 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP B 154 " --> pdb=" O GLN B 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.587A 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: 6.281A pdb=" N ILE C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 140 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 156 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA9, first strand: chain 'D' and resid 63 through 66 removed outlier: 5.452A pdb=" N LYS D 64 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU D 71 " --> pdb=" O LYS D 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN D 137 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.819A pdb=" N ALA E 149 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.203A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 247 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 323 through 326 Processing sheet with id=AB4, first strand: chain 'F' and resid 228 through 229 removed outlier: 3.684A pdb=" N ASP F 303 " --> pdb=" O GLY F 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.871A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 179 through 182 Processing sheet with id=AB8, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 90 removed outlier: 4.242A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 153 through 157 removed outlier: 4.071A pdb=" N GLY I 40 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL I 202 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY I 217 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'I' and resid 63 through 67 removed outlier: 3.626A pdb=" N CYS I 72 " --> pdb=" O HIS I 64 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE I 70 " --> pdb=" O MET I 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 240 through 247 removed outlier: 4.379A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.275A pdb=" N GLU J 30 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR J 34 " --> pdb=" O GLU J 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 46 removed outlier: 3.727A pdb=" N VAL J 45 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE J 49 " --> pdb=" O VAL J 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.323A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 22 through 24 removed outlier: 6.817A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.664A pdb=" N GLN K 43 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 224 through 228 removed outlier: 6.528A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 119 through 121 removed outlier: 7.030A pdb=" N ALA L 119 " --> pdb=" O ALA L 126 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR L 124 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 133 through 135 removed outlier: 4.084A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP L 204 " --> pdb=" O GLY L 207 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 261 through 265 removed outlier: 4.993A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY M 328 " --> pdb=" O THR M 325 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 168 through 172 removed outlier: 6.619A pdb=" N THR M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 236 " --> pdb=" O TYR M 248 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 132 through 134 Processing sheet with id=AD7, first strand: chain 'N' and resid 24 through 26 removed outlier: 6.596A pdb=" N LEU N 24 " --> pdb=" O LYS N 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.682A pdb=" N ARG N 112 " --> pdb=" O GLU N 115 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 167 through 171 removed outlier: 5.568A pdb=" N LEU a 35 " --> pdb=" O GLN a 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL a 221 " --> pdb=" O VAL a 234 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 66 through 70 removed outlier: 6.422A pdb=" N ILE a 73 " --> pdb=" O VAL a 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 158 through 161 removed outlier: 3.518A pdb=" N VAL b 42 " --> pdb=" O VAL b 211 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN b 207 " --> pdb=" O ALA b 46 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER b 131 " --> pdb=" O SER b 75 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'b' and resid 63 through 67 removed outlier: 6.283A pdb=" N VAL b 70 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP b 154 " --> pdb=" O GLN b 146 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 167 through 170 removed outlier: 3.586A pdb=" N ARG c 222 " --> pdb=" O ARG c 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 71 through 75 removed outlier: 6.281A pdb=" N ILE c 78 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE c 140 " --> pdb=" O THR c 156 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR c 156 " --> pdb=" O PHE c 140 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'd' and resid 63 through 66 removed outlier: 5.452A pdb=" N LYS d 64 " --> pdb=" O LEU d 71 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU d 71 " --> pdb=" O LYS d 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN d 137 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LYS d 141 " --> pdb=" O ASN d 137 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'e' and resid 267 through 270 removed outlier: 3.819A pdb=" N ALA e 149 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'e' and resid 167 through 171 removed outlier: 6.204A pdb=" N ILE e 174 " --> pdb=" O VAL e 170 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP e 247 " --> pdb=" O GLY e 250 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU e 253 " --> pdb=" O TYR e 265 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 323 through 326 Processing sheet with id=AF3, first strand: chain 'f' and resid 228 through 229 removed outlier: 3.683A pdb=" N ASP f 303 " --> pdb=" O GLY f 306 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'g' and resid 67 through 69 removed outlier: 3.871A pdb=" N ALA g 142 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 179 through 182 Processing sheet with id=AF7, first strand: chain 'h' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'h' and resid 88 through 90 removed outlier: 4.243A pdb=" N VAL h 165 " --> pdb=" O LEU h 177 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 153 through 157 removed outlier: 4.072A pdb=" N GLY i 40 " --> pdb=" O TYR i 37 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL i 202 " --> pdb=" O GLY i 217 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY i 217 " --> pdb=" O VAL i 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 49 through 50 Processing sheet with id=AG2, first strand: chain 'i' and resid 63 through 67 removed outlier: 3.626A pdb=" N CYS i 72 " --> pdb=" O HIS i 64 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE i 70 " --> pdb=" O MET i 66 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'i' and resid 240 through 247 removed outlier: 4.221A pdb=" N LYS i 242 " --> pdb=" O LEU j 199 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS j 194 " --> pdb=" O THR j 191 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 28 through 30 removed outlier: 6.275A pdb=" N GLU j 30 " --> pdb=" O THR j 34 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR j 34 " --> pdb=" O GLU j 30 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 42 through 46 removed outlier: 3.726A pdb=" N VAL j 45 " --> pdb=" O ILE j 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE j 49 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'k' and resid 140 through 143 removed outlier: 4.323A pdb=" N VAL k 191 " --> pdb=" O ILE k 202 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 22 through 24 removed outlier: 6.817A pdb=" N ASN k 22 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'k' and resid 36 through 40 removed outlier: 6.664A pdb=" N GLN k 43 " --> pdb=" O LEU k 39 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 224 through 228 removed outlier: 6.509A pdb=" N HIS l 277 " --> pdb=" O LYS l 285 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS l 285 " --> pdb=" O HIS l 277 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N HIS l 279 " --> pdb=" O TRP l 283 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TRP l 283 " --> pdb=" O HIS l 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'l' and resid 119 through 121 removed outlier: 7.056A pdb=" N ALA l 119 " --> pdb=" O ALA l 126 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR l 124 " --> pdb=" O THR l 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'l' and resid 133 through 135 removed outlier: 4.104A pdb=" N MET l 199 " --> pdb=" O THR l 143 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP l 204 " --> pdb=" O GLY l 207 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 261 through 265 removed outlier: 4.994A pdb=" N THR m 135 " --> pdb=" O ASP m 150 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY m 328 " --> pdb=" O THR m 325 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'm' and resid 168 through 172 removed outlier: 6.619A pdb=" N THR m 175 " --> pdb=" O LEU m 171 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL m 236 " --> pdb=" O TYR m 248 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'n' and resid 132 through 134 Processing sheet with id=AH6, first strand: chain 'n' and resid 24 through 26 removed outlier: 6.596A pdb=" N LEU n 24 " --> pdb=" O LYS n 31 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'n' and resid 39 through 41 removed outlier: 3.684A pdb=" N ARG n 112 " --> pdb=" O GLU n 115 " (cutoff:3.500A) 2504 hydrogen bonds defined for protein. 7128 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: 17.10 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14490 1.33 - 1.45: 7834 1.45 - 1.57: 27352 1.57 - 1.69: 0 1.69 - 1.81: 512 Bond restraints: 50188 Sorted by residual: bond pdb=" C7 N2E L 401 " pdb=" N3 N2E L 401 " ideal model delta sigma weight residual 1.388 1.288 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C7 N2E l 401 " pdb=" N3 N2E l 401 " ideal model delta sigma weight residual 1.388 1.288 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C7 N2E l 401 " pdb=" N8 N2E l 401 " ideal model delta sigma weight residual 1.339 1.433 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C7 N2E L 401 " pdb=" N8 N2E L 401 " ideal model delta sigma weight residual 1.339 1.432 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C7 N2E l 401 " pdb=" N6 N2E l 401 " ideal model delta sigma weight residual 1.327 1.244 0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 50183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 66854 2.41 - 4.83: 958 4.83 - 7.24: 66 7.24 - 9.65: 14 9.65 - 12.07: 6 Bond angle restraints: 67898 Sorted by residual: angle pdb=" CA GLY f 236 " pdb=" C GLY f 236 " pdb=" N MET f 237 " ideal model delta sigma weight residual 114.58 118.53 -3.95 8.60e-01 1.35e+00 2.11e+01 angle pdb=" CA GLY F 236 " pdb=" C GLY F 236 " pdb=" N MET F 237 " ideal model delta sigma weight residual 114.58 118.53 -3.95 8.60e-01 1.35e+00 2.11e+01 angle pdb=" N VAL K 122 " pdb=" CA VAL K 122 " pdb=" C VAL K 122 " ideal model delta sigma weight residual 113.53 109.37 4.16 9.80e-01 1.04e+00 1.80e+01 angle pdb=" N VAL k 122 " pdb=" CA VAL k 122 " pdb=" C VAL k 122 " ideal model delta sigma weight residual 113.53 109.40 4.13 9.80e-01 1.04e+00 1.78e+01 angle pdb=" C CYS g 42 " pdb=" N LYS g 43 " pdb=" CA LYS g 43 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 ... (remaining 67893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 27079 17.88 - 35.77: 2406 35.77 - 53.65: 421 53.65 - 71.54: 146 71.54 - 89.42: 70 Dihedral angle restraints: 30122 sinusoidal: 11774 harmonic: 18348 Sorted by residual: