Starting phenix.real_space_refine on Sun Feb 18 11:55:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fs8_29417/02_2024/8fs8_29417_updated.pdb" } resolution = 3.04 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 68 5.49 5 Mg 4 5.21 5 S 114 5.16 5 C 13702 2.51 5 N 3764 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21906 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3489 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2503 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 9, 'TRANS': 309} Chain: "C" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2586 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain: "D" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2616 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2620 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 317} Chain breaks: 2 Chain: "F" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2216 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 7 Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2303 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 4, 'TRANS': 285} Chain breaks: 2 Chain: "H" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2296 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 5 Chain: "I" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "J" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 201 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.69, per 1000 atoms: 0.53 Number of scatterers: 21906 At special positions: 0 Unit cell: (122.544, 129.996, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 114 16.00 P 68 15.00 Mg 4 11.99 O 4254 8.00 N 3764 7.00 C 13702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 3.5 seconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 18 sheets defined 44.0% alpha, 12.7% beta 21 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 9.55 Creating SS restraints... Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.901A pdb=" N GLU A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 162 through 175 removed outlier: 4.162A pdb=" N PHE A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 210 Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 374 through 390 removed outlier: 5.455A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY A 390 " --> pdb=" O THR A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.518A pdb=" N MET A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.654A pdb=" N LEU A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 470 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 484 through 496 Proline residue: A 489 - end of helix removed outlier: 4.479A pdb=" N CYS A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 74 removed outlier: 7.596A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 3.912A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 156 Processing helix chain 'B' and resid 170 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 275 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 321 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 42 Processing helix chain 'C' and resid 59 through 70 removed outlier: 3.971A pdb=" N ILE C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.838A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.753A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 293 through 312 removed outlier: 3.539A pdb=" N VAL C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.716A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 85 through 91 removed outlier: 4.074A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.823A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.549A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 207 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 229 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 310 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 21 through 32 removed outlier: 4.237A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 4.087A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 291 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 333 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 15 through 29 Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 97 through 112 Processing helix chain 'F' and resid 214 through 219 Processing helix chain 'F' and resid 241 through 251 removed outlier: 4.394A pdb=" N ALA F 245 " --> pdb=" O GLU F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 424 removed outlier: 3.780A pdb=" N VAL F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 removed outlier: 4.230A pdb=" N LEU G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 87 through 93 Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 239 through 245 removed outlier: 4.739A pdb=" N LYS G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 329 removed outlier: 3.550A pdb=" N THR G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 26 Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 98 through 101 No H-bonds generated for 'chain 'H' and resid 98 through 101' Processing helix chain 'H' and resid 163 through 166 No H-bonds generated for 'chain 'H' and resid 163 through 166' Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 327 through 338 removed outlier: 3.522A pdb=" N ASN H 331 " --> pdb=" O LYS H 327 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) Proline residue: H 337 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 184 through 186 Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.588A pdb=" N LEU B 161 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 143 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.731A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 3.710A pdb=" N GLY D 65 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.217A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU E 94 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN E 141 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE E 96 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR E 97 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN E 86 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 4 through 7 Processing sheet with id= G, first strand: chain 'F' and resid 91 through 95 Processing sheet with id= H, first strand: chain 'F' and resid 67 through 71 removed outlier: 3.636A pdb=" N GLN F 463 " --> pdb=" O THR F 71 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 427 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET F 231 " --> pdb=" O ILE F 432 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 154 through 156 Processing sheet with id= J, first strand: chain 'F' and resid 159 through 162 removed outlier: 3.559A pdb=" N PHE F 160 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 