dihedral pdb=" CA TYR k 25 " pdb=" C TYR k 25 " pdb=" N TYR k 26 " pdb=" CA TYR k 26 " ideal model delta harmonic sigma weight residual 180.00 154.10 25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA TYR K 25 " pdb=" C TYR K 25 " pdb=" N TYR K 26 " pdb=" CA TYR K 26 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+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 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 30119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4903 0.041 - 0.083: 2005 0.083 - 0.124: 564 0.124 - 0.166: 66 0.166 - 0.207: 10 Chirality restraints: 7548 Sorted by residual: chirality pdb=" CB ILE j 189 " pdb=" CA ILE j 189 " pdb=" CG1 ILE j 189 " pdb=" CG2 ILE j 189 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE J 189 " pdb=" CA ILE J 189 " pdb=" CG1 ILE J 189 " pdb=" CG2 ILE J 189 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ASP N 113 " pdb=" N ASP N 113 " pdb=" C ASP N 113 " pdb=" CB ASP N 113 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 ... (remaining 7545 not shown) Planarity restraints: 8804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO l 300 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C PRO l 300 " -0.064 2.00e-02 2.50e+03 pdb=" O PRO l 300 " 0.024 2.00e-02 2.50e+03 pdb=" N SER l 301 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER d 11 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO d 12 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO d 12 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO d 12 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 11 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO D 12 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 12 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 12 " 0.033 5.00e-02 4.00e+02 ... (remaining 8801 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 573 2.62 - 3.19: 43773 3.19 - 3.76: 72738 3.76 - 4.33: 105317 4.33 - 4.90: 180831 Nonbonded interactions: 403232 Sorted by model distance: nonbonded pdb=" OG SER H 191 " pdb=" O PHE h 188 " model vdw 2.048 3.040 nonbonded pdb=" OH TYR J 136 " pdb=" OE1 GLU J 151 " model vdw 2.068 3.040 nonbonded pdb=" OH TYR j 136 " pdb=" OE1 GLU j 151 " model vdw 2.069 3.040 nonbonded pdb=" OH TYR L 124 " pdb=" OE1 GLU M 272 " model vdw 2.069 3.040 nonbonded pdb=" OH TYR l 124 " pdb=" OE1 GLU m 272 " model vdw 2.078 3.040 ... (remaining 403227 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: 0.990 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: 1.390 Check model and map are aligned: 0.300 Set scattering table: 0.340 Process input model: 85.610 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.300 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.007 0.100 50188 Z= 0.483 Angle : 0.786 12.067 67898 Z= 0.469 Chirality : 0.047 0.207 7548 Planarity : 0.004 0.061 8804 Dihedral : 15.067 89.423 18406 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.84 % Allowed : 7.39 % Favored : 91.77 % 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: -3.18 (0.09), residues: 6306 helix: -1.65 (0.09), residues: 2196 sheet: -1.81 (0.12), residues: 1484 loop : -2.57 (0.10), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 215 HIS 0.007 0.001 HIS m 224 PHE 0.020 0.002 PHE g 22 TYR 0.017 0.002 TYR h 218 ARG 0.012 0.001 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1461 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1417 time to evaluate : 4.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.8610 (mttt) cc_final: 0.8398 (mttm) REVERT: A 77 MET cc_start: 0.8318 (mmt) cc_final: 0.7754 (mmt) REVERT: A 94 GLU cc_start: 0.7642 (tp30) cc_final: 0.7387 (tp30) REVERT: A 98 TYR cc_start: 0.8910 (t80) cc_final: 0.8557 (t80) REVERT: B 37 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8271 (mtpp) REVERT: B 56 ASP cc_start: 0.8349 (t0) cc_final: 0.7866 (t0) REVERT: B 100 ASN cc_start: 0.8813 (t0) cc_final: 0.8401 (t0) REVERT: B 107 GLN cc_start: 0.8603 (mm110) cc_final: 0.8225 (mm-40) REVERT: B 210 ARG cc_start: 0.8027 (ptt90) cc_final: 0.7613 (ptt90) REVERT: B 226 ASP cc_start: 0.6886 (t0) cc_final: 0.6427 (t0) REVERT: C 26 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 165 TRP cc_start: 0.8693 (m100) cc_final: 0.8329 (m100) REVERT: C 237 LYS cc_start: 0.8300 (tptm) cc_final: 0.8022 (tptm) REVERT: C 238 HIS cc_start: 0.6689 (t-90) cc_final: 0.6263 (t70) REVERT: C 260 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6793 (ptm160) REVERT: D 4 ASP cc_start: 0.7628 (p0) cc_final: 0.7152 (p0) REVERT: D 109 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7495 (mtm110) REVERT: D 117 LYS cc_start: 0.8838 (tttt) cc_final: 0.8618 (ttpt) REVERT: D 136 PHE cc_start: 0.8868 (m-80) cc_final: 0.8567 (m-80) REVERT: E 113 ASN cc_start: 0.8594 (m-40) cc_final: 0.8314 (m-40) REVERT: E 118 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: E 141 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7867 (ttt90) REVERT: E 231 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7390 (ptmm) REVERT: E 251 PRO cc_start: 0.9052 (Cg_exo) cc_final: 0.8776 (Cg_endo) REVERT: E 283 GLU cc_start: 0.7230 (pp20) cc_final: 0.6681 (pp20) REVERT: F 220 GLU cc_start: 0.6965 (mp0) cc_final: 0.6199 (mt-10) REVERT: F 373 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8184 (mtmt) REVERT: F 401 PHE cc_start: 0.6152 (t80) cc_final: 0.5840 (t80) REVERT: G 14 VAL cc_start: 0.9004 (t) cc_final: 0.8778 (m) REVERT: I 58 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8277 (mttp) REVERT: I 101 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8037 (mmtm) REVERT: J 201 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8422 (mtpt) REVERT: K 1 MET cc_start: 0.5875 (mmm) cc_final: 0.4927 (mmm) REVERT: L 138 ASP cc_start: 0.7137 (t0) cc_final: 0.6839 (t0) REVERT: L 166 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8161 (tm-30) REVERT: M 164 ASP cc_start: 0.8031 (t70) cc_final: 0.7770 (t0) REVERT: N 26 TYR cc_start: 0.8256 (t80) cc_final: 0.7932 (t80) REVERT: N 83 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7973 (mp0) REVERT: N 94 GLN cc_start: 0.8449 (tp40) cc_final: 0.8151 (tp40) REVERT: N 95 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8691 (mtmm) REVERT: N 163 MET cc_start: 0.7486 (tpp) cc_final: 0.7176 (tpp) REVERT: a 77 MET cc_start: 0.8311 (mmt) cc_final: 0.7842 (mmt) REVERT: a 98 TYR cc_start: 0.9035 (t80) cc_final: 0.8773 (t80) REVERT: a 141 ASP cc_start: 0.8350 (p0) cc_final: 0.8137 (p0) REVERT: b 107 GLN cc_start: 0.8497 (mm110) cc_final: 0.8112 (mm-40) REVERT: b 210 ARG cc_start: 0.7999 (ptt90) cc_final: 0.7567 (ptt90) REVERT: b 215 ARG cc_start: 0.7317 (ptt-90) cc_final: 0.6625 (ptp90) REVERT: b 226 ASP cc_start: 0.6672 (t0) cc_final: 0.6197 (t0) REVERT: c 26 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7589 (mm-30) REVERT: c 234 ASP cc_start: 0.7684 (t0) cc_final: 0.7466 (t0) REVERT: c 238 HIS cc_start: 0.6560 (t-90) cc_final: 0.5896 (t70) REVERT: d 117 LYS cc_start: 0.8846 (tttt) cc_final: 0.8643 (ttpt) REVERT: d 136 PHE cc_start: 0.8854 (m-80) cc_final: 0.8512 (m-80) REVERT: d 138 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7129 (mm-30) REVERT: d 215 ARG cc_start: 0.8460 (ttp-110) cc_final: 0.8062 (ttp80) REVERT: e 113 ASN cc_start: 0.8556 (m-40) cc_final: 0.8202 (m-40) REVERT: e 118 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: e 231 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7465 (ptmm) REVERT: e 283 GLU cc_start: 0.7376 (pp20) cc_final: 0.7141 (pp20) REVERT: f 220 GLU cc_start: 0.6803 (mp0) cc_final: 0.6186 (mp0) REVERT: f 271 ASN cc_start: 0.8645 (m110) cc_final: 0.8379 (m110) REVERT: f 302 TYR cc_start: 0.8144 (t80) cc_final: 0.7892 (t80) REVERT: f 305 GLN cc_start: 0.8438 (mt0) cc_final: 0.8127 (mp10) REVERT: f 373 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8122 (mtmt) REVERT: f 401 PHE cc_start: 0.6272 (t80) cc_final: 0.5854 (t80) REVERT: h 120 TYR cc_start: 0.9130 (t80) cc_final: 0.8908 (t80) REVERT: h 198 LYS cc_start: 0.8089 (mppt) cc_final: 0.7884 (mmtt) REVERT: i 58 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8179 (mttp) REVERT: i 101 LYS cc_start: 0.8687 (mmtp) cc_final: 0.8092 (mmpt) REVERT: i 172 LYS cc_start: 0.7806 (pttm) cc_final: 0.7598 (mttp) REVERT: i 195 ASP cc_start: 0.8061 (t70) cc_final: 0.7849 (t70) REVERT: j 3 ILE cc_start: 0.8720 (mp) cc_final: 0.8435 (mm) REVERT: j 91 ILE cc_start: 0.8696 (pt) cc_final: 0.8399 (mt) REVERT: j 201 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8258 (mtpt) REVERT: k 1 MET cc_start: 0.5929 (mmm) cc_final: 0.4918 (mmm) REVERT: k 180 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7766 (tpt90) REVERT: l 166 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8124 (tm-30) REVERT: m 152 ARG cc_start: 0.8501 (ttt180) cc_final: 0.7921 (ttt180) REVERT: m 164 ASP cc_start: 0.8039 (t70) cc_final: 0.7745 (t0) REVERT: n 83 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8002 (mt-10) REVERT: n 94 GLN cc_start: 0.8415 (tp40) cc_final: 0.8142 (tp40) REVERT: n 95 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8543 (mtmm) REVERT: n 163 MET cc_start: 0.7509 (tpp) cc_final: 0.7283 (tpp) REVERT: n 168 ASP cc_start: 0.7487 (m-30) cc_final: 0.7276 (m-30) REVERT: n 215 LYS cc_start: 0.8659 (mttm) cc_final: 0.8429 (mttt) outliers start: 44 outliers final: 11 residues processed: 1448 average time/residue: 0.5555 time to fit residues: 1272.6141 Evaluate side-chains 1076 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1061 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain a residue 97 ASP Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain e residue 118 GLU Chi-restraints excluded: chain e residue 231 LYS Chi-restraints excluded: chain f residue 245 ASP Chi-restraints excluded: chain i residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 525 optimal weight: 1.9990 chunk 471 optimal weight: 0.2980 chunk 261 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 318 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 487 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 564 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 50 GLN A 195 GLN A 207 GLN B 143 HIS B 207 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN C 257 HIS D 18 GLN E 252 GLN F 190 ASN F 194 ASN F 195 ASN F 225 GLN F 259 ASN F 271 ASN F 311 GLN F 343 HIS G 64 ASN H 63 ASN H 107 GLN H 264 GLN I 64 HIS I 201 GLN J 68 GLN J 169 GLN K 38 GLN K 64 ASN K 72 GLN K 73 HIS K 125 GLN K 136 GLN L 279 HIS M 165 GLN M 180 ASN M 244 HIS M 280 ASN M 282 GLN a 21 GLN a 50 GLN a 165 HIS a 195 GLN a 207 GLN b 143 HIS b 207 GLN c 175 GLN d 18 GLN e 252 GLN f 190 ASN f 194 ASN f 195 ASN f 225 GLN f 259 ASN f 305 GLN f 311 GLN g 64 ASN h 63 ASN h 107 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 144 ASN h 264 GLN i 64 HIS i 194 ASN ** j 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 72 GLN k 136 GLN l 279 HIS m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 244 HIS m 280 ASN m 282 GLN Total number of N/Q/H flips: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 50188 Z= 0.184 Angle : 0.553 7.771 67898 Z= 0.298 Chirality : 0.043 0.161 7548 Planarity : 0.004 0.060 8804 Dihedral : 4.944 58.975 7032 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.89 % Allowed : 14.47 % Favored : 83.65 % 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: -1.48 (0.10), residues: 6306 helix: 0.37 (0.11), residues: 2212 sheet: -1.21 (0.13), residues: 1480 loop : -1.98 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 215 HIS 0.008 0.001 HIS F 343 PHE 0.011 0.001 PHE l 105 TYR 0.019 0.001 TYR H 218 ARG 0.006 0.000 ARG a 85 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1217 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8433 (mmt) cc_final: 0.7820 (mmt) REVERT: A 94 GLU cc_start: 0.7808 (tp30) cc_final: 0.7558 (tp30) REVERT: A 98 TYR cc_start: 0.8980 (t80) cc_final: 0.8485 (t80) REVERT: A 99 GLN cc_start: 0.8355 (tp40) cc_final: 0.8047 (tp40) REVERT: A 141 ASP cc_start: 0.8088 (p0) cc_final: 0.7621 (p0) REVERT: B 56 ASP cc_start: 0.8386 (t0) cc_final: 0.7922 (t0) REVERT: B 98 MET cc_start: 0.7536 (ttm) cc_final: 0.7280 (ttt) REVERT: B 107 GLN cc_start: 0.8429 (mm110) cc_final: 0.8076 (mm-40) REVERT: B 154 TRP cc_start: 0.7417 (m-90) cc_final: 0.7050 (m100) REVERT: B 183 GLU cc_start: 0.6801 (mp0) cc_final: 0.6137 (tt0) REVERT: B 210 ARG cc_start: 0.7900 (ptt90) cc_final: 0.7497 (ptt90) REVERT: B 226 ASP cc_start: 0.6658 (t0) cc_final: 0.6262 (t0) REVERT: C 26 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7535 (mm-30) REVERT: C 116 LEU cc_start: 0.8768 (tp) cc_final: 0.8342 (tp) REVERT: C 141 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8290 (mt) REVERT: C 165 TRP cc_start: 0.8754 (m100) cc_final: 0.8314 (m100) REVERT: C 221 MET cc_start: 0.7895 (tpt) cc_final: 0.7466 (tpt) REVERT: C 238 HIS cc_start: 0.6736 (t-90) cc_final: 0.6339 (t70) REVERT: D 4 ASP cc_start: 0.7286 (p0) cc_final: 0.7070 (p0) REVERT: D 117 LYS cc_start: 0.8814 (tttt) cc_final: 0.8565 (ttpt) REVERT: D 171 TYR cc_start: 0.7105 (t80) cc_final: 0.6805 (t80) REVERT: E 189 VAL cc_start: 0.8696 (t) cc_final: 0.8427 (m) REVERT: E 338 ILE cc_start: 0.8533 (mm) cc_final: 0.8089 (mm) REVERT: F 220 GLU cc_start: 0.7046 (mp0) cc_final: 0.6353 (mt-10) REVERT: F 319 TYR cc_start: 0.8211 (m-80) cc_final: 0.7915 (m-10) REVERT: F 373 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8268 (mtmt) REVERT: F 401 PHE cc_start: 0.6147 (t80) cc_final: 0.5899 (t80) REVERT: G 175 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7890 (mm-30) REVERT: H 221 ASP cc_start: 0.8255 (t0) cc_final: 0.8039 (t0) REVERT: I 101 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8083 (mmtt) REVERT: J 118 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7568 (mt-10) REVERT: K 1 MET cc_start: 0.5755 (mmm) cc_final: 0.4938 (mmm) REVERT: K 28 LYS cc_start: 0.8729 (mtpp) cc_final: 0.8512 (ttpp) REVERT: K 179 LYS cc_start: 0.8800 (mttp) cc_final: 0.8586 (mttt) REVERT: K 180 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7750 (tpt90) REVERT: L 138 ASP cc_start: 0.7189 (t0) cc_final: 0.6954 (t0) REVERT: M 233 PHE cc_start: 0.8396 (m-80) cc_final: 0.8125 (m-80) REVERT: N 26 TYR cc_start: 0.8068 (t80) cc_final: 0.7800 (t80) REVERT: N 68 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7254 (mp0) REVERT: N 94 GLN cc_start: 0.8410 (tp40) cc_final: 0.7954 (tp40) REVERT: N 95 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8594 (mtmm) REVERT: a 27 LYS cc_start: 0.8759 (mttt) cc_final: 0.8547 (mttm) REVERT: a 77 MET cc_start: 0.8458 (mmt) cc_final: 0.7897 (mmt) REVERT: a 98 TYR cc_start: 0.9118 (t80) cc_final: 0.8779 (t80) REVERT: a 99 GLN cc_start: 0.8392 (tp40) cc_final: 0.8024 (tp40) REVERT: a 141 ASP cc_start: 0.8125 (p0) cc_final: 0.7860 (p0) REVERT: a 178 MET cc_start: 0.8520 (tpp) cc_final: 0.8051 (mmt) REVERT: b 67 ASP cc_start: 0.8366 (m-30) cc_final: 0.8126 (m-30) REVERT: b 68 GLU cc_start: 0.7617 (pp20) cc_final: 0.7285 (pm20) REVERT: b 100 ASN cc_start: 0.8715 (t0) cc_final: 0.8288 (t0) REVERT: b 107 GLN cc_start: 0.8440 (mm110) cc_final: 0.8035 (mm-40) REVERT: b 183 GLU cc_start: 0.6906 (mp0) cc_final: 0.6227 (tt0) REVERT: b 210 ARG cc_start: 0.7861 (ptt90) cc_final: 0.7481 (ptt90) REVERT: b 226 ASP cc_start: 0.6571 (t0) cc_final: 0.6153 (t0) REVERT: c 26 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7544 (mm-30) REVERT: c 69 GLU cc_start: 0.7102 (tt0) cc_final: 0.6890 (mt-10) REVERT: c 116 LEU cc_start: 0.8819 (tp) cc_final: 0.8431 (tp) REVERT: c 119 ILE cc_start: 0.9135 (tp) cc_final: 0.8782 (tt) REVERT: c 221 MET cc_start: 0.7848 (tpt) cc_final: 0.7437 (tpt) REVERT: c 238 HIS cc_start: 0.6590 (t-90) cc_final: 0.6119 (t70) REVERT: d 117 LYS cc_start: 0.8844 (tttt) cc_final: 0.8614 (ttpt) REVERT: d 120 GLN cc_start: 0.8051 (tt0) cc_final: 0.7719 (tt0) REVERT: f 220 GLU cc_start: 0.6811 (mp0) cc_final: 0.6099 (mt-10) REVERT: f 302 TYR cc_start: 0.8052 (t80) cc_final: 0.7826 (t80) REVERT: f 319 TYR cc_start: 0.8208 (m-80) cc_final: 0.7938 (m-10) REVERT: f 373 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8137 (mtmt) REVERT: f 401 PHE cc_start: 0.6105 (t80) cc_final: 0.5796 (t80) REVERT: h 120 TYR cc_start: 0.9131 (t80) cc_final: 0.8770 (t80) REVERT: h 198 LYS cc_start: 0.8071 (mppt) cc_final: 0.7846 (mmtt) REVERT: i 54 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7998 (tp) REVERT: i 71 MET cc_start: 0.7439 (mmt) cc_final: 0.7218 (mmm) REVERT: j 3 ILE cc_start: 0.8795 (mp) cc_final: 0.8463 (mm) REVERT: j 201 LYS cc_start: 0.8557 (mmtp) cc_final: 0.8266 (mtpt) REVERT: k 1 MET cc_start: 0.5821 (mmm) cc_final: 0.4972 (mmm) REVERT: k 180 ARG cc_start: 0.8021 (ttp-110) cc_final: 0.7673 (tpt90) REVERT: m 152 ARG cc_start: 0.8518 (ttt180) cc_final: 0.8047 (ttt180) REVERT: m 164 ASP cc_start: 0.7925 (t70) cc_final: 0.7670 (t0) REVERT: n 83 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7864 (mp0) REVERT: n 94 GLN cc_start: 0.8446 (tp40) cc_final: 0.8164 (tp40) REVERT: n 95 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8524 (mtmm) outliers start: 99 outliers final: 59 residues processed: 1267 average time/residue: 0.4941 time to fit residues: 1029.4367 Evaluate side-chains 1099 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1038 time to evaluate : 4.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 134 GLU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 300 MET Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain f residue 187 GLU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 78 ILE Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 134 GLU Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 313 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 470 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 565 optimal weight: 6.9990 chunk 611 optimal weight: 0.9990 chunk 503 optimal weight: 7.9990 chunk 561 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 453 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN F 194 ASN F 195 ASN F 225 GLN F 282 GLN F 311 GLN G 64 ASN I 115 HIS I 201 GLN J 26 ASN ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 137 ASN M 165 GLN M 280 ASN N 66 ASN a 51 HIS b 207 GLN e 113 ASN e 314 ASN f 195 ASN f 282 GLN f 311 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 115 HIS j 26 ASN k 68 ASN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 50188 Z= 0.447 Angle : 0.651 8.508 67898 Z= 0.347 Chirality : 0.047 0.165 7548 Planarity : 0.005 0.055 8804 Dihedral : 4.976 34.990 7010 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.95 % Allowed : 17.21 % Favored : 78.84 % 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: -1.29 (0.10), residues: 6306 helix: 0.56 (0.11), residues: 2228 sheet: -1.08 (0.13), residues: 1500 loop : -1.94 (0.11), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 215 HIS 0.014 0.001 HIS a 51 PHE 0.022 0.002 PHE j 69 TYR 0.039 0.002 TYR H 218 ARG 0.007 0.001 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1061 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8419 (mmt) cc_final: 0.7807 (mmt) REVERT: A 94 GLU cc_start: 0.7786 (tp30) cc_final: 0.7578 (tp30) REVERT: A 141 ASP cc_start: 0.8133 (p0) cc_final: 0.7744 (p0) REVERT: A 166 ILE cc_start: 0.9027 (mt) cc_final: 0.8813 (mm) REVERT: A 184 ARG cc_start: 0.8238 (tpt90) cc_final: 0.7979 (tpp-160) REVERT: B 98 MET cc_start: 0.7607 (ttm) cc_final: 0.7406 (ttp) REVERT: B 100 ASN cc_start: 0.8743 (t0) cc_final: 0.8376 (t0) REVERT: B 154 TRP cc_start: 0.7469 (m-90) cc_final: 0.7156 (m100) REVERT: B 210 ARG cc_start: 0.8003 (ptt90) cc_final: 0.7478 (ptt90) REVERT: B 215 ARG cc_start: 0.7057 (ptt-90) cc_final: 0.6441 (ptp-170) REVERT: B 226 ASP cc_start: 0.6656 (t0) cc_final: 0.6227 (t0) REVERT: C 26 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7607 (mm-30) REVERT: C 165 TRP cc_start: 0.8809 (m100) cc_final: 0.8443 (m100) REVERT: C 221 MET cc_start: 0.7992 (tpt) cc_final: 0.7499 (tpt) REVERT: C 238 HIS cc_start: 0.6778 (t-90) cc_final: 0.6427 (t70) REVERT: D 4 ASP cc_start: 0.7265 (p0) cc_final: 0.6934 (p0) REVERT: D 117 LYS cc_start: 0.8867 (tttt) cc_final: 0.8592 (ttpt) REVERT: D 120 GLN cc_start: 0.8137 (tt0) cc_final: 0.7839 (tt0) REVERT: D 230 GLU cc_start: 0.6502 (pp20) cc_final: 0.6077 (tm-30) REVERT: F 220 GLU cc_start: 0.7210 (mp0) cc_final: 0.6504 (mt-10) REVERT: F 311 GLN cc_start: 0.8465 (tt0) cc_final: 0.8260 (tt0) REVERT: F 373 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8240 (mtmt) REVERT: F 401 PHE cc_start: 0.6170 (t80) cc_final: 0.5847 (t80) REVERT: H 145 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7742 (ptt90) REVERT: J 99 ARG cc_start: 0.8754 (tmt-80) cc_final: 0.8430 (ttt-90) REVERT: J 190 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8782 (p) REVERT: K 1 MET cc_start: 0.5726 (mmm) cc_final: 0.4729 (mmm) REVERT: K 179 LYS cc_start: 0.8834 (mttp) cc_final: 0.8594 (mttt) REVERT: K 180 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7697 (tpt90) REVERT: L 138 ASP cc_start: 0.7226 (t0) cc_final: 0.6996 (t0) REVERT: M 152 ARG cc_start: 0.8332 (ttt180) cc_final: 0.7973 (ttt180) REVERT: M 164 ASP cc_start: 0.8025 (t70) cc_final: 0.7798 (t0) REVERT: N 26 TYR cc_start: 0.8180 (t80) cc_final: 0.7933 (t80) REVERT: N 68 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7372 (mp0) REVERT: N 94 GLN cc_start: 0.8371 (tp40) cc_final: 0.8057 (tp40) REVERT: a 77 MET cc_start: 0.8484 (mmt) cc_final: 0.7846 (mmt) REVERT: a 141 ASP cc_start: 0.8224 (p0) cc_final: 0.7858 (p0) REVERT: a 166 ILE cc_start: 0.9038 (mt) cc_final: 0.8826 (mm) REVERT: b 210 ARG cc_start: 0.7928 (ptt90) cc_final: 0.7472 (ptt90) REVERT: b 215 ARG cc_start: 0.7086 (ptt-90) cc_final: 0.6489 (ptp-170) REVERT: b 226 ASP cc_start: 0.6648 (t0) cc_final: 0.6169 (t0) REVERT: c 26 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7745 (mm-30) REVERT: c 165 TRP cc_start: 0.8804 (m100) cc_final: 0.8367 (m100) REVERT: c 174 ASP cc_start: 0.7332 (p0) cc_final: 0.6963 (p0) REVERT: c 221 MET cc_start: 0.7985 (tpt) cc_final: 0.7436 (tpt) REVERT: c 234 ASP cc_start: 0.7317 (t0) cc_final: 0.7098 (t70) REVERT: c 238 HIS cc_start: 0.6682 (t-90) cc_final: 0.6331 (t70) REVERT: d 17 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8005 (m-10) REVERT: d 117 LYS cc_start: 0.8863 (tttt) cc_final: 0.8612 (ttpt) REVERT: d 120 GLN cc_start: 0.8080 (tt0) cc_final: 0.7790 (tt0) REVERT: f 220 GLU cc_start: 0.7030 (mp0) cc_final: 0.6318 (mt-10) REVERT: f 247 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7248 (ptm160) REVERT: f 302 TYR cc_start: 0.8133 (t80) cc_final: 0.7918 (t80) REVERT: f 311 GLN cc_start: 0.8508 (tt0) cc_final: 0.8296 (tt0) REVERT: f 373 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8195 (mtmt) REVERT: g 32 ASP cc_start: 0.7138 (m-30) cc_final: 0.6924 (m-30) REVERT: h 120 TYR cc_start: 0.9117 (t80) cc_final: 0.8792 (t80) REVERT: j 201 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8390 (mtpt) REVERT: k 1 MET cc_start: 0.5808 (mmm) cc_final: 0.4771 (mmm) REVERT: k 125 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: k 177 GLU cc_start: 0.8454 (tp30) cc_final: 0.8110 (tp30) REVERT: k 181 ARG cc_start: 0.8807 (mmt180) cc_final: 0.8558 (tpp-160) REVERT: l 138 ASP cc_start: 0.7229 (t0) cc_final: 0.6999 (t0) REVERT: m 152 ARG cc_start: 0.8515 (ttt180) cc_final: 0.8054 (ttt180) REVERT: m 164 ASP cc_start: 0.7995 (t70) cc_final: 0.7741 (t0) REVERT: m 212 LYS cc_start: 0.7788 (ttpp) cc_final: 0.7574 (mtmm) REVERT: n 59 MET cc_start: 0.7914 (tpp) cc_final: 0.7564 (tpp) REVERT: n 83 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8006 (mt-10) REVERT: n 205 HIS cc_start: 0.6965 (m90) cc_final: 0.6750 (m90) outliers start: 207 outliers final: 146 residues processed: 1186 average time/residue: 0.5434 time to fit residues: 1072.6954 Evaluate side-chains 1128 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 978 time to evaluate : 4.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 198 LYS Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 129 GLU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 60 ILE Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 115 ASP Chi-restraints excluded: chain c residue 141 LEU Chi-restraints excluded: chain c residue 253 GLU Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 314 ASN Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 225 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 218 TYR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 242 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 32 ILE Chi-restraints excluded: chain i residue 54 ILE Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 91 ILE Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain l residue 143 THR Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 198 LYS Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 559 optimal weight: 0.7980 chunk 425 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 270 optimal weight: 0.9980 chunk 379 optimal weight: 6.9990 chunk 567 optimal weight: 1.9990 chunk 601 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 538 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN F 194 ASN F 195 ASN F 271 ASN G 23 GLN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN M 165 GLN M 280 ASN M 303 ASN N 66 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN f 194 ASN f 195 ASN ** g 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 60 GLN k 64 ASN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 303 ASN n 66 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 50188 Z= 0.203 Angle : 0.538 8.104 67898 Z= 0.287 Chirality : 0.043 0.157 7548 Planarity : 0.004 0.054 8804 Dihedral : 4.534 32.764 7008 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.17 % Allowed : 19.29 % Favored : 77.54 % 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: -0.74 (0.10), residues: 6306 helix: 1.10 (0.11), residues: 2222 sheet: -0.86 (0.13), residues: 1498 loop : -1.66 (0.11), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 215 HIS 0.005 0.001 HIS F 343 PHE 0.013 0.001 PHE K 8 TYR 0.021 0.001 TYR H 218 ARG 0.005 0.000 ARG i 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1087 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8371 (mmt) cc_final: 0.7842 (mmt) REVERT: A 87 LEU cc_start: 0.8953 (tp) cc_final: 0.8684 (tp) REVERT: A 141 ASP cc_start: 0.8029 (p0) cc_final: 0.7741 (p0) REVERT: A 184 ARG cc_start: 0.8149 (tpt90) cc_final: 0.7892 (tpp-160) REVERT: B 18 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8184 (pt) REVERT: B 98 MET cc_start: 0.7491 (ttm) cc_final: 0.7261 (ttt) REVERT: B 107 GLN cc_start: 0.8499 (mm110) cc_final: 0.8173 (mm-40) REVERT: B 210 ARG cc_start: 0.7905 (ptt90) cc_final: 0.7398 (ptt90) REVERT: B 215 ARG cc_start: 0.6764 (ptt-90) cc_final: 0.6262 (ptp-170) REVERT: B 226 ASP cc_start: 0.6684 (t0) cc_final: 0.6260 (t0) REVERT: C 26 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 141 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8278 (mt) REVERT: C 165 TRP cc_start: 0.8760 (m100) cc_final: 0.8294 (m100) REVERT: C 215 ARG cc_start: 0.6846 (ttp-170) cc_final: 0.6053 (tpt170) REVERT: C 221 MET cc_start: 0.7950 (tpt) cc_final: 0.7486 (tpt) REVERT: C 254 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7447 (tt) REVERT: D 4 ASP cc_start: 0.7236 (p0) cc_final: 0.6982 (p0) REVERT: D 117 LYS cc_start: 0.8853 (tttt) cc_final: 0.8600 (ttpt) REVERT: D 120 GLN cc_start: 0.8040 (tt0) cc_final: 0.7723 (tt0) REVERT: D 230 GLU cc_start: 0.6638 (pp20) cc_final: 0.6203 (tm-30) REVERT: E 338 ILE cc_start: 0.8343 (mm) cc_final: 0.8034 (mm) REVERT: F 220 GLU cc_start: 0.7140 (mp0) cc_final: 0.6495 (mt-10) REVERT: F 247 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6831 (ttm-80) REVERT: F 319 TYR cc_start: 0.8122 (m-80) cc_final: 0.7867 (m-10) REVERT: F 373 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8227 (mtmt) REVERT: F 401 PHE cc_start: 0.5937 (t80) cc_final: 0.5624 (t80) REVERT: G 175 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7943 (mm-30) REVERT: H 221 ASP cc_start: 0.8287 (t0) cc_final: 0.8078 (t0) REVERT: J 118 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7576 (mt-10) REVERT: K 125 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: K 179 LYS cc_start: 0.8768 (mttp) cc_final: 0.8509 (mttt) REVERT: K 180 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7613 (tpt90) REVERT: L 138 ASP cc_start: 0.7220 (t0) cc_final: 0.6936 (t0) REVERT: M 311 ARG cc_start: 0.8455 (mmm160) cc_final: 0.8192 (mmt180) REVERT: N 26 TYR cc_start: 0.8095 (t80) cc_final: 0.7768 (t80) REVERT: N 94 GLN cc_start: 0.8378 (tp40) cc_final: 0.7995 (tp40) REVERT: N 205 HIS cc_start: 0.6778 (m-70) cc_final: 0.6439 (m90) REVERT: a 77 MET cc_start: 0.8424 (mmt) cc_final: 0.7830 (mmt) REVERT: a 141 ASP cc_start: 0.8111 (p0) cc_final: 0.7702 (p0) REVERT: b 67 ASP cc_start: 0.8442 (m-30) cc_final: 0.8195 (m-30) REVERT: b 107 GLN cc_start: 0.8551 (mm110) cc_final: 0.8227 (mm-40) REVERT: b 210 ARG cc_start: 0.7897 (ptt90) cc_final: 0.7565 (ptt90) REVERT: b 215 ARG cc_start: 0.6891 (ptt-90) cc_final: 0.6311 (ptp-170) REVERT: b 226 ASP cc_start: 0.6629 (t0) cc_final: 0.6178 (t0) REVERT: c 26 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7744 (mm-30) REVERT: c 29 GLN cc_start: 0.7905 (mm110) cc_final: 0.7651 (mt0) REVERT: c 165 TRP cc_start: 0.8752 (m100) cc_final: 0.8294 (m100) REVERT: c 215 ARG cc_start: 0.6706 (ttp-170) cc_final: 0.5906 (tpt170) REVERT: c 221 MET cc_start: 0.7892 (tpt) cc_final: 0.7476 (tpt) REVERT: c 234 ASP cc_start: 0.7124 (t0) cc_final: 0.6906 (t70) REVERT: c 238 HIS cc_start: 0.6644 (t-90) cc_final: 0.6342 (t70) REVERT: c 254 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7455 (tt) REVERT: d 17 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7980 (m-10) REVERT: d 117 LYS cc_start: 0.8854 (tttt) cc_final: 0.8601 (ttpt) REVERT: d 120 GLN cc_start: 0.8019 (tt0) cc_final: 0.7719 (tt0) REVERT: d 230 GLU cc_start: 0.6452 (pp20) cc_final: 0.6024 (tm-30) REVERT: e 207 MET cc_start: 0.8561 (ttt) cc_final: 0.8329 (ttt) REVERT: f 220 GLU cc_start: 0.7006 (mp0) cc_final: 0.6200 (mt-10) REVERT: f 247 ARG cc_start: 0.7765 (tpp-160) cc_final: 0.7196 (ptm160) REVERT: f 302 TYR cc_start: 0.8074 (t80) cc_final: 0.7835 (t80) REVERT: f 305 GLN cc_start: 0.8331 (mp10) cc_final: 0.7802 (mp10) REVERT: f 319 TYR cc_start: 0.8122 (m-80) cc_final: 0.7880 (m-10) REVERT: f 373 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8102 (mtmt) REVERT: i 212 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8185 (p) REVERT: j 3 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8494 (mm) REVERT: j 99 ARG cc_start: 0.8709 (tmt-80) cc_final: 0.8449 (ttt-90) REVERT: j 118 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7587 (mt-10) REVERT: j 201 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8465 (mtpt) REVERT: k 69 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7468 (mtm-85) REVERT: m 152 ARG cc_start: 0.8374 (ttt180) cc_final: 0.7919 (ttt180) REVERT: m 164 ASP cc_start: 0.7977 (t70) cc_final: 0.7733 (t0) REVERT: n 83 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7862 (mp0) REVERT: n 94 GLN cc_start: 0.8524 (tp40) cc_final: 0.8126 (tp40) outliers start: 166 outliers final: 103 residues processed: 1184 average time/residue: 0.4968 time to fit residues: 976.3594 Evaluate side-chains 1137 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1026 time to evaluate : 4.155 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 211 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 500 optimal weight: 7.9990 chunk 341 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 447 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 513 optimal weight: 3.9990 chunk 415 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 6.9990 chunk 539 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN F 194 ASN F 195 ASN F 311 GLN G 64 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 GLN M 165 GLN M 280 ASN N 66 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN f 195 ASN f 311 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN n 66 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 50188 Z= 0.347 Angle : 0.596 9.575 67898 Z= 0.317 Chirality : 0.045 0.166 7548 Planarity : 0.004 0.054 8804 Dihedral : 4.679 32.400 7004 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.54 % Allowed : 20.10 % Favored : 75.36 % 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: -0.74 (0.10), residues: 6306 helix: 1.06 (0.11), residues: 2230 sheet: -0.80 (0.13), residues: 1492 loop : -1.66 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 215 HIS 0.006 0.001 HIS F 343 PHE 0.022 0.002 PHE f 401 TYR 0.035 0.001 TYR H 218 ARG 0.009 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1037 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8410 (mmt) cc_final: 0.7856 (mmt) REVERT: A 87 LEU cc_start: 0.8993 (tp) cc_final: 0.8734 (tp) REVERT: A 141 ASP cc_start: 0.8059 (p0) cc_final: 0.7809 (p0) REVERT: A 184 ARG cc_start: 0.8227 (tpt90) cc_final: 0.7981 (tpp-160) REVERT: B 18 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8185 (pt) REVERT: B 56 ASP cc_start: 0.8477 (t0) cc_final: 0.7983 (t0) REVERT: B 98 MET cc_start: 0.7547 (ttm) cc_final: 0.7295 (ttt) REVERT: B 107 GLN cc_start: 0.8536 (mm110) cc_final: 0.8187 (mm-40) REVERT: B 210 ARG cc_start: 0.7870 (ptt90) cc_final: 0.7406 (ptt90) REVERT: B 215 ARG cc_start: 0.6727 (ptt-90) cc_final: 0.6230 (ptp-170) REVERT: B 226 ASP cc_start: 0.6615 (t0) cc_final: 0.6155 (t0) REVERT: C 26 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 165 TRP cc_start: 0.8791 (m100) cc_final: 0.8298 (m100) REVERT: C 221 MET cc_start: 0.8006 (tpt) cc_final: 0.7482 (tpt) REVERT: C 254 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7470 (tt) REVERT: D 4 ASP cc_start: 0.7255 (p0) cc_final: 0.6931 (p0) REVERT: D 117 LYS cc_start: 0.8857 (tttt) cc_final: 0.8585 (ttpt) REVERT: D 120 GLN cc_start: 0.8103 (tt0) cc_final: 0.7798 (tt0) REVERT: D 230 GLU cc_start: 0.6763 (pp20) cc_final: 0.6441 (tm-30) REVERT: E 338 ILE cc_start: 0.8429 (mm) cc_final: 0.8068 (mm) REVERT: F 220 GLU cc_start: 0.7204 (mp0) cc_final: 0.6534 (mt-10) REVERT: F 311 GLN cc_start: 0.8386 (tt0) cc_final: 0.8181 (tt0) REVERT: F 319 TYR cc_start: 0.8083 (m-80) cc_final: 0.7818 (m-10) REVERT: F 373 LYS cc_start: 0.8665 (mmmt) cc_final: 0.8203 (mtmt) REVERT: F 401 PHE cc_start: 0.6044 (t80) cc_final: 0.5665 (t80) REVERT: G 231 MET cc_start: 0.6698 (tpt) cc_final: 0.6344 (tpp) REVERT: H 145 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7624 (ptt90) REVERT: J 126 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8525 (pt) REVERT: K 111 ASP cc_start: 0.8217 (m-30) cc_final: 0.7868 (m-30) REVERT: K 179 LYS cc_start: 0.8836 (mttp) cc_final: 0.8624 (mttm) REVERT: K 180 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7628 (tpt90) REVERT: M 164 ASP cc_start: 0.8049 (t70) cc_final: 0.7795 (t0) REVERT: M 183 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: M 311 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8226 (mmt180) REVERT: N 26 TYR cc_start: 0.8184 (t80) cc_final: 0.7888 (t80) REVERT: N 94 GLN cc_start: 0.8406 (tp40) cc_final: 