405 through 411 removed outlier: 3.521A pdb=" N ILE F 284 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL F 267 " --> pdb=" O GLU F 280 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 280 " --> pdb=" O VAL F 267 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 11 through 15 Processing sheet with id= M, first strand: chain 'G' and resid 36 through 41 Processing sheet with id= N, first strand: chain 'G' and resid 45 through 52 removed outlier: 3.549A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL G 264 " --> pdb=" O ASP G 260 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 270 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS G 159 " --> pdb=" O LEU G 214 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU G 214 " --> pdb=" O LYS G 159 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 232 through 238 removed outlier: 3.959A pdb=" N GLU G 189 " --> pdb=" O GLU G 185 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 3 through 7 removed outlier: 6.483A pdb=" N GLU H 139 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE H 116 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL H 137 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE H 118 " --> pdb=" O ILE H 135 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE H 135 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 295 through 297 removed outlier: 3.839A pdb=" N ASN H 228 " --> pdb=" O PHE H 353 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE H 353 " --> pdb=" O ASN H 228 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN H 348 " --> pdb=" O GLN H 365 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN H 365 " --> pdb=" O ASN H 348 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN H 363 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H 38 " --> pdb=" O THR H 35 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N MET H 44 " --> pdb=" O ASP H 29 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASP H 29 " --> pdb=" O MET H 44 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 321 through 325 removed outlier: 3.652A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 7.69 Time building geometry restraints manager: 10.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7083 1.36 - 1.51: 5957 1.51 - 1.65: 9184 1.65 - 1.80: 69 1.80 - 1.95: 100 Bond restraints: 22393 Sorted by residual: bond pdb=" N ILE F 468 " pdb=" CA ILE F 468 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.44e+00 bond pdb=" N ASN E 103 " pdb=" CA ASN E 103 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.46e+00 bond pdb=" N LEU B 133 " pdb=" CA LEU B 133 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.27e-02 6.20e+03 6.86e+00 bond pdb=" C SER E 175 " pdb=" N PRO E 176 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.85e+00 bond pdb=" N ASP E 100 " pdb=" CA ASP E 100 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.33e-02 5.65e+03 6.42e+00 ... (remaining 22388 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.69: 869 106.69 - 114.05: 13281 114.05 - 121.42: 10939 121.42 - 128.78: 5245 128.78 - 136.15: 163 Bond angle restraints: 30497 Sorted by residual: angle pdb=" N GLU C 332 " pdb=" CA GLU C 332 " pdb=" C GLU C 332 " ideal model delta sigma weight residual 113.23 107.05 6.18 1.24e+00 6.50e-01 2.49e+01 angle pdb=" CA GLY E 102 " pdb=" C GLY E 102 " pdb=" O GLY E 102 " ideal model delta sigma weight residual 121.18 117.19 3.99 8.80e-01 1.29e+00 2.05e+01 angle pdb=" N THR H 290 " pdb=" CA THR H 290 " pdb=" C THR H 290 " ideal model delta sigma weight residual 114.04 109.20 4.84 1.24e+00 6.50e-01 1.52e+01 angle pdb=" N ASN B 136 " pdb=" CA ASN B 136 " pdb=" C ASN B 136 " ideal model delta sigma weight residual 113.28 108.61 4.67 1.22e+00 6.72e-01 1.47e+01 angle pdb=" N ASN C 333 " pdb=" CA ASN C 333 " pdb=" C ASN C 333 " ideal model delta sigma weight residual 113.18 108.65 4.53 1.21e+00 6.83e-01 1.40e+01 ... (remaining 30492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.25: 12710 23.25 - 46.50: 615 46.50 - 69.75: 210 69.75 - 93.00: 9 93.00 - 116.25: 1 Dihedral angle restraints: 13545 sinusoidal: 5965 harmonic: 7580 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -176.26 116.25 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" CA ASN C 180 " pdb=" CB ASN C 180 " pdb=" CG ASN C 180 " pdb=" OD1 ASN C 180 " ideal model delta sinusoidal sigma weight residual -90.00 -159.37 69.37 2 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" O1B AGS D 401 " pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " pdb=" PG AGS D 401 " ideal model delta sinusoidal sigma weight residual 68.91 157.20 -88.29 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 13542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2548 0.035 - 0.071: 709 0.071 - 0.106: 216 0.106 - 0.141: 51 0.141 - 0.177: 3 Chirality restraints: 3527 Sorted by residual: chirality pdb=" CB ILE G 137 " pdb=" CA ILE G 137 " pdb=" CG1 ILE G 137 " pdb=" CG2 ILE G 137 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ASP E 100 " pdb=" N ASP E 100 " pdb=" C ASP E 100 " pdb=" CB ASP E 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CA ILE F 468 " pdb=" N ILE F 468 " pdb=" C ILE F 468 " pdb=" CB ILE F 468 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 3524 not shown) Planarity restraints: 3643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 217 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C LEU D 217 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU D 217 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 218 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " -0.023 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" N9 DG I 28 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 131 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C MET B 131 " -0.030 2.00e-02 2.50e+03 pdb=" O MET B 131 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 132 " 0.010 2.00e-02 2.50e+03 ... (remaining 3640 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 208 2.58 - 3.16: 18341 3.16 - 3.74: 36608 3.74 - 4.32: 49489 4.32 - 4.90: 81427 Nonbonded interactions: 186073 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR C 60 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR B 56 " pdb="MG MG B 402 " model vdw 2.218 2.170 nonbonded pdb=" O GLN A 207 " pdb=" OG SER A 211 " model vdw 2.236 2.440 ... (remaining 186068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.030 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: 0.020 Extract box with map and model: 16.670 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 64.660 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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 : 0.002 0.039 22393 Z= 0.155 Angle : 0.534 6.692 30497 Z= 0.330 Chirality : 0.038 0.177 3527 Planarity : 0.003 0.044 3643 Dihedral : 14.335 116.254 8601 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.29 % Allowed : 7.31 % Favored : 89.40 % 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: 0.66 (0.18), residues: 2532 helix: 1.71 (0.16), residues: 1165 sheet: -0.66 (0.24), residues: 525 loop : -0.53 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 259 HIS 0.004 0.000 HIS E 18 PHE 0.010 0.001 PHE A 201 TYR 0.009 0.001 TYR A 67 ARG 0.002 0.000 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 554 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7846 (tt0) cc_final: 0.7187 (tm-30) REVERT: A 163 MET cc_start: 0.6551 (mtm) cc_final: 0.5838 (mtm) REVERT: A 174 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.5957 (ptm160) REVERT: A 196 ASP cc_start: 0.7677 (t0) cc_final: 0.7437 (t0) REVERT: A 225 GLU cc_start: 0.7597 (tt0) cc_final: 0.6991 (mp0) REVERT: A 289 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6540 (mtmm) REVERT: A 374 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6511 (tp30) REVERT: A 436 HIS cc_start: 0.4305 (m-70) cc_final: 0.3828 (m-70) REVERT: A 443 PHE cc_start: 0.7430 (t80) cc_final: 0.7159 (t80) REVERT: B 38 LYS cc_start: 0.7533 (tmmm) cc_final: 0.7070 (mtmt) REVERT: B 146 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7182 (mt0) REVERT: B 152 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 272 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7508 (mmm160) REVERT: C 250 SER cc_start: 0.7262 (m) cc_final: 0.6947 (p) REVERT: C 256 TRP cc_start: 0.8091 (OUTLIER) cc_final: 0.6403 (t60) REVERT: D 83 TYR cc_start: 0.7239 (m-80) cc_final: 0.6940 (m-80) REVERT: E 19 ASN cc_start: 0.6100 (m110) cc_final: 0.5824 (m-40) REVERT: E 32 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6420 (mp10) REVERT: E 34 ARG cc_start: 0.7177 (ptp90) cc_final: 0.6107 (ptm160) REVERT: E 68 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7140 (tm) REVERT: E 221 ARG cc_start: 0.6469 (mtp180) cc_final: 0.6129 (mtp-110) REVERT: E 329 ASP cc_start: 0.8077 (p0) cc_final: 0.7866 (p0) REVERT: F 109 ARG cc_start: 0.7665 (mpt90) cc_final: 0.7443 (mmt180) REVERT: F 120 THR cc_start: 0.6685 (OUTLIER) cc_final: 0.6259 (m) REVERT: F 162 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6174 (tm-30) REVERT: F 263 HIS cc_start: 0.6296 (t-90) cc_final: 0.6059 (t-90) REVERT: F 293 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6871 (tt0) REVERT: F 422 TYR cc_start: 0.7459 (t80) cc_final: 0.7185 (t80) REVERT: F 461 ARG cc_start: 0.5767 (OUTLIER) cc_final: 0.5475 (ptm160) REVERT: G 40 PHE cc_start: 0.7072 (m-80) cc_final: 0.6498 (m-80) REVERT: G 188 ASP cc_start: 0.7642 (m-30) cc_final: 0.7349 (m-30) REVERT: G 270 LEU cc_start: 0.6031 (tt) cc_final: 0.5573 (mp) REVERT: G 321 GLN cc_start: 0.8006 (tt0) cc_final: 0.7620 (mp10) REVERT: H 158 ASP cc_start: 0.7336 (p0) cc_final: 0.7096 (p0) REVERT: H 282 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6317 (mm) REVERT: H 320 LYS cc_start: 0.7100 (mmtm) cc_final: 0.6756 (mmtm) REVERT: H 352 TRP cc_start: 0.7723 (m-90) cc_final: 0.7523 (m-90) REVERT: H 364 MET cc_start: 0.7705 (ptm) cc_final: 0.7302 (ptt) outliers start: 77 outliers final: 24 residues processed: 600 average time/residue: 0.3524 time to fit residues: 319.5599 Evaluate side-chains 390 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 357 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 282 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 10.0000 chunk 197 optimal weight: 0.0970 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 236 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 355 ASN A 368 ASN A 409 ASN A 436 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 333 ASN ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN G 9 ASN H 27 GLN H 132 ASN H 295 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22393 Z= 0.161 Angle : 0.503 8.267 30497 Z= 0.266 Chirality : 0.040 0.156 3527 Planarity : 0.004 0.034 3643 Dihedral : 16.375 101.299 3517 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.59 % Allowed : 12.01 % Favored : 84.40 % 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: 0.64 (0.18), residues: 2532 helix: 1.63 (0.16), residues: 1181 sheet: -0.64 (0.24), residues: 524 loop : -0.50 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 42 HIS 0.008 0.001 HIS F 203 PHE 0.020 0.001 PHE B 96 TYR 0.023 0.001 TYR A 67 ARG 0.005 0.000 ARG A 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 373 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLN cc_start: 0.7877 (tt0) cc_final: 0.7186 (tm-30) REVERT: A 163 MET cc_start: 0.6663 (mtm) cc_final: 0.5953 (mtm) REVERT: A 178 MET cc_start: 0.7176 (mpp) cc_final: 0.6885 (mpp) REVERT: A 196 ASP cc_start: 0.7882 (t0) cc_final: 0.7542 (t0) REVERT: A 225 GLU cc_start: 0.7608 (tt0) cc_final: 0.6867 (mp0) REVERT: A 289 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6497 (mtmm) REVERT: A 306 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7236 (mt0) REVERT: A 374 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6595 (tp30) REVERT: A 436 HIS cc_start: 0.4759 (m90) cc_final: 0.4489 (m90) REVERT: B 38 LYS cc_start: 0.7511 (tmmm) cc_final: 0.7084 (mtmt) REVERT: B 133 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (mt) REVERT: B 272 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7690 (mmm160) REVERT: C 205 MET cc_start: 0.7251 (mmt) cc_final: 0.7021 (mmt) REVERT: C 250 SER cc_start: 0.7233 (m) cc_final: 0.6868 (p) REVERT: D 227 ASP cc_start: 0.7896 (t0) cc_final: 0.6645 (t70) REVERT: D 255 GLN cc_start: 0.7711 (tp40) cc_final: 0.7494 (mt0) REVERT: E 19 ASN cc_start: 0.6153 (m110) cc_final: 0.5868 (m-40) REVERT: E 32 GLN cc_start: 0.7165 (mm-40) cc_final: 0.6382 (mp10) REVERT: E 34 ARG cc_start: 0.7312 (ptp90) cc_final: 0.6130 (ptm160) REVERT: E 221 ARG cc_start: 0.6459 (mtp180) cc_final: 0.6161 (mtp-110) REVERT: E 329 ASP cc_start: 0.8115 (p0) cc_final: 0.7900 (p0) REVERT: F 120 THR cc_start: 0.6646 (OUTLIER) cc_final: 0.6260 (m) REVERT: F 293 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6861 (tt0) REVERT: F 461 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5456 (ptm160) REVERT: G 40 PHE cc_start: 0.7127 (m-80) cc_final: 0.6911 (m-80) REVERT: G 188 ASP cc_start: 0.7589 (m-30) cc_final: 0.7315 (m-30) REVERT: G 270 LEU cc_start: 0.6291 (tt) cc_final: 0.5715 (mp) REVERT: G 321 GLN cc_start: 0.8082 (tt0) cc_final: 0.7707 (mp10) REVERT: H 6 THR cc_start: 0.7439 (p) cc_final: 0.7215 (p) REVERT: H 158 ASP cc_start: 0.7444 (p0) cc_final: 0.7105 (p0) REVERT: H 253 LYS cc_start: 0.8190 (tmtm) cc_final: 0.7884 (tptt) REVERT: H 320 LYS cc_start: 0.6936 (mmtm) cc_final: 0.6671 (mmtm) REVERT: H 375 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7064 (mt-10) outliers start: 84 outliers final: 50 residues processed: 429 average time/residue: 0.3267 time to fit residues: 217.8436 Evaluate side-chains 392 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 336 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 256 TRP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 0.0170 chunk 255 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 92 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN F 261 HIS F 263 HIS G 218 GLN H 57 GLN H 132 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22393 Z= 0.358 Angle : 0.630 8.190 30497 Z= 0.328 Chirality : 0.044 0.180 3527 Planarity : 0.005 0.050 3643 Dihedral : 16.432 95.212 3509 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 4.87 % Allowed : 13.21 % Favored : 81.92 % 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: -0.21 (0.17), residues: 2532 helix: 0.84 (0.15), residues: 1187 sheet: -0.94 (0.23), residues: 529 loop : -0.86 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 324 HIS 0.009 0.002 HIS E 18 PHE 0.019 0.002 PHE E 305 TYR 0.024 0.002 TYR A 67 ARG 0.006 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 346 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6921 (mtm) cc_final: 0.6210 (mtm) REVERT: A 184 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 196 ASP cc_start: 0.7942 (t0) cc_final: 0.7572 (t0) REVERT: A 225 GLU cc_start: 0.7690 (tt0) cc_final: 0.7051 (mp0) REVERT: A 289 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6548 (mtmm) REVERT: A 450 ARG cc_start: 0.6451 (ptt-90) cc_final: 0.6229 (ptt-90) REVERT: B 38 LYS cc_start: 0.7534 (tmmm) cc_final: 0.6992 (mtmt) REVERT: B 67 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.5909 (mm) REVERT: B 243 SER cc_start: 0.8693 (m) cc_final: 0.8418 (p) REVERT: B 272 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7707 (mmm160) REVERT: C 98 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7374 (ttpt) REVERT: C 250 SER cc_start: 0.7386 (m) cc_final: 0.6764 (p) REVERT: D 83 TYR cc_start: 0.7058 (m-80) cc_final: 0.6854 (m-80) REVERT: D 155 ARG cc_start: 0.7969 (mmp-170) cc_final: 0.7621 (mmm160) REVERT: D 160 TYR cc_start: 0.8289 (m-80) cc_final: 0.8078 (m-80) REVERT: D 353 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7263 (mp) REVERT: E 19 ASN cc_start: 0.6370 (m110) cc_final: 0.6100 (m110) REVERT: E 32 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6421 (mp10) REVERT: E 34 ARG cc_start: 0.7438 (ptp90) cc_final: 0.6246 (ptm160) REVERT: E 210 ARG cc_start: 0.6248 (tpp80) cc_final: 0.5752 (mmt180) REVERT: E 221 ARG cc_start: 0.6652 (mtp180) cc_final: 0.6229 (mtp-110) REVERT: F 293 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6920 (tt0) REVERT: F 421 LEU cc_start: 0.7890 (mt) cc_final: 0.7685 (mt) REVERT: F 461 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.4976 (ptm-80) REVERT: F 472 LYS cc_start: 0.7241 (mtmm) cc_final: 0.6864 (mtmm) REVERT: G 9 ASN cc_start: 0.8259 (m-40) cc_final: 0.7913 (m-40) REVERT: G 96 MET cc_start: 0.6932 (tpt) cc_final: 0.6732 (tpt) REVERT: G 168 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7076 (tmtt) REVERT: G 188 ASP cc_start: 0.7709 (m-30) cc_final: 0.7403 (m-30) REVERT: G 321 GLN cc_start: 0.8102 (tt0) cc_final: 0.7705 (mp10) REVERT: G 325 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8740 (mt-10) REVERT: H 6 THR cc_start: 0.7503 (p) cc_final: 0.7129 (p) REVERT: H 158 ASP cc_start: 0.7505 (p0) cc_final: 0.7117 (p0) REVERT: H 253 LYS cc_start: 0.8027 (tmtm) cc_final: 0.7752 (tptt) REVERT: H 320 LYS cc_start: 0.6840 (mmtm) cc_final: 0.6569 (mmtm) outliers start: 114 outliers final: 77 residues processed: 424 average time/residue: 0.3504 time to fit residues: 232.2206 Evaluate side-chains 405 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 322 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 151 GLN Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 224 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 388 ASN A 409 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 128 ASN H 57 GLN H 295 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22393 Z= 0.173 Angle : 0.506 7.853 30497 Z= 0.266 Chirality : 0.040 0.149 3527 Planarity : 0.004 0.075 3643 Dihedral : 16.203 94.992 3503 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.62 % Allowed : 15.18 % Favored : 80.21 % 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 (0.17), residues: 2532 helix: 1.10 (0.15), residues: 1189 sheet: -0.89 (0.23), residues: 528 loop : -0.76 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 42 HIS 0.006 0.001 HIS H 295 PHE 0.032 0.002 PHE H 353 TYR 0.024 0.001 TYR A 67 ARG 0.004 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 350 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6846 (mtm) cc_final: 0.6159 (mtm) REVERT: A 178 MET cc_start: 0.7244 (mpp) cc_final: 0.6888 (mpp) REVERT: A 184 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 196 ASP cc_start: 0.7856 (t0) cc_final: 0.7488 (t0) REVERT: A 225 GLU cc_start: 0.7659 (tt0) cc_final: 0.7042 (mp0) REVERT: A 289 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6608 (mtmm) REVERT: A 359 MET cc_start: 0.7707 (ttp) cc_final: 0.7503 (ptm) REVERT: B 38 LYS cc_start: 0.7589 (tmmm) cc_final: 0.7010 (mtmt) REVERT: B 243 SER cc_start: 0.8700 (m) cc_final: 0.8433 (p) REVERT: B 272 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7792 (mmm160) REVERT: C 98 LYS cc_start: 0.7784 (ttpt) cc_final: 0.7266 (ttpt) REVERT: C 205 MET cc_start: 0.7659 (mmt) cc_final: 0.7404 (mmt) REVERT: C 250 SER cc_start: 0.7425 (m) cc_final: 0.6860 (p) REVERT: D 83 TYR cc_start: 0.7090 (m-80) cc_final: 0.6822 (m-80) REVERT: D 207 GLN cc_start: 0.7672 (tp40) cc_final: 0.7059 (tp40) REVERT: D 353 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7231 (mp) REVERT: E 32 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6373 (mp10) REVERT: E 34 ARG cc_start: 0.7410 (ptp90) cc_final: 0.5540 (ptm160) REVERT: E 52 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.4764 (mpt90) REVERT: E 135 TYR cc_start: 0.4964 (OUTLIER) cc_final: 0.3984 (m-80) REVERT: E 221 ARG cc_start: 0.6596 (mtp180) cc_final: 0.6206 (mtp-110) REVERT: F 111 MET cc_start: 0.5376 (mmm) cc_final: 0.5082 (mmt) REVERT: F 162 GLU cc_start: 0.6183 (tm-30) cc_final: 0.5646 (tm-30) REVERT: F 228 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5660 (tp) REVERT: F 293 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6949 (tt0) REVERT: F 461 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.5131 (ptm160) REVERT: F 472 LYS cc_start: 0.7252 (mtmm) cc_final: 0.6872 (mtmm) REVERT: G 9 ASN cc_start: 0.8273 (m-40) cc_final: 0.7908 (m-40) REVERT: G 96 MET cc_start: 0.6949 (tpt) cc_final: 0.6596 (tpt) REVERT: G 168 LYS cc_start: 0.7935 (ttmt) cc_final: 0.7163 (tttt) REVERT: G 188 ASP cc_start: 0.7680 (m-30) cc_final: 0.7390 (m-30) REVERT: G 206 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7439 (mtpp) REVERT: G 321 GLN cc_start: 0.8084 (tt0) cc_final: 0.7717 (mp10) REVERT: G 325 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8740 (mt-10) REVERT: H 6 THR cc_start: 0.7206 (p) cc_final: 0.6278 (p) REVERT: H 81 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7286 (mt) REVERT: H 158 ASP cc_start: 0.7527 (p0) cc_final: 0.7108 (p0) REVERT: H 253 LYS cc_start: 0.8028 (tmtm) cc_final: 0.7756 (tptt) outliers start: 108 outliers final: 69 residues processed: 424 average time/residue: 0.3299 time to fit residues: 222.0529 Evaluate side-chains 403 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 324 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 409 ASN Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 187 optimal weight: 0.4980 chunk 103 optimal weight: 0.5980 chunk 214 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 225 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 260 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22393 Z= 0.176 Angle : 0.504 8.013 30497 Z= 0.264 Chirality : 0.040 0.147 3527 Planarity : 0.003 0.048 3643 Dihedral : 16.126 99.187 3503 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.62 % Allowed : 15.65 % Favored : 79.73 % 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: 0.14 (0.17), residues: 2532 helix: 1.15 (0.15), residues: 1192 sheet: -0.86 (0.23), residues: 531 loop : -0.65 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 42 HIS 0.006 0.001 HIS E 18 PHE 0.032 0.001 PHE H 353 TYR 0.021 0.001 TYR A 67 ARG 0.004 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 340 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6863 (mtm) cc_final: 0.6129 (mtm) REVERT: A 178 MET cc_start: 0.7184 (mpp) cc_final: 0.6803 (mpp) REVERT: A 184 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7921 (mp) REVERT: A 196 ASP cc_start: 0.7878 (t0) cc_final: 0.7482 (t0) REVERT: A 225 GLU cc_start: 0.7649 (tt0) cc_final: 0.7044 (mp0) REVERT: A 250 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6217 (mmt) REVERT: A 289 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6643 (mtmm) REVERT: B 38 LYS cc_start: 0.7620 (tmmm) cc_final: 0.7017 (mtmt) REVERT: B 243 SER cc_start: 0.8706 (m) cc_final: 0.8439 (p) REVERT: B 272 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7807 (mmm160) REVERT: C 98 LYS cc_start: 0.7876 (ttpt) cc_final: 0.7343 (ttpt) REVERT: C 205 MET cc_start: 0.7642 (mmt) cc_final: 0.7356 (mmt) REVERT: C 250 SER cc_start: 0.7388 (m) cc_final: 0.6817 (p) REVERT: D 83 TYR cc_start: 0.7076 (m-80) cc_final: 0.6808 (m-80) REVERT: D 207 GLN cc_start: 0.7682 (tp40) cc_final: 0.7078 (tp40) REVERT: D 353 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7165 (mp) REVERT: E 32 GLN cc_start: 0.7101 (mm-40) cc_final: 0.6400 (mt0) REVERT: E 34 ARG cc_start: 0.7455 (ptp90) cc_final: 0.5621 (ptm160) REVERT: E 52 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.4465 (mpt90) REVERT: E 135 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.3977 (m-80) REVERT: E 210 ARG cc_start: 0.6353 (tpp80) cc_final: 0.5821 (mmt180) REVERT: E 221 ARG cc_start: 0.6588 (mtp180) cc_final: 0.6198 (mtp-110) REVERT: F 111 MET cc_start: 0.5297 (mmm) cc_final: 0.5019 (mmt) REVERT: F 119 MET cc_start: 0.5630 (tmm) cc_final: 0.5149 (tmm) REVERT: F 162 GLU cc_start: 0.6270 (tm-30) cc_final: 0.5938 (tm-30) REVERT: F 228 ILE cc_start: 0.5820 (OUTLIER) cc_final: 0.5595 (tp) REVERT: F 293 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6909 (tt0) REVERT: F 461 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5152 (ptm160) REVERT: F 472 LYS cc_start: 0.7269 (mtmm) cc_final: 0.6802 (mtmt) REVERT: G 9 ASN cc_start: 0.8281 (m-40) cc_final: 0.7922 (m-40) REVERT: G 96 MET cc_start: 0.7091 (tpt) cc_final: 0.6875 (tpt) REVERT: G 168 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7167 (tttt) REVERT: G 188 ASP cc_start: 0.7648 (m-30) cc_final: 0.7392 (m-30) REVERT: G 206 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7392 (mtpp) REVERT: G 321 GLN cc_start: 0.8080 (tt0) cc_final: 0.7715 (mp10) REVERT: G 325 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8737 (mt-10) REVERT: H 63 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.6098 (pt0) REVERT: H 81 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7296 (mt) REVERT: H 158 ASP cc_start: 0.7517 (p0) cc_final: 0.7100 (p0) REVERT: H 253 LYS cc_start: 0.8013 (tmtm) cc_final: 0.7753 (tptt) REVERT: H 320 LYS cc_start: 0.7365 (mmtm) cc_final: 0.7124 (mttp) outliers start: 108 outliers final: 76 residues processed: 410 average time/residue: 0.3300 time to fit residues: 211.6692 Evaluate side-chains 416 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 328 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 87 ASN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 147 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 HIS H 122 ASN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22393 Z= 0.166 Angle : 0.497 7.839 30497 Z= 0.261 Chirality : 0.040 0.144 3527 Planarity : 0.003 0.049 3643 Dihedral : 16.044 104.467 3503 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.66 % Allowed : 16.20 % Favored : 79.14 % 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: 0.24 (0.17), residues: 2532 helix: 1.24 (0.16), residues: 1191 sheet: -0.82 (0.23), residues: 532 loop : -0.62 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 42 HIS 0.007 0.001 HIS F 441 PHE 0.035 0.001 PHE H 353 TYR 0.021 0.001 TYR A 67 ARG 0.003 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 340 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6852 (mtm) cc_final: 0.6119 (mtm) REVERT: A 175 TYR cc_start: 0.7866 (m-80) cc_final: 0.7208 (m-80) REVERT: A 178 MET cc_start: 0.7215 (mpp) cc_final: 0.6840 (mpp) REVERT: A 196 ASP cc_start: 0.7881 (t0) cc_final: 0.7473 (t0) REVERT: A 225 GLU cc_start: 0.7634 (tt0) cc_final: 0.7008 (mp0) REVERT: A 250 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6165 (mmt) REVERT: A 289 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6703 (mtmm) REVERT: B 38 LYS cc_start: 0.7600 (tmmm) cc_final: 0.7028 (mtmt) REVERT: B 67 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5903 (mm) REVERT: B 243 SER cc_start: 0.8719 (m) cc_final: 0.8451 (p) REVERT: B 272 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7837 (mmm160) REVERT: C 98 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7352 (ttpt) REVERT: C 132 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7182 (tpm-80) REVERT: C 205 MET cc_start: 0.7618 (mmt) cc_final: 0.7302 (mmt) REVERT: C 250 SER cc_start: 0.7428 (m) cc_final: 0.6846 (p) REVERT: D 83 TYR cc_start: 0.7071 (m-80) cc_final: 0.6806 (m-80) REVERT: D 207 GLN cc_start: 0.7726 (tp40) cc_final: 0.7121 (tp40) REVERT: E 19 ASN cc_start: 0.6274 (m110) cc_final: 0.5723 (m110) REVERT: E 32 GLN cc_start: 0.6933 (mm-40) cc_final: 0.6261 (mt0) REVERT: E 34 ARG cc_start: 0.7444 (ptp90) cc_final: 0.5598 (ptm160) REVERT: E 52 ARG cc_start: 0.5985 (OUTLIER) cc_final: 0.4285 (mpt90) REVERT: E 135 TYR cc_start: 0.4918 (OUTLIER) cc_final: 0.3970 (m-80) REVERT: E 210 ARG cc_start: 0.6371 (tpp80) cc_final: 0.5829 (mmt180) REVERT: E 221 ARG cc_start: 0.6589 (mtp180) cc_final: 0.6295 (mtp-110) REVERT: F 8 ASN cc_start: 0.6692 (t0) cc_final: 0.6179 (m-40) REVERT: F 119 MET cc_start: 0.5596 (tmm) cc_final: 0.5353 (tmm) REVERT: F 162 GLU cc_start: 0.6419 (tm-30) cc_final: 0.5849 (tm-30) REVERT: F 228 ILE cc_start: 0.5794 (OUTLIER) cc_final: 0.5520 (tp) REVERT: F 293 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6888 (tt0) REVERT: F 413 LYS cc_start: 0.7857 (mptt) cc_final: 0.7614 (mtpp) REVERT: F 461 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5113 (ptm160) REVERT: F 472 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6778 (mtmt) REVERT: G 9 ASN cc_start: 0.8297 (m-40) cc_final: 0.7917 (m-40) REVERT: G 96 MET cc_start: 0.7166 (tpt) cc_final: 0.6828 (tpt) REVERT: G 168 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7156 (tttt) REVERT: G 188 ASP cc_start: 0.7636 (m-30) cc_final: 0.7371 (m-30) REVERT: G 206 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7359 (mtpp) REVERT: G 321 GLN cc_start: 0.8081 (tt0) cc_final: 0.7700 (mp10) REVERT: G 325 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8728 (mp0) REVERT: H 81 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7302 (mt) REVERT: H 158 ASP cc_start: 0.7614 (p0) cc_final: 0.7175 (p0) REVERT: H 288 ILE cc_start: 0.7765 (mp) cc_final: 0.7545 (mt) outliers start: 109 outliers final: 76 residues processed: 413 average time/residue: 0.3199 time to fit residues: 206.8855 Evaluate side-chains 408 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 321 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 118 ASN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 87 ASN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 245 ILE Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 0.0170 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22393 Z= 0.194 Angle : 0.511 8.067 30497 Z= 0.266 Chirality : 0.040 0.152 3527 Planarity : 0.003 0.041 3643 Dihedral : 15.991 109.597 3499 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.87 % Allowed : 16.25 % Favored : 78.88 % 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: 0.22 (0.17), residues: 2532 helix: 1.20 (0.15), residues: 1198 sheet: -0.78 (0.23), residues: 532 loop : -0.64 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 290 HIS 0.013 0.001 HIS F 291 PHE 0.034 0.002 PHE H 353 TYR 0.018 0.001 TYR A 67 ARG 0.005 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 336 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6831 (mtm) cc_final: 0.6095 (mtm) REVERT: A 175 TYR cc_start: 0.7963 (m-80) cc_final: 0.7205 (m-80) REVERT: A 184 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 196 ASP cc_start: 0.7906 (t0) cc_final: 0.7474 (t0) REVERT: A 225 GLU cc_start: 0.7681 (tt0) cc_final: 0.7040 (mp0) REVERT: A 250 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6232 (mmt) REVERT: A 289 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6719 (mtmm) REVERT: B 38 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7027 (mtmt) REVERT: B 67 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.5882 (mm) REVERT: B 243 SER cc_start: 0.8737 (m) cc_final: 0.8467 (p) REVERT: B 272 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7844 (mmm160) REVERT: C 98 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7381 (ttpt) REVERT: C 205 MET cc_start: 0.7691 (mmt) cc_final: 0.7483 (mmt) REVERT: C 250 SER cc_start: 0.7295 (m) cc_final: 0.6714 (p) REVERT: D 207 GLN cc_start: 0.7729 (tp40) cc_final: 0.7124 (tp40) REVERT: D 318 PHE cc_start: 0.7256 (t80) cc_final: 0.6799 (t80) REVERT: D 353 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6990 (mp) REVERT: E 19 ASN cc_start: 0.6215 (m110) cc_final: 0.5968 (m-40) REVERT: E 31 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6934 (p0) REVERT: E 32 GLN cc_start: 0.6897 (mm-40) cc_final: 0.5664 (mp10) REVERT: E 34 ARG cc_start: 0.7466 (ptp90) cc_final: 0.5598 (ptm160) REVERT: E 52 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.4444 (mpt90) REVERT: E 135 TYR cc_start: 0.4968 (OUTLIER) cc_final: 0.4117 (m-80) REVERT: E 221 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6239 (mtp-110) REVERT: F 119 MET cc_start: 0.5585 (tmm) cc_final: 0.5376 (tmm) REVERT: F 162 GLU cc_start: 0.6475 (tm-30) cc_final: 0.5906 (tm-30) REVERT: F 228 ILE cc_start: 0.5860 (OUTLIER) cc_final: 0.5561 (tp) REVERT: F 246 PHE cc_start: 0.7145 (t80) cc_final: 0.6731 (t80) REVERT: F 293 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6849 (tt0) REVERT: F 421 LEU cc_start: 0.8006 (mt) cc_final: 0.7770 (mt) REVERT: F 461 ARG cc_start: 0.5646 (OUTLIER) cc_final: 0.4886 (ptm160) REVERT: F 472 LYS cc_start: 0.7340 (mtmm) cc_final: 0.6803 (mtmt) REVERT: G 9 ASN cc_start: 0.8308 (m-40) cc_final: 0.7932 (m-40) REVERT: G 96 MET cc_start: 0.7125 (tpt) cc_final: 0.6856 (tpt) REVERT: G 168 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7169 (tttt) REVERT: G 188 ASP cc_start: 0.7712 (m-30) cc_final: 0.7462 (m-30) REVERT: G 206 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.7296 (mtpp) REVERT: G 321 GLN cc_start: 0.8079 (tt0) cc_final: 0.7708 (mp10) REVERT: G 325 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8744 (mp0) REVERT: H 81 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7320 (mt) REVERT: H 158 ASP cc_start: 0.7666 (p0) cc_final: 0.7189 (p0) REVERT: H 253 LYS cc_start: 0.8026 (tmtm) cc_final: 0.7780 (tptt) outliers start: 114 outliers final: 86 residues processed: 409 average time/residue: 0.3207 time to fit residues: 205.4371 Evaluate side-chains 426 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 326 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 365 GLU Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 87 ASN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 261 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 362 ASN B 26 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22393 Z= 0.361 Angle : 0.617 8.607 30497 Z= 0.319 Chirality : 0.044 0.159 3527 Planarity : 0.004 0.044 3643 Dihedral : 16.138 113.463 3499 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.75 % Allowed : 16.80 % Favored : 78.45 % 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: -0.33 (0.17), residues: 2532 helix: 0.69 (0.15), residues: 1200 sheet: -0.90 (0.23), residues: 525 loop : -0.93 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 69 HIS 0.008 0.001 HIS B 232 PHE 0.030 0.002 PHE H 353 TYR 0.020 0.002 TYR D 83 ARG 0.007 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 334 time to evaluate : 2.519 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.6920 (mtm) cc_final: 0.6212 (mtm) REVERT: A 184 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8008 (mp) REVERT: A 196 ASP cc_start: 0.7920 (t0) cc_final: 0.7521 (t0) REVERT: A 225 GLU cc_start: 0.7742 (tt0) cc_final: 0.7113 (mp0) REVERT: A 250 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6286 (mmt) REVERT: A 289 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6710 (mtmm) REVERT: B 38 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7042 (mtmt) REVERT: B 67 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.5932 (mm) REVERT: B 272 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7823 (mmm160) REVERT: C 98 LYS cc_start: 0.7992 (ttpt) cc_final: 0.7460 (ttpt) REVERT: C 250 SER cc_start: 0.7444 (m) cc_final: 0.6692 (p) REVERT: D 207 GLN cc_start: 0.7811 (tp40) cc_final: 0.7183 (tp40) REVERT: D 255 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7580 (mt0) REVERT: D 353 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7183 (mp) REVERT: E 19 ASN cc_start: 0.6372 (m110) cc_final: 0.5920 (m110) REVERT: E 32 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6079 (mt0) REVERT: E 34 ARG cc_start: 0.7358 (ptp90) cc_final: 0.5559 (ptm160) REVERT: E 52 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4476 (mpt90) REVERT: E 135 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4227 (m-80) REVERT: E 221 ARG cc_start: 0.6734 (mtp180) cc_final: 0.6305 (mtp-110) REVERT: F 111 MET cc_start: 0.5631 (mmt) cc_final: 0.5334 (mmt) REVERT: F 119 MET cc_start: 0.5595 (tmm) cc_final: 0.5350 (tmm) REVERT: F 162 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6153 (tm-30) REVERT: F 228 ILE cc_start: 0.5841 (OUTLIER) cc_final: 0.5518 (tp) REVERT: F 246 PHE cc_start: 0.7221 (t80) cc_final: 0.6834 (t80) REVERT: F 293 GLU cc_start: 0.7480 (mt-10) cc_final: 0.6983 (tt0) REVERT: F 421 LEU cc_start: 0.7997 (mt) cc_final: 0.7768 (mt) REVERT: F 461 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4597 (ptm160) REVERT: F 472 LYS cc_start: 0.7435 (mtmm) cc_final: 0.6914 (mtmt) REVERT: G 9 ASN cc_start: 0.8389 (m-40) cc_final: 0.7963 (m-40) REVERT: G 96 MET cc_start: 0.7177 (tpt) cc_final: 0.6865 (mmm) REVERT: G 188 ASP cc_start: 0.7766 (m-30) cc_final: 0.7496 (m-30) REVERT: G 206 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7341 (mtpp) REVERT: G 321 GLN cc_start: 0.8070 (tt0) cc_final: 0.7724 (mp10) REVERT: H 158 ASP cc_start: 0.7660 (p0) cc_final: 0.7162 (p0) REVERT: H 253 LYS cc_start: 0.7988 (tmtm) cc_final: 0.7741 (tptt) REVERT: H 288 ILE cc_start: 0.7920 (mp) cc_final: 0.7698 (mt) REVERT: H 320 LYS cc_start: 0.7472 (mmtm) cc_final: 0.7085 (mttp) outliers start: 111 outliers final: 79 residues processed: 403 average time/residue: 0.3322 time to fit residues: 207.4994 Evaluate side-chains 403 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 312 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 161 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 87 ASN Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 259 MET Chi-restraints excluded: chain G residue 266 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 310 MET Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 7.9990 chunk 240 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 233 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 101 optimal weight: 0.0570 chunk 183 optimal weight: 0.0000 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 232 optimal weight: 0.7980 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 362 ASN C 317 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22393 Z= 0.161 Angle : 0.522 13.095 30497 Z= 0.271 Chirality : 0.040 0.152 3527 Planarity : 0.003 0.042 3643 Dihedral : 15.926 114.864 3497 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.38 % Allowed : 18.77 % Favored : 77.85 % 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 (0.17), residues: 2532 helix: 1.08 (0.15), residues: 1197 sheet: -0.72 (0.23), residues: 527 loop : -0.71 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 42 HIS 0.007 0.001 HIS F 441 PHE 0.051 0.001 PHE H 240 TYR 0.020 0.001 TYR A 67 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 335 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6841 (mtm) cc_final: 0.6105 (mtm) REVERT: A 184 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 196 ASP cc_start: 0.7882 (t0) cc_final: 0.7483 (t0) REVERT: A 225 GLU cc_start: 0.7640 (tt0) cc_final: 0.7009 (mp0) REVERT: A 250 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6223 (mmt) REVERT: A 289 LYS cc_start: 0.7218 (OUTLIER) cc_final: 0.6734 (mtmm) REVERT: A 306 GLN cc_start: 0.7824 (tm-30) cc_final: 0.6873 (mt0) REVERT: B 38 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7056 (mtmt) REVERT: B 67 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.5923 (mm) REVERT: B 129 ARG cc_start: 0.7439 (tpt170) cc_final: 0.6852 (tpp80) REVERT: B 243 SER cc_start: 0.8749 (m) cc_final: 0.8487 (p) REVERT: B 272 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7839 (mmm160) REVERT: C 98 LYS cc_start: 0.7928 (ttpt) cc_final: 0.7382 (ttpt) REVERT: C 132 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7286 (tpm-80) REVERT: C 205 MET cc_start: 0.7566 (mmt) cc_final: 0.7283 (mmt) REVERT: C 250 SER cc_start: 0.7259 (m) cc_final: 0.6738 (p) REVERT: D 207 GLN cc_start: 0.7661 (tp40) cc_final: 0.7059 (tp40) REVERT: D 255 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7501 (mt0) REVERT: D 318 PHE cc_start: 0.7127 (t80) cc_final: 0.6850 (t80) REVERT: E 32 GLN cc_start: 0.6735 (mm-40) cc_final: 0.5991 (mt0) REVERT: E 34 ARG cc_start: 0.7369 (ptp90) cc_final: 0.5462 (ptm160) REVERT: E 82 LYS cc_start: 0.6183 (ptmm) cc_final: 0.5794 (ttpp) REVERT: E 135 TYR cc_start: 0.5047 (OUTLIER) cc_final: 0.4140 (m-80) REVERT: E 221 ARG cc_start: 0.6659 (mtp180) cc_final: 0.6250 (mtp-110) REVERT: E 329 ASP cc_start: 0.8139 (p0) cc_final: 0.7790 (p0) REVERT: F 162 GLU cc_start: 0.6479 (tm-30) cc_final: 0.5960 (tm-30) REVERT: F 228 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5507 (tp) REVERT: F 293 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6855 (tt0) REVERT: F 296 TRP cc_start: 0.7955 (t-100) cc_final: 0.7669 (t-100) REVERT: F 413 LYS cc_start: 0.7878 (mptt) cc_final: 0.7663 (mtpp) REVERT: F 421 LEU cc_start: 0.7983 (mt) cc_final: 0.7751 (mt) REVERT: F 461 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.4697 (ptm160) REVERT: G 9 ASN cc_start: 0.8381 (m-40) cc_final: 0.7987 (m-40) REVERT: G 96 MET cc_start: 0.7185 (tpt) cc_final: 0.6699 (tmm) REVERT: G 188 ASP cc_start: 0.7737 (m-30) cc_final: 0.7514 (m-30) REVERT: G 206 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7343 (mtpp) REVERT: G 321 GLN cc_start: 0.7993 (tt0) cc_final: 0.7762 (mp10) REVERT: H 158 ASP cc_start: 0.7673 (p0) cc_final: 0.7214 (p0) REVERT: H 253 LYS cc_start: 0.8012 (tmtm) cc_final: 0.7763 (tptt) outliers start: 79 outliers final: 61 residues processed: 383 average time/residue: 0.3169 time to fit residues: 190.6994 Evaluate side-chains 387 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 315 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 298 ILE Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.7980 chunk 246 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 171 optimal weight: 0.0770 chunk 259 optimal weight: 6.9990 chunk 238 optimal weight: 0.0970 chunk 206 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 HIS C 317 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22393 Z= 0.163 Angle : 0.519 12.899 30497 Z= 0.269 Chirality : 0.039 0.156 3527 Planarity : 0.003 0.041 3643 Dihedral : 15.890 119.059 3497 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.38 % Allowed : 19.15 % Favored : 77.47 % 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: 0.22 (0.17), residues: 2532 helix: 1.16 (0.15), residues: 1196 sheet: -0.66 (0.23), residues: 527 loop : -0.66 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 69 HIS 0.006 0.001 HIS F 441 PHE 0.032 0.001 PHE H 353 TYR 0.019 0.001 TYR A 67 ARG 0.005 0.000 ARG A 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 326 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.6830 (mtm) cc_final: 0.6103 (mtm) REVERT: A 184 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7937 (mp) REVERT: A 196 ASP cc_start: 0.7884 (t0) cc_final: 0.7481 (t0) REVERT: A 204 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7365 (mm) REVERT: A 225 GLU cc_start: 0.7646 (tt0) cc_final: 0.7000 (mp0) REVERT: A 250 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6207 (mmt) REVERT: A 289 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6820 (mtmm) REVERT: A 306 GLN cc_start: 0.7835 (tm-30) cc_final: 0.6884 (mt0) REVERT: B 38 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7061 (mtmt) REVERT: B 67 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.5907 (mm) REVERT: B 243 SER cc_start: 0.8758 (m) cc_final: 0.8488 (p) REVERT: B 272 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7837 (mmm160) REVERT: C 98 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7340 (ttpt) REVERT: C 205 MET cc_start: 0.7609 (mmt) cc_final: 0.7339 (mmt) REVERT: C 250 SER cc_start: 0.7244 (m) cc_final: 0.6704 (p) REVERT: D 207 GLN cc_start: 0.7680 (tp40) cc_final: 0.7085 (tp40) REVERT: D 255 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7505 (mt0) REVERT: E 32 GLN cc_start: 0.6741 (mm-40) cc_final: 0.5676 (mt0) REVERT: E 34 ARG cc_start: 0.7379 (ptp90) cc_final: 0.5486 (ptm160) REVERT: E 82 LYS cc_start: 0.6249 (ptmm) cc_final: 0.5828 (ttpp) REVERT: E 135 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.4172 (m-80) REVERT: E 221 ARG cc_start: 0.6655 (mtp180) cc_final: 0.6244 (mtp-110) REVERT: E 329 ASP cc_start: 0.8149 (p0) cc_final: 0.7807 (p0) REVERT: F 111 MET cc_start: 0.5784 (mmt) cc_final: 0.5335 (mmt) REVERT: F 162 GLU cc_start: 0.6461 (tm-30) cc_final: 0.5902 (tm-30) REVERT: F 228 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5544 (tp) REVERT: F 246 PHE cc_start: 0.7147 (t80) cc_final: 0.6677 (t80) REVERT: F 293 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6878 (tt0) REVERT: F 296 TRP cc_start: 0.7927 (t-100) cc_final: 0.7652 (t-100) REVERT: F 413 LYS cc_start: 0.7873 (mptt) cc_final: 0.7646 (mtpp) REVERT: F 421 LEU cc_start: 0.7993 (mt) cc_final: 0.7766 (mt) REVERT: F 461 ARG cc_start: 0.5751 (OUTLIER) cc_final: 0.4742 (ptm160) REVERT: G 9 ASN cc_start: 0.8345 (m-40) cc_final: 0.7932 (m-40) REVERT: G 96 MET cc_start: 0.7141 (tpt) cc_final: 0.6813 (mmm) REVERT: G 188 ASP cc_start: 0.7766 (m-30) cc_final: 0.7547 (m-30) REVERT: G 206 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7322 (mtpp) REVERT: G 321 GLN cc_start: 0.8008 (tt0) cc_final: 0.7749 (mp10) REVERT: H 158 ASP cc_start: 0.7658 (p0) cc_final: 0.7200 (p0) REVERT: H 253 LYS cc_start: 0.8019 (tmtm) cc_final: 0.7765 (tptt) REVERT: H 352 TRP cc_start: 0.7828 (m-90) cc_final: 0.7259 (m-90) outliers start: 79 outliers final: 59 residues processed: 375 average time/residue: 0.3250 time to fit residues: 192.1958 Evaluate side-chains 390 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 173 VAL Chi-restraints excluded: chain D residue 206 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 135 TYR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 461 ARG Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 470 ARG Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 79 HIS Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain H residue 34 VAL Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 135 ILE Chi-restraints excluded: chain H residue 166 TYR Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 284 MET Chi-restraints excluded: chain H residue 335 ILE Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 317 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** H 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 HIS ** H 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.174604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138505 restraints weight = 27692.267| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 2.07 r_work: 0.3620 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22393 Z= 0.229 Angle : 0.543 12.948 30497 Z= 0.281 Chirality : 0.041 0.156 3527 Planarity : 0.004 0.042 3643 Dihedral : 15.914 120.645 3497 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.33 % Allowed : 19.11 % Favored : 77.55 % 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: 0.08 (0.17), residues: 2532 helix: 1.05 (0.15), residues: 1193 sheet: -0.69 (0.23), residues: 526 loop : -0.77 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 69 HIS 0.015 0.001 HIS A 436 PHE 0.029 0.002 PHE H 353 TYR 0.025 0.001 TYR A 67 ARG 0.006 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5621.32 seconds wall clock time: 102 minutes 25.79 seconds (6145.79 seconds total)