0.7994 (tp-100) REVERT: a 77 MET cc_start: 0.8469 (mmt) cc_final: 0.7812 (mmt) REVERT: a 141 ASP cc_start: 0.8137 (p0) cc_final: 0.7705 (p0) REVERT: b 100 ASN cc_start: 0.8663 (t0) cc_final: 0.8291 (t0) REVERT: b 107 GLN cc_start: 0.8578 (mm110) cc_final: 0.8234 (mm-40) REVERT: b 121 GLN cc_start: 0.8097 (tt0) cc_final: 0.7839 (tp40) REVERT: b 210 ARG cc_start: 0.7886 (ptt90) cc_final: 0.7342 (ptt90) REVERT: b 215 ARG cc_start: 0.6868 (ptt-90) cc_final: 0.6298 (ptp-170) REVERT: b 226 ASP cc_start: 0.6613 (t0) cc_final: 0.6154 (t0) REVERT: c 26 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7769 (mm-30) REVERT: c 165 TRP cc_start: 0.8806 (m100) cc_final: 0.8424 (m100) REVERT: c 215 ARG cc_start: 0.6805 (ttp-170) cc_final: 0.6006 (tpt170) REVERT: c 221 MET cc_start: 0.8018 (tpt) cc_final: 0.7414 (tpt) REVERT: c 234 ASP cc_start: 0.7226 (t0) cc_final: 0.7016 (t70) REVERT: c 238 HIS cc_start: 0.6722 (t-90) cc_final: 0.6453 (t70) REVERT: c 254 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7470 (tt) REVERT: d 17 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: d 46 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6749 (mm-30) REVERT: d 117 LYS cc_start: 0.8861 (tttt) cc_final: 0.8614 (ttpt) REVERT: d 120 GLN cc_start: 0.8160 (tt0) cc_final: 0.7816 (tt0) REVERT: d 230 GLU cc_start: 0.6792 (pp20) cc_final: 0.6466 (tm-30) REVERT: f 220 GLU cc_start: 0.7097 (mp0) cc_final: 0.6427 (mt-10) REVERT: f 247 ARG cc_start: 0.7834 (tpp-160) cc_final: 0.7209 (ptm160) REVERT: f 302 TYR cc_start: 0.8079 (t80) cc_final: 0.7823 (t80) REVERT: f 305 GLN cc_start: 0.8411 (mp10) cc_final: 0.7854 (mp10) REVERT: f 311 GLN cc_start: 0.8414 (tt0) cc_final: 0.8198 (tt0) REVERT: f 319 TYR cc_start: 0.8088 (m-80) cc_final: 0.7829 (m-10) REVERT: f 373 LYS cc_start: 0.8597 (mmmt) cc_final: 0.8181 (mtmt) REVERT: f 403 MET cc_start: 0.4263 (tpp) cc_final: 0.3095 (mmt) REVERT: j 3 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8538 (mm) REVERT: j 99 ARG cc_start: 0.8744 (tmt-80) cc_final: 0.8470 (ttt-90) REVERT: j 126 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8498 (pt) REVERT: j 201 LYS cc_start: 0.8700 (mmtp) cc_final: 0.8472 (mtpt) REVERT: k 177 GLU cc_start: 0.8498 (tp30) cc_final: 0.8132 (tp30) REVERT: l 138 ASP cc_start: 0.7201 (t0) cc_final: 0.6994 (t0) REVERT: m 152 ARG cc_start: 0.8415 (ttt180) cc_final: 0.7950 (ttt180) REVERT: m 164 ASP cc_start: 0.7993 (t70) cc_final: 0.7741 (t0) REVERT: m 183 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: n 83 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7892 (mp0) REVERT: n 94 GLN cc_start: 0.8557 (tp40) cc_final: 0.8186 (tp40) outliers start: 238 outliers final: 176 residues processed: 1193 average time/residue: 0.4784 time to fit residues: 956.2739 Evaluate side-chains 1178 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 992 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 145 ARG Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 184 ASP Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 111 MET Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 327 LEU Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain f residue 355 HIS Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 99 SER Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain h residue 269 SER Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 143 THR Chi-restraints excluded: chain l residue 160 MET Chi-restraints excluded: chain l residue 227 VAL Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 257 GLU Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 202 optimal weight: 6.9990 chunk 541 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 601 optimal weight: 1.9990 chunk 499 optimal weight: 6.9990 chunk 278 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 315 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN F 194 ASN F 195 ASN F 271 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN a 207 GLN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN g 23 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 GLN m 165 GLN ** m 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 280 ASN m 303 ASN n 66 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 50188 Z= 0.241 Angle : 0.552 11.338 67898 Z= 0.294 Chirality : 0.043 0.181 7548 Planarity : 0.004 0.056 8804 Dihedral : 4.517 31.594 7004 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.35 % Allowed : 20.74 % Favored : 74.90 % 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: -0.52 (0.10), residues: 6306 helix: 1.27 (0.11), residues: 2224 sheet: -0.71 (0.13), residues: 1500 loop : -1.54 (0.11), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.005 0.001 HIS F 343 PHE 0.015 0.001 PHE K 8 TYR 0.025 0.001 TYR h 218 ARG 0.007 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1250 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1022 time to evaluate : 4.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8234 (ttm) cc_final: 0.7913 (tpp) REVERT: A 77 MET cc_start: 0.8405 (mmt) cc_final: 0.7851 (mmt) REVERT: A 87 LEU cc_start: 0.8977 (tp) cc_final: 0.8714 (tp) REVERT: A 141 ASP cc_start: 0.7969 (p0) cc_final: 0.7687 (p0) REVERT: A 184 ARG cc_start: 0.8185 (tpt90) cc_final: 0.7954 (tpp-160) REVERT: B 18 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8181 (pt) REVERT: B 56 ASP cc_start: 0.8445 (t0) cc_final: 0.7951 (t0) REVERT: B 98 MET cc_start: 0.7496 (ttm) cc_final: 0.7262 (ttt) REVERT: B 107 GLN cc_start: 0.8498 (mm110) cc_final: 0.8166 (mm-40) REVERT: B 210 ARG cc_start: 0.7891 (ptt90) cc_final: 0.7406 (ptt90) REVERT: B 215 ARG cc_start: 0.6573 (ptt-90) cc_final: 0.6138 (ptp-170) REVERT: B 226 ASP cc_start: 0.6634 (t0) cc_final: 0.6240 (t0) REVERT: C 26 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 141 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8288 (mt) REVERT: C 165 TRP cc_start: 0.8775 (m100) cc_final: 0.8274 (m100) REVERT: C 221 MET cc_start: 0.8002 (tpt) cc_final: 0.7495 (tpt) REVERT: C 254 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7493 (tt) REVERT: D 4 ASP cc_start: 0.7221 (p0) cc_final: 0.6886 (p0) REVERT: D 117 LYS cc_start: 0.8860 (tttt) cc_final: 0.8596 (ttpt) REVERT: D 120 GLN cc_start: 0.8074 (tt0) cc_final: 0.7776 (tt0) REVERT: D 230 GLU cc_start: 0.6683 (pp20) cc_final: 0.6359 (tm-30) REVERT: F 220 GLU cc_start: 0.7198 (mp0) cc_final: 0.6490 (mt-10) REVERT: F 319 TYR cc_start: 0.8048 (m-80) cc_final: 0.7809 (m-10) REVERT: F 373 LYS cc_start: 0.8656 (mmmt) cc_final: 0.8062 (mtmm) REVERT: G 175 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7971 (mm-30) REVERT: G 231 MET cc_start: 0.6678 (tpt) cc_final: 0.6365 (tpp) REVERT: J 126 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8510 (pt) REVERT: K 1 MET cc_start: 0.5376 (OUTLIER) cc_final: 0.4439 (mmm) REVERT: K 125 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: K 179 LYS cc_start: 0.8831 (mttp) cc_final: 0.8569 (mttt) REVERT: K 180 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7610 (tpt90) REVERT: M 164 ASP cc_start: 0.8017 (t70) cc_final: 0.7754 (t0) REVERT: M 183 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: N 26 TYR cc_start: 0.8113 (t80) cc_final: 0.7789 (t80) REVERT: N 94 GLN cc_start: 0.8422 (tp40) cc_final: 0.7987 (tp-100) REVERT: a 77 MET cc_start: 0.8409 (mmt) cc_final: 0.7712 (mmt) REVERT: a 141 ASP cc_start: 0.8081 (p0) cc_final: 0.7816 (p0) REVERT: b 18 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8138 (pt) REVERT: b 107 GLN cc_start: 0.8538 (mm110) cc_final: 0.8200 (mm-40) REVERT: b 210 ARG cc_start: 0.7925 (ptt90) cc_final: 0.7373 (ptt90) REVERT: b 215 ARG cc_start: 0.6654 (ptt-90) cc_final: 0.6174 (ptp-170) REVERT: c 26 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7984 (mm-30) REVERT: c 165 TRP cc_start: 0.8777 (m100) cc_final: 0.8303 (m100) REVERT: c 215 ARG cc_start: 0.6605 (ttp-170) cc_final: 0.5997 (tpt170) REVERT: c 221 MET cc_start: 0.7963 (tpt) cc_final: 0.7480 (tpt) REVERT: c 234 ASP cc_start: 0.7129 (t0) cc_final: 0.6924 (t70) REVERT: c 238 HIS cc_start: 0.6716 (t-90) cc_final: 0.6477 (t70) REVERT: c 254 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7473 (tt) REVERT: d 17 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: d 46 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6779 (mm-30) REVERT: d 117 LYS cc_start: 0.8845 (tttt) cc_final: 0.8606 (ttpt) REVERT: d 120 GLN cc_start: 0.8042 (tt0) cc_final: 0.7796 (tt0) REVERT: d 230 GLU cc_start: 0.6776 (pp20) cc_final: 0.6436 (tm-30) REVERT: f 220 GLU cc_start: 0.7084 (mp0) cc_final: 0.6354 (mt-10) REVERT: f 247 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7204 (ptm160) REVERT: f 302 TYR cc_start: 0.8068 (t80) cc_final: 0.7809 (t80) REVERT: f 319 TYR cc_start: 0.8080 (m-80) cc_final: 0.7828 (m-10) REVERT: f 373 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8195 (mtmt) REVERT: f 403 MET cc_start: 0.4343 (tpp) cc_final: 0.2887 (mmt) REVERT: i 47 THR cc_start: 0.8175 (p) cc_final: 0.7925 (p) REVERT: j 3 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8522 (mm) REVERT: j 99 ARG cc_start: 0.8719 (tmt-80) cc_final: 0.8377 (ttt-90) REVERT: j 126 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8518 (pt) REVERT: j 201 LYS cc_start: 0.8721 (mmtp) cc_final: 0.8465 (mtpt) REVERT: k 1 MET cc_start: 0.5434 (OUTLIER) cc_final: 0.4483 (mmm) REVERT: k 125 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: k 177 GLU cc_start: 0.8491 (tp30) cc_final: 0.8123 (tp30) REVERT: l 138 ASP cc_start: 0.7223 (t0) cc_final: 0.6964 (t0) REVERT: m 152 ARG cc_start: 0.8346 (ttt180) cc_final: 0.7877 (ttt180) REVERT: m 164 ASP cc_start: 0.7964 (t70) cc_final: 0.7696 (t0) REVERT: m 183 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: n 83 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7858 (mp0) REVERT: n 94 GLN cc_start: 0.8565 (tp40) cc_final: 0.8167 (tp40) outliers start: 228 outliers final: 161 residues processed: 1171 average time/residue: 0.4718 time to fit residues: 922.0114 Evaluate side-chains 1156 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 980 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 212 CYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 168 CYS Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 SER Chi-restraints excluded: chain e residue 157 THR Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 221 LEU Chi-restraints excluded: chain f residue 239 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 245 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 81 ASP Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain m residue 300 MET Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 580 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 342 optimal weight: 0.9990 chunk 439 optimal weight: 0.9990 chunk 340 optimal weight: 9.9990 chunk 506 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 chunk 599 optimal weight: 6.9990 chunk 375 optimal weight: 8.9990 chunk 365 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 187 HIS B 207 GLN C 129 GLN F 194 ASN F 195 ASN F 271 ASN F 311 GLN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 GLN c 129 GLN f 195 ASN f 311 GLN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 GLN m 170 GLN m 180 ASN m 280 ASN n 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50188 Z= 0.164 Angle : 0.523 12.816 67898 Z= 0.277 Chirality : 0.042 0.164 7548 Planarity : 0.004 0.058 8804 Dihedral : 4.278 30.148 7004 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.49 % Allowed : 22.21 % Favored : 74.29 % 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: -0.25 (0.11), residues: 6306 helix: 1.54 (0.11), residues: 2228 sheet: -0.58 (0.13), residues: 1492 loop : -1.41 (0.11), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP l 165 HIS 0.004 0.001 HIS D 164 PHE 0.012 0.001 PHE F 401 TYR 0.018 0.001 TYR H 218 ARG 0.007 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1060 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8362 (mmt) cc_final: 0.7769 (mmt) REVERT: A 87 LEU cc_start: 0.8955 (tp) cc_final: 0.8723 (tp) REVERT: A 98 TYR cc_start: 0.9164 (t80) cc_final: 0.8851 (t80) REVERT: A 141 ASP cc_start: 0.7864 (p0) cc_final: 0.7564 (p0) REVERT: A 181 LEU cc_start: 0.8557 (mt) cc_final: 0.8175 (mt) REVERT: A 184 ARG cc_start: 0.8132 (tpt90) cc_final: 0.7922 (tpp-160) REVERT: B 18 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8177 (pt) REVERT: B 56 ASP cc_start: 0.8466 (t0) cc_final: 0.7976 (t0) REVERT: B 98 MET cc_start: 0.7420 (ttm) cc_final: 0.7209 (ttt) REVERT: B 107 GLN cc_start: 0.8458 (mm110) cc_final: 0.8151 (mm-40) REVERT: B 187 HIS cc_start: 0.7163 (t-90) cc_final: 0.6818 (t70) REVERT: B 210 ARG cc_start: 0.7813 (ptt90) cc_final: 0.7426 (ptt90) REVERT: B 215 ARG cc_start: 0.6413 (ptt-90) cc_final: 0.6105 (ptp-170) REVERT: B 226 ASP cc_start: 0.6679 (t0) cc_final: 0.6293 (t0) REVERT: C 8 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7534 (mtm-85) REVERT: C 26 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 116 LEU cc_start: 0.8730 (tp) cc_final: 0.8417 (tp) REVERT: C 141 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8250 (mt) REVERT: C 165 TRP cc_start: 0.8742 (m100) cc_final: 0.8271 (m100) REVERT: C 221 MET cc_start: 0.7979 (tpt) cc_final: 0.7508 (tpt) REVERT: C 254 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7241 (tt) REVERT: D 4 ASP cc_start: 0.7216 (p0) cc_final: 0.6970 (p0) REVERT: D 117 LYS cc_start: 0.8839 (tttt) cc_final: 0.8603 (ttpt) REVERT: D 120 GLN cc_start: 0.7982 (tt0) cc_final: 0.7670 (tt0) REVERT: D 188 PHE cc_start: 0.8731 (t80) cc_final: 0.8522 (t80) REVERT: D 230 GLU cc_start: 0.6662 (pp20) cc_final: 0.6111 (tm-30) REVERT: E 191 HIS cc_start: 0.8419 (t70) cc_final: 0.8107 (t70) REVERT: E 249 LYS cc_start: 0.7920 (mttm) cc_final: 0.6709 (tptp) REVERT: F 247 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.6932 (ptm160) REVERT: F 311 GLN cc_start: 0.8312 (tt0) cc_final: 0.8087 (tt0) REVERT: F 319 TYR cc_start: 0.8032 (m-80) cc_final: 0.7796 (m-10) REVERT: F 373 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8172 (mtmt) REVERT: G 175 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7635 (mm-30) REVERT: G 231 MET cc_start: 0.6710 (tpt) cc_final: 0.6442 (tpp) REVERT: J 50 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8856 (t) REVERT: J 126 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8514 (pt) REVERT: J 127 ILE cc_start: 0.8736 (pt) cc_final: 0.8348 (mt) REVERT: K 125 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: K 180 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7628 (tpt90) REVERT: M 152 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7439 (ttt180) REVERT: M 164 ASP cc_start: 0.7948 (t70) cc_final: 0.7699 (t0) REVERT: M 183 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: N 26 TYR cc_start: 0.7978 (t80) cc_final: 0.7744 (t80) REVERT: N 94 GLN cc_start: 0.8383 (tp40) cc_final: 0.7864 (tp-100) REVERT: a 77 MET cc_start: 0.8423 (mmt) cc_final: 0.7769 (mmt) REVERT: a 141 ASP cc_start: 0.7934 (p0) cc_final: 0.7660 (p0) REVERT: b 100 ASN cc_start: 0.8511 (t0) cc_final: 0.8175 (t0) REVERT: b 107 GLN cc_start: 0.8488 (mm110) cc_final: 0.8164 (mm-40) REVERT: b 117 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8440 (tm-30) REVERT: b 210 ARG cc_start: 0.7801 (ptt90) cc_final: 0.7439 (ptt90) REVERT: c 26 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7945 (mm-30) REVERT: c 165 TRP cc_start: 0.8747 (m100) cc_final: 0.8256 (m100) REVERT: c 221 MET cc_start: 0.7955 (tpt) cc_final: 0.7508 (tpt) REVERT: c 238 HIS cc_start: 0.6776 (t-90) cc_final: 0.6480 (t70) REVERT: c 254 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7352 (tt) REVERT: d 17 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.8084 (m-10) REVERT: d 46 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6753 (mm-30) REVERT: d 117 LYS cc_start: 0.8839 (tttt) cc_final: 0.8627 (ttpt) REVERT: d 120 GLN cc_start: 0.7939 (tt0) cc_final: 0.7713 (tt0) REVERT: d 230 GLU cc_start: 0.6806 (pp20) cc_final: 0.6478 (tm-30) REVERT: e 191 HIS cc_start: 0.8447 (t70) cc_final: 0.7769 (t-170) REVERT: e 248 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7055 (tt0) REVERT: e 263 THR cc_start: 0.8859 (m) cc_final: 0.8590 (p) REVERT: f 247 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.7159 (ptm160) REVERT: f 302 TYR cc_start: 0.8020 (t80) cc_final: 0.7803 (t80) REVERT: f 311 GLN cc_start: 0.8322 (tt0) cc_final: 0.8105 (tt0) REVERT: f 319 TYR cc_start: 0.8058 (m-80) cc_final: 0.7807 (m-10) REVERT: f 373 LYS cc_start: 0.8563 (mmmt) cc_final: 0.8195 (mtmt) REVERT: f 403 MET cc_start: 0.4188 (tpp) cc_final: 0.3012 (tpp) REVERT: i 47 THR cc_start: 0.8090 (p) cc_final: 0.7823 (p) REVERT: j 3 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8500 (mm) REVERT: j 50 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8852 (t) REVERT: j 99 ARG cc_start: 0.8683 (tmt-80) cc_final: 0.8400 (ttt-90) REVERT: j 126 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8480 (pt) REVERT: j 201 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8508 (mtpt) REVERT: k 177 GLU cc_start: 0.8471 (tp30) cc_final: 0.8118 (tp30) REVERT: k 181 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8449 (tpp-160) REVERT: m 152 ARG cc_start: 0.8252 (ttt180) cc_final: 0.7874 (ttt180) REVERT: m 183 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7341 (tt0) outliers start: 183 outliers final: 123 residues processed: 1177 average time/residue: 0.4795 time to fit residues: 942.6193 Evaluate side-chains 1125 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 988 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 399 ASP Chi-restraints excluded: chain G residue 31 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 13 ASP Chi-restraints excluded: chain d residue 17 PHE Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 211 TYR Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 90 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 125 GLN Chi-restraints excluded: chain k residue 181 ARG Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 370 optimal weight: 0.1980 chunk 239 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 117 optimal weight: 0.0570 chunk 116 optimal weight: 0.3980 chunk 381 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 471 optimal weight: 10.0000 overall best weight: 1.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN B 207 GLN F 194 ASN F 271 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN M 280 ASN ** b 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 GLN f 195 ASN g 64 ASN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 GLN m 280 ASN n 66 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50188 Z= 0.200 Angle : 0.541 13.828 67898 Z= 0.285 Chirality : 0.043 0.158 7548 Planarity : 0.004 0.058 8804 Dihedral : 4.270 29.675 7004 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.76 % Allowed : 22.77 % Favored : 73.47 % 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: -0.17 (0.11), residues: 6306 helix: 1.58 (0.11), residues: 2226 sheet: -0.52 (0.13), residues: 1498 loop : -1.35 (0.11), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.004 0.001 HIS F 343 PHE 0.027 0.001 PHE F 401 TYR 0.022 0.001 TYR H 218 ARG 0.010 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1005 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8409 (mmt) cc_final: 0.7816 (mmt) REVERT: A 87 LEU cc_start: 0.8978 (tp) cc_final: 0.8753 (tp) REVERT: A 141 ASP cc_start: 0.7884 (p0) cc_final: 0.7555 (p0) REVERT: A 181 LEU cc_start: 0.8553 (mt) cc_final: 0.8132 (mt) REVERT: A 184 ARG cc_start: 0.8123 (tpt90) cc_final: 0.7918 (tpp-160) REVERT: B 18 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8175 (pt) REVERT: B 98 MET cc_start: 0.7452 (ttm) cc_final: 0.7233 (ttt) REVERT: B 107 GLN cc_start: 0.8509 (mm110) cc_final: 0.8103 (mm-40) REVERT: B 210 ARG cc_start: 0.7801 (ptt90) cc_final: 0.7412 (ptt90) REVERT: B 215 ARG cc_start: 0.6447 (ptt-90) cc_final: 0.6080 (ptp-170) REVERT: B 226 ASP cc_start: 0.6664 (t0) cc_final: 0.6287 (t0) REVERT: C 26 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7731 (mm-30) REVERT: C 141 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8275 (mt) REVERT: C 165 TRP cc_start: 0.8736 (m100) cc_final: 0.8236 (m100) REVERT: C 221 MET cc_start: 0.8120 (tpt) cc_final: 0.7596 (tpt) REVERT: C 254 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7327 (tt) REVERT: D 4 ASP cc_start: 0.7193 (p0) cc_final: 0.6918 (p0) REVERT: D 117 LYS cc_start: 0.8836 (tttt) cc_final: 0.8598 (ttpt) REVERT: D 120 GLN cc_start: 0.7926 (tt0) cc_final: 0.7679 (tt0) REVERT: D 230 GLU cc_start: 0.6639 (pp20) cc_final: 0.5868 (tm-30) REVERT: D 234 GLU cc_start: 0.3895 (OUTLIER) cc_final: 0.3170 (pt0) REVERT: E 249 LYS cc_start: 0.7917 (mttm) cc_final: 0.6721 (tptp) REVERT: F 247 ARG cc_start: 0.7215 (mtp-110) cc_final: 0.6791 (ttm-80) REVERT: F 311 GLN cc_start: 0.8279 (tt0) cc_final: 0.8032 (tt0) REVERT: F 319 TYR cc_start: 0.8007 (m-80) cc_final: 0.7771 (m-10) REVERT: F 373 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8017 (mtmm) REVERT: G 175 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7620 (mm-30) REVERT: G 231 MET cc_start: 0.6732 (tpt) cc_final: 0.6442 (tpp) REVERT: J 50 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8839 (t) REVERT: J 126 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8535 (pt) REVERT: J 127 ILE cc_start: 0.8745 (pt) cc_final: 0.8379 (mt) REVERT: K 125 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: K 180 ARG cc_start: 0.8192 (ttp80) cc_final: 0.7631 (tpt90) REVERT: M 152 ARG cc_start: 0.8033 (ttt180) cc_final: 0.7445 (ttt180) REVERT: M 183 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: N 26 TYR cc_start: 0.8031 (t80) cc_final: 0.7731 (t80) REVERT: N 94 GLN cc_start: 0.8360 (tp40) cc_final: 0.7866 (tp-100) REVERT: N 159 ARG cc_start: 0.8588 (tpt-90) cc_final: 0.8336 (ttt-90) REVERT: a 77 MET cc_start: 0.8458 (mmt) cc_final: 0.7715 (mmt) REVERT: a 141 ASP cc_start: 0.7936 (p0) cc_final: 0.7668 (p0) REVERT: b 18 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8132 (pt) REVERT: b 100 ASN cc_start: 0.8520 (t0) cc_final: 0.8176 (t0) REVERT: b 107 GLN cc_start: 0.8516 (mm110) cc_final: 0.8096 (mm-40) REVERT: b 204 GLU cc_start: 0.7105 (mp0) cc_final: 0.6686 (mp0) REVERT: b 210 ARG cc_start: 0.7782 (ptt90) cc_final: 0.7284 (ptt90) REVERT: c 26 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7914 (mm-30) REVERT: c 165 TRP cc_start: 0.8742 (m100) cc_final: 0.8238 (m100) REVERT: c 175 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8030 (mm-40) REVERT: c 221 MET cc_start: 0.8058 (tpt) cc_final: 0.7557 (tpt) REVERT: c 238 HIS cc_start: 0.6808 (t-90) cc_final: 0.6549 (t70) REVERT: c 254 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7335 (tt) REVERT: d 117 LYS cc_start: 0.8834 (tttt) cc_final: 0.8619 (ttpt) REVERT: d 120 GLN cc_start: 0.7909 (tt0) cc_final: 0.7697 (tt0) REVERT: d 230 GLU cc_start: 0.6844 (pp20) cc_final: 0.6325 (tm-30) REVERT: d 234 GLU cc_start: 0.3991 (OUTLIER) cc_final: 0.3339 (pt0) REVERT: e 195 GLU cc_start: 0.7830 (mp0) cc_final: 0.7495 (mm-30) REVERT: e 263 THR cc_start: 0.8868 (m) cc_final: 0.8553 (p) REVERT: f 247 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7148 (ptm160) REVERT: f 302 TYR cc_start: 0.8065 (t80) cc_final: 0.7797 (t80) REVERT: f 373 LYS cc_start: 0.8584 (mmmt) cc_final: 0.8206 (mtmt) REVERT: f 403 MET cc_start: 0.4036 (tpp) cc_final: 0.2994 (tpp) REVERT: i 47 THR cc_start: 0.8098 (p) cc_final: 0.7839 (p) REVERT: i 66 MET cc_start: 0.8632 (mmm) cc_final: 0.8260 (mtp) REVERT: j 3 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8492 (mm) REVERT: j 50 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8853 (t) REVERT: j 99 ARG cc_start: 0.8684 (tmt-80) cc_final: 0.8386 (ttt-90) REVERT: j 126 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8553 (pt) REVERT: j 149 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7810 (tpp) REVERT: j 201 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8523 (mtpt) REVERT: k 1 MET cc_start: 0.5466 (OUTLIER) cc_final: 0.4538 (mmm) REVERT: k 177 GLU cc_start: 0.8496 (tp30) cc_final: 0.8120 (tp30) REVERT: k 181 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8321 (mmp80) REVERT: m 152 ARG cc_start: 0.8278 (ttt180) cc_final: 0.7923 (ttt180) REVERT: m 183 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: n 58 MET cc_start: 0.7690 (mmm) cc_final: 0.7452 (mmm) outliers start: 197 outliers final: 152 residues processed: 1141 average time/residue: 0.4758 time to fit residues: 905.3648 Evaluate side-chains 1153 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 983 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain M residue 318 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 13 ASP Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 SER Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 289 MET Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 90 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 245 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 149 MET Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 181 ARG Chi-restraints excluded: chain k residue 188 TYR Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 193 LEU Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 545 optimal weight: 0.9990 chunk 574 optimal weight: 8.9990 chunk 524 optimal weight: 0.8980 chunk 558 optimal weight: 7.9990 chunk 336 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 504 optimal weight: 3.9990 chunk 528 optimal weight: 0.9990 chunk 556 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN ** B 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN D 223 GLN F 194 ASN F 195 ASN F 271 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN b 207 GLN f 195 ASN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 201 GLN ** j 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 165 GLN m 280 ASN n 66 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50188 Z= 0.203 Angle : 0.549 13.796 67898 Z= 0.289 Chirality : 0.043 0.153 7548 Planarity : 0.004 0.059 8804 Dihedral : 4.263 29.562 7004 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.87 % Allowed : 22.79 % Favored : 73.34 % 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: -0.10 (0.11), residues: 6306 helix: 1.61 (0.11), residues: 2224 sheet: -0.47 (0.13), residues: 1510 loop : -1.29 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 165 HIS 0.004 0.001 HIS F 343 PHE 0.027 0.001 PHE F 401 TYR 0.022 0.001 TYR H 218 ARG 0.009 0.000 ARG I 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1200 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 997 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8395 (mmt) cc_final: 0.7812 (mmt) REVERT: A 87 LEU cc_start: 0.8971 (tp) cc_final: 0.8718 (tp) REVERT: A 141 ASP cc_start: 0.7889 (p0) cc_final: 0.7534 (p0) REVERT: A 178 MET cc_start: 0.8147 (mmt) cc_final: 0.7881 (mmt) REVERT: A 181 LEU cc_start: 0.8398 (mt) cc_final: 0.7957 (mt) REVERT: A 184 ARG cc_start: 0.8115 (tpt90) cc_final: 0.7892 (tpp-160) REVERT: B 18 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8172 (pt) REVERT: B 98 MET cc_start: 0.7452 (ttm) cc_final: 0.7213 (ttt) REVERT: B 100 ASN cc_start: 0.8511 (t0) cc_final: 0.8235 (t0) REVERT: B 107 GLN cc_start: 0.8488 (mm110) cc_final: 0.8080 (mm-40) REVERT: B 210 ARG cc_start: 0.7788 (ptt90) cc_final: 0.7422 (ptt90) REVERT: B 215 ARG cc_start: 0.6482 (ptt-90) cc_final: 0.6088 (ptp-170) REVERT: B 226 ASP cc_start: 0.6687 (t0) cc_final: 0.6295 (t0) REVERT: C 26 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7733 (mm-30) REVERT: C 141 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8273 (mt) REVERT: C 165 TRP cc_start: 0.8732 (m100) cc_final: 0.8254 (m100) REVERT: C 221 MET cc_start: 0.8132 (tpt) cc_final: 0.7562 (tpt) REVERT: C 254 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7335 (tt) REVERT: D 4 ASP cc_start: 0.7190 (p0) cc_final: 0.6860 (p0) REVERT: D 117 LYS cc_start: 0.8840 (tttt) cc_final: 0.8607 (ttpt) REVERT: D 120 GLN cc_start: 0.7920 (tt0) cc_final: 0.7683 (tt0) REVERT: D 234 GLU cc_start: 0.3917 (OUTLIER) cc_final: 0.3480 (pt0) REVERT: E 207 MET cc_start: 0.8484 (ttt) cc_final: 0.8246 (ttt) REVERT: E 249 LYS cc_start: 0.7933 (mttm) cc_final: 0.6735 (tptp) REVERT: F 247 ARG cc_start: 0.7233 (mtp-110) cc_final: 0.6966 (ptm160) REVERT: F 305 GLN cc_start: 0.8799 (mp10) cc_final: 0.7879 (mp10) REVERT: F 311 GLN cc_start: 0.8271 (tt0) cc_final: 0.8035 (tt0) REVERT: F 319 TYR cc_start: 0.8002 (m-80) cc_final: 0.7762 (m-10) REVERT: F 373 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8421 (mmtm) REVERT: G 231 MET cc_start: 0.6767 (tpt) cc_final: 0.6491 (tpp) REVERT: J 126 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8564 (pt) REVERT: J 127 ILE cc_start: 0.8757 (pt) cc_final: 0.8413 (mt) REVERT: K 125 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: K 180 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7651 (tpt90) REVERT: M 152 ARG cc_start: 0.8029 (ttt180) cc_final: 0.7438 (ttt180) REVERT: M 183 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: N 26 TYR cc_start: 0.8037 (t80) cc_final: 0.7684 (t80) REVERT: N 94 GLN cc_start: 0.8340 (tp40) cc_final: 0.7896 (tp-100) REVERT: N 159 ARG cc_start: 0.8589 (tpt-90) cc_final: 0.8328 (ttt-90) REVERT: a 77 MET cc_start: 0.8451 (mmt) cc_final: 0.7699 (mmt) REVERT: a 94 GLU cc_start: 0.7878 (tp30) cc_final: 0.7518 (tp30) REVERT: a 141 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7640 (p0) REVERT: b 18 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8132 (pt) REVERT: b 100 ASN cc_start: 0.8549 (t0) cc_final: 0.8193 (t0) REVERT: b 107 GLN cc_start: 0.8487 (mm110) cc_final: 0.8088 (mm-40) REVERT: b 204 GLU cc_start: 0.7154 (mp0) cc_final: 0.6732 (mp0) REVERT: b 210 ARG cc_start: 0.7671 (ptt90) cc_final: 0.7243 (ptt90) REVERT: c 26 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7890 (mm-30) REVERT: c 165 TRP cc_start: 0.8742 (m100) cc_final: 0.8236 (m100) REVERT: c 175 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7968 (mm-40) REVERT: c 221 MET cc_start: 0.8054 (tpt) cc_final: 0.7535 (tpt) REVERT: c 238 HIS cc_start: 0.6753 (t-90) cc_final: 0.6519 (t70) REVERT: c 254 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7364 (tt) REVERT: d 46 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6702 (mm-30) REVERT: d 117 LYS cc_start: 0.8835 (tttt) cc_final: 0.8615 (ttpt) REVERT: d 230 GLU cc_start: 0.6858 (pp20) cc_final: 0.6337 (tm-30) REVERT: d 234 GLU cc_start: 0.3978 (OUTLIER) cc_final: 0.3330 (pt0) REVERT: e 195 GLU cc_start: 0.7832 (mp0) cc_final: 0.7495 (mm-30) REVERT: e 249 LYS cc_start: 0.7813 (mttm) cc_final: 0.6637 (tptp) REVERT: e 263 THR cc_start: 0.8862 (m) cc_final: 0.8578 (p) REVERT: e 324 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: f 247 ARG cc_start: 0.7770 (tpp-160) cc_final: 0.7156 (ptm160) REVERT: f 303 ASP cc_start: 0.7864 (p0) cc_final: 0.7546 (p0) REVERT: f 305 GLN cc_start: 0.8744 (mp10) cc_final: 0.7875 (mp10) REVERT: f 319 TYR cc_start: 0.8043 (m-80) cc_final: 0.7719 (m-10) REVERT: f 373 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8198 (mtmt) REVERT: f 403 MET cc_start: 0.4021 (tpp) cc_final: 0.2985 (tpp) REVERT: i 47 THR cc_start: 0.8109 (p) cc_final: 0.7820 (p) REVERT: i 66 MET cc_start: 0.8639 (mmm) cc_final: 0.8265 (mtp) REVERT: j 3 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8487 (mm) REVERT: j 50 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8851 (t) REVERT: j 99 ARG cc_start: 0.8684 (tmt-80) cc_final: 0.8380 (ttt-90) REVERT: j 126 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8561 (pt) REVERT: k 1 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4486 (mmm) REVERT: k 111 ASP cc_start: 0.7921 (m-30) cc_final: 0.7602 (m-30) REVERT: k 177 GLU cc_start: 0.8501 (tp30) cc_final: 0.8108 (tp30) REVERT: k 181 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8134 (mmp80) REVERT: m 183 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: m 231 TYR cc_start: 0.8276 (t80) cc_final: 0.7886 (t80) REVERT: n 58 MET cc_start: 0.7678 (mmm) cc_final: 0.7450 (mmm) outliers start: 203 outliers final: 161 residues processed: 1134 average time/residue: 0.4754 time to fit residues: 901.7465 Evaluate side-chains 1155 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 976 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain M residue 318 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 13 ASP Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 SER Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 324 ASP Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 90 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 245 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 50 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 14 VAL Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 181 ARG Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 193 LEU Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 366 optimal weight: 1.9990 chunk 590 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 619 optimal weight: 0.9980 chunk 570 optimal weight: 0.9980 chunk 493 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 381 optimal weight: 0.1980 chunk 302 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 165 HIS B 207 GLN D 223 GLN F 194 ASN F 195 ASN F 271 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 303 ASN a 72 ASN b 207 GLN d 120 GLN f 194 ASN f 195 ASN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 125 GLN m 165 GLN m 280 ASN n 66 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50188 Z= 0.235 Angle : 0.564 13.915 67898 Z= 0.297 Chirality : 0.043 0.153 7548 Planarity : 0.004 0.059 8804 Dihedral : 4.321 29.557 7004 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.84 % Allowed : 22.92 % Favored : 73.24 % 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: -0.12 (0.11), residues: 6306 helix: 1.58 (0.11), residues: 2226 sheet: -0.45 (0.13), residues: 1502 loop : -1.30 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 165 HIS 0.008 0.001 HIS E 191 PHE 0.032 0.001 PHE F 401 TYR 0.025 0.001 TYR H 218 ARG 0.010 0.000 ARG I 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 994 time to evaluate : 4.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8415 (mmt) cc_final: 0.7818 (mmt) REVERT: A 87 LEU cc_start: 0.8978 (tp) cc_final: 0.8729 (tp) REVERT: A 98 TYR cc_start: 0.9178 (t80) cc_final: 0.8888 (t80) REVERT: A 141 ASP cc_start: 0.7893 (p0) cc_final: 0.7532 (p0) REVERT: A 178 MET cc_start: 0.8177 (mmt) cc_final: 0.7912 (mmt) REVERT: A 184 ARG cc_start: 0.8147 (tpt90) cc_final: 0.7927 (tpp-160) REVERT: B 18 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8171 (pt) REVERT: B 56 ASP cc_start: 0.8472 (t0) cc_final: 0.7930 (t0) REVERT: B 98 MET cc_start: 0.7449 (ttm) cc_final: 0.7231 (ttt) REVERT: B 100 ASN cc_start: 0.8548 (t0) cc_final: 0.8239 (t0) REVERT: B 107 GLN cc_start: 0.8493 (mm110) cc_final: 0.8087 (mm-40) REVERT: B 174 LYS cc_start: 0.6986 (pptt) cc_final: 0.6096 (pttp) REVERT: B 210 ARG cc_start: 0.7859 (ptt90) cc_final: 0.7386 (ptt90) REVERT: B 215 ARG cc_start: 0.6429 (ptt-90) cc_final: 0.6093 (ptp-170) REVERT: B 226 ASP cc_start: 0.6744 (t0) cc_final: 0.6314 (t0) REVERT: C 26 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 141 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8272 (mt) REVERT: C 165 TRP cc_start: 0.8740 (m100) cc_final: 0.8307 (m100) REVERT: C 221 MET cc_start: 0.8131 (tpt) cc_final: 0.7548 (tpt) REVERT: C 254 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7347 (tt) REVERT: D 4 ASP cc_start: 0.7212 (p0) cc_final: 0.6868 (p0) REVERT: D 117 LYS cc_start: 0.8847 (tttt) cc_final: 0.8604 (ttpt) REVERT: D 120 GLN cc_start: 0.7947 (tt0) cc_final: 0.7716 (tt0) REVERT: D 234 GLU cc_start: 0.3983 (OUTLIER) cc_final: 0.3533 (pt0) REVERT: E 169 GLU cc_start: 0.7820 (pt0) cc_final: 0.7553 (pt0) REVERT: E 191 HIS cc_start: 0.8389 (t70) cc_final: 0.7571 (t-170) REVERT: E 207 MET cc_start: 0.8449 (ttt) cc_final: 0.8246 (ttt) REVERT: E 249 LYS cc_start: 0.7943 (mttm) cc_final: 0.6754 (tptp) REVERT: F 247 ARG cc_start: 0.7253 (mtp-110) cc_final: 0.6968 (ptm160) REVERT: F 305 GLN cc_start: 0.8837 (mp10) cc_final: 0.7920 (mp10) REVERT: F 311 GLN cc_start: 0.8269 (tt0) cc_final: 0.8067 (tt0) REVERT: F 319 TYR cc_start: 0.8005 (m-80) cc_final: 0.7754 (m-10) REVERT: F 401 PHE cc_start: 0.6563 (t80) cc_final: 0.6331 (t80) REVERT: G 231 MET cc_start: 0.6788 (tpt) cc_final: 0.6519 (tpp) REVERT: I 47 THR cc_start: 0.8130 (p) cc_final: 0.7864 (p) REVERT: J 126 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8595 (pt) REVERT: J 127 ILE cc_start: 0.8732 (pt) cc_final: 0.8403 (mt) REVERT: K 1 MET cc_start: 0.5352 (OUTLIER) cc_final: 0.4447 (mmm) REVERT: K 125 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: K 180 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7622 (tpt90) REVERT: M 152 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7469 (ttt180) REVERT: M 183 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: N 26 TYR cc_start: 0.8075 (t80) cc_final: 0.7726 (t80) REVERT: N 94 GLN cc_start: 0.8325 (tp40) cc_final: 0.7919 (tp-100) REVERT: N 159 ARG cc_start: 0.8607 (tpt-90) cc_final: 0.8407 (ttt-90) REVERT: a 77 MET cc_start: 0.8430 (mmt) cc_final: 0.7672 (mmt) REVERT: a 141 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7629 (p0) REVERT: b 18 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8142 (pt) REVERT: b 98 MET cc_start: 0.8028 (tmt) cc_final: 0.7654 (tmm) REVERT: b 100 ASN cc_start: 0.8589 (t0) cc_final: 0.8257 (t0) REVERT: b 107 GLN cc_start: 0.8495 (mm110) cc_final: 0.8079 (mm-40) REVERT: b 204 GLU cc_start: 0.7183 (mp0) cc_final: 0.6771 (mp0) REVERT: b 210 ARG cc_start: 0.7672 (ptt90) cc_final: 0.7264 (ptt90) REVERT: c 165 TRP cc_start: 0.8761 (m100) cc_final: 0.8244 (m100) REVERT: c 221 MET cc_start: 0.8071 (tpt) cc_final: 0.7508 (tpt) REVERT: c 238 HIS cc_start: 0.6822 (t-90) cc_final: 0.6481 (t70) REVERT: c 254 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7342 (tt) REVERT: d 117 LYS cc_start: 0.8852 (tttt) cc_final: 0.8621 (ttpt) REVERT: d 230 GLU cc_start: 0.6822 (pp20) cc_final: 0.6326 (tm-30) REVERT: d 234 GLU cc_start: 0.4036 (OUTLIER) cc_final: 0.3362 (pt0) REVERT: e 195 GLU cc_start: 0.7811 (mp0) cc_final: 0.7464 (mm-30) REVERT: e 207 MET cc_start: 0.8552 (ttt) cc_final: 0.8283 (ttt) REVERT: e 249 LYS cc_start: 0.7823 (mttm) cc_final: 0.6637 (tptp) REVERT: e 263 THR cc_start: 0.8899 (m) cc_final: 0.8565 (p) REVERT: e 324 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: f 247 ARG cc_start: 0.7806 (tpp-160) cc_final: 0.7154 (ptm160) REVERT: f 319 TYR cc_start: 0.8047 (m-80) cc_final: 0.7729 (m-10) REVERT: f 373 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8193 (mtmt) REVERT: i 47 THR cc_start: 0.8136 (p) cc_final: 0.7856 (p) REVERT: i 66 MET cc_start: 0.8582 (mmm) cc_final: 0.8274 (mtp) REVERT: j 3 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8505 (mm) REVERT: j 99 ARG cc_start: 0.8689 (tmt-80) cc_final: 0.8356 (ttt-90) REVERT: j 126 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8589 (pt) REVERT: k 1 MET cc_start: 0.5405 (OUTLIER) cc_final: 0.4497 (mmm) REVERT: k 177 GLU cc_start: 0.8507 (tp30) cc_final: 0.8122 (tp30) REVERT: k 181 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8326 (mmp80) REVERT: m 164 ASP cc_start: 0.7921 (t70) cc_final: 0.7644 (t0) REVERT: m 183 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: m 231 TYR cc_start: 0.8284 (t80) cc_final: 0.7942 (t80) REVERT: n 58 MET cc_start: 0.7712 (mmm) cc_final: 0.7496 (mmm) REVERT: n 148 GLN cc_start: 0.7605 (tt0) cc_final: 0.7338 (tt0) outliers start: 201 outliers final: 173 residues processed: 1129 average time/residue: 0.4805 time to fit residues: 904.9637 Evaluate side-chains 1164 residues out of total 5242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 973 time to evaluate : 4.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 56 PHE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 13 ASP Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 234 GLU Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain F residue 271 ASN Chi-restraints excluded: chain F residue 355 HIS Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ILE Chi-restraints excluded: chain H residue 239 GLU Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 263 THR Chi-restraints excluded: chain I residue 65 TYR Chi-restraints excluded: chain I residue 90 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 216 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 111 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain J residue 190 VAL Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 92 SER Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 188 TYR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 160 MET Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 286 ILE Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 179 SER Chi-restraints excluded: chain M residue 183 GLN Chi-restraints excluded: chain M residue 237 VAL Chi-restraints excluded: chain M residue 256 THR Chi-restraints excluded: chain M residue 259 PHE Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 GLU Chi-restraints excluded: chain M residue 317 ASP Chi-restraints excluded: chain M residue 318 SER Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain N residue 77 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 141 ASP Chi-restraints excluded: chain a residue 156 VAL Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 208 SER Chi-restraints excluded: chain a residue 246 VAL Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 18 ILE Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 32 THR Chi-restraints excluded: chain c residue 50 MET Chi-restraints excluded: chain c residue 56 PHE Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 176 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 254 LEU Chi-restraints excluded: chain d residue 11 SER Chi-restraints excluded: chain d residue 13 ASP Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain d residue 147 THR Chi-restraints excluded: chain d residue 234 GLU Chi-restraints excluded: chain e residue 147 VAL Chi-restraints excluded: chain e residue 156 SER Chi-restraints excluded: chain e residue 172 SER Chi-restraints excluded: chain e residue 324 ASP Chi-restraints excluded: chain e residue 331 THR Chi-restraints excluded: chain e residue 334 GLU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain f residue 199 THR Chi-restraints excluded: chain f residue 380 VAL Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 32 ASP Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 42 CYS Chi-restraints excluded: chain g residue 124 THR Chi-restraints excluded: chain g residue 163 VAL Chi-restraints excluded: chain g residue 171 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain g residue 216 VAL Chi-restraints excluded: chain g residue 227 VAL Chi-restraints excluded: chain h residue 56 THR Chi-restraints excluded: chain h residue 201 MET Chi-restraints excluded: chain h residue 230 THR Chi-restraints excluded: chain h residue 231 ILE Chi-restraints excluded: chain h residue 239 GLU Chi-restraints excluded: chain h residue 243 ILE Chi-restraints excluded: chain h residue 263 THR Chi-restraints excluded: chain i residue 65 TYR Chi-restraints excluded: chain i residue 90 SER Chi-restraints excluded: chain i residue 129 LEU Chi-restraints excluded: chain i residue 148 THR Chi-restraints excluded: chain i residue 212 THR Chi-restraints excluded: chain i residue 245 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 39 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 111 SER Chi-restraints excluded: chain j residue 126 LEU Chi-restraints excluded: chain j residue 166 ILE Chi-restraints excluded: chain j residue 189 ILE Chi-restraints excluded: chain j residue 190 VAL Chi-restraints excluded: chain j residue 199 LEU Chi-restraints excluded: chain k residue 1 MET Chi-restraints excluded: chain k residue 3 GLU Chi-restraints excluded: chain k residue 4 THR Chi-restraints excluded: chain k residue 14 VAL Chi-restraints excluded: chain k residue 44 LEU Chi-restraints excluded: chain k residue 92 SER Chi-restraints excluded: chain k residue 121 VAL Chi-restraints excluded: chain k residue 181 ARG Chi-restraints excluded: chain l residue 131 MET Chi-restraints excluded: chain l residue 232 ILE Chi-restraints excluded: chain l residue 286 ILE Chi-restraints excluded: chain m residue 183 GLN Chi-restraints excluded: chain m residue 193 LEU Chi-restraints excluded: chain m residue 237 VAL Chi-restraints excluded: chain m residue 256 THR Chi-restraints excluded: chain m residue 259 PHE Chi-restraints excluded: chain m residue 263 THR Chi-restraints excluded: chain m residue 295 GLU Chi-restraints excluded: chain n residue 7 VAL Chi-restraints excluded: chain n residue 45 SER Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain n residue 66 ASN Chi-restraints excluded: chain n residue 77 ASP Chi-restraints excluded: chain n residue 116 THR Chi-restraints excluded: chain n residue 130 ASP Chi-restraints excluded: chain n residue 212 CYS Chi-restraints excluded: chain n residue 218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 622 random chunks: chunk 391 optimal weight: 9.9990 chunk 525 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 454 optimal weight: 0.9980 chunk 72 optimal weight: 0.0170 chunk 137 optimal weight: 0.5980 chunk 494 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 507 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 165 HIS B 207 GLN C 238 HIS D 223 GLN F 194 ASN F 195 ASN F 271 ASN ** H 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN a 72 ASN b 207 GLN f 194 ASN ** h 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 169 GLN m 165 GLN m 280 ASN n 66 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.150002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125886 restraints weight = 64134.396| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.98 r_work: 0.3214 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 50188 Z= 0.147 Angle : 0.537 14.402 67898 Z= 0.283 Chirality : 0.042 0.167 7548 Planarity : 0.004 0.058 8804 Dihedral : 4.127 28.855 7004 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.92 % Allowed : 24.06 % Favored : 73.02 % 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: 0.05 (0.11), residues: 6306 helix: 1.71 (0.11), residues: 2240 sheet: -0.34 (0.13), residues: 1488 loop : -1.22 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 145 HIS 0.006 0.001 HIS E 191 PHE 0.027 0.001 PHE F 401 TYR 0.017 0.001 TYR B 74 ARG 0.010 0.000 ARG I 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15003.11 seconds wall clock time: 259 minutes 35.79 seconds (15575.79 seconds total)