Starting phenix.real_space_refine on Sun Jun 15 19:18:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4k_42971/06_2025/8v4k_42971.cif" } resolution = 3.1 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= 0.002 sd= 0.021 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 12 5.49 5 Mg 4 5.21 5 S 116 5.16 5 C 11053 2.51 5 N 3022 2.21 5 O 3351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B GLU 435": not complete - not flipped Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17559 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3379 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3345 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 47 Classifications: {'peptide': 9} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 7} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3379 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3303 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3963 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 35, 'TRANS': 465} Chain breaks: 3 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 1, ' ZN': 1, 'G2P': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.66, per 1000 atoms: 0.66 Number of scatterers: 17559 At special positions: 0 Unit cell: (130.725, 124.5, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 116 16.00 P 12 15.00 Mg 4 11.99 O 3351 8.00 N 3022 7.00 C 11053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied TRANS " UNK B 431 " - " ALA B 430 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 503 " pdb="ZN ZN B 503 " - pdb=" ND1 HIS E 252 " pdb="ZN ZN B 503 " - pdb=" ND1 HIS E 434 " 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 14 sheets defined 47.7% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.973A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.829A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.705A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.910A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.958A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.712A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.620A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.584A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.983A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.036A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.192A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.689A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.873A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.603A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.913A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.525A pdb=" N VAL B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 176 " --> pdb=" O PRO B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 180 through 196 removed outlier: 4.285A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.881A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.578A pdb=" N LEU B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.655A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 295 through 299' Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.622A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.551A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.976A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.180A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.970A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.930A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.044A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 85 removed outlier: 4.622A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 85' Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 128 removed outlier: 4.263A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.473A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.761A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.874A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.796A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.839A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.980A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET C 398 " --> pdb=" O LYS C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.946A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.070A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 46 removed outlier: 3.987A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.644A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.898A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.706A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.926A pdb=" N SER D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.587A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.810A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.762A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.703A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 295 through 299' Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.597A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.602A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.891A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.023A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 425 removed outlier: 3.871A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.733A pdb=" N PHE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 270 " --> pdb=" O LEU E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 310 through 315 removed outlier: 3.888A pdb=" N TYR E 315 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 340 Processing helix chain 'E' and resid 451 through 467 removed outlier: 4.570A pdb=" N TYR E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Proline residue: E 462 - end of helix Processing helix chain 'E' and resid 480 through 485 removed outlier: 3.566A pdb=" N MET E 484 " --> pdb=" O GLU E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 497 Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 551 through 569 removed outlier: 3.671A pdb=" N PHE E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 601 removed outlier: 3.641A pdb=" N ARG E 601 " --> pdb=" O VAL E 597 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.939A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.743A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.239A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.678A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.933A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.027A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.663A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.558A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.725A pdb=" N ARG E 111 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR E 112 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG E 118 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'E' and resid 189 through 198 removed outlier: 7.203A pdb=" N VAL E 205 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N SER E 212 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE E 284 " --> pdb=" O SER E 212 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG E 243 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS E 287 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N PHE E 245 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE E 289 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 247 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE E 244 " --> pdb=" O TYR E 429 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL E 431 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE E 246 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU E 433 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER E 248 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N GLY E 435 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 216 through 220 removed outlier: 3.843A pdb=" N ARG E 238 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 795 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2937 1.31 - 1.44: 4959 1.44 - 1.57: 9877 1.57 - 1.69: 19 1.69 - 1.82: 185 Bond restraints: 17977 Sorted by residual: bond pdb=" O3B G2P B 502 " pdb=" PG G2P B 502 " ideal model delta sigma weight residual 1.716 1.609 0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" O3B G2P D 502 " pdb=" PG G2P D 502 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C PHE D 260 " pdb=" N PRO D 261 " ideal model delta sigma weight residual 1.334 1.391 -0.057 1.51e-02 4.39e+03 1.40e+01 bond pdb=" O5' G2P B 502 " pdb=" PA G2P B 502 " ideal model delta sigma weight residual 1.656 1.587 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O5' G2P D 502 " pdb=" PA G2P D 502 " ideal model delta sigma weight residual 1.656 1.587 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 17972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 23632 2.57 - 5.14: 698 5.14 - 7.72: 79 7.72 - 10.29: 18 10.29 - 12.86: 8 Bond angle restraints: 24435 Sorted by residual: angle pdb=" PA GTP C 502 " pdb=" O3A GTP C 502 " pdb=" PB GTP C 502 " ideal model delta sigma weight residual 120.50 133.36 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " ideal model delta sigma weight residual 120.50 133.32 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" N GLY A 148 " pdb=" CA GLY A 148 " pdb=" C GLY A 148 " ideal model delta sigma weight residual 112.49 117.60 -5.11 1.21e+00 6.83e-01 1.78e+01 angle pdb=" C GLY D 400 " pdb=" N GLU D 401 " pdb=" CA GLU D 401 " ideal model delta sigma weight residual 124.31 131.28 -6.97 1.67e+00 3.59e-01 1.74e+01 angle pdb=" C LEU E 460 " pdb=" N TYR E 461 " pdb=" CA TYR E 461 " ideal model delta sigma weight residual 120.09 125.12 -5.03 1.25e+00 6.40e-01 1.62e+01 ... (remaining 24430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.02: 10350 28.02 - 56.03: 298 56.03 - 84.05: 39 84.05 - 112.07: 5 112.07 - 140.09: 8 Dihedral angle restraints: 10700 sinusoidal: 4235 harmonic: 6465 Sorted by residual: dihedral pdb=" C8 GTP A 502 " pdb=" C1' GTP A 502 " pdb=" N9 GTP A 502 " pdb=" O4' GTP A 502 " ideal model delta sinusoidal sigma weight residual 104.59 -35.49 140.09 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C8 GTP C 502 " pdb=" C1' GTP C 502 " pdb=" N9 GTP C 502 " pdb=" O4' GTP C 502 " ideal model delta sinusoidal sigma weight residual 104.59 -34.73 139.32 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" C5' GTP C 502 " pdb=" O5' GTP C 502 " pdb=" PA GTP C 502 " pdb=" O3A GTP C 502 " ideal model delta sinusoidal sigma weight residual 69.27 -156.96 -133.77 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 10697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2237 0.081 - 0.163: 383 0.163 - 0.244: 36 0.244 - 0.326: 1 0.326 - 0.407: 2 Chirality restraints: 2659 Sorted by residual: chirality pdb=" CA GLU B1001 " pdb=" N GLU B1001 " pdb=" C GLU B1001 " pdb=" CB GLU B1001 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL E 25 " pdb=" CA VAL E 25 " pdb=" CG1 VAL E 25 " pdb=" CG2 VAL E 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE C 265 " pdb=" CA ILE C 265 " pdb=" CG1 ILE C 265 " pdb=" CG2 ILE C 265 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2656 not shown) Planarity restraints: 3194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 432 " -0.018 2.00e-02 2.50e+03 2.35e-02 1.11e+01 pdb=" CG TYR A 432 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 432 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 432 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 432 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 432 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 432 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 432 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 120 " -0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" CG ASP A 120 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A 120 " -0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 120 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 267 " -0.050 5.00e-02 4.00e+02 7.64e-02 9.34e+00 pdb=" N PRO D 268 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.042 5.00e-02 4.00e+02 ... (remaining 3191 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 12 2.35 - 2.99: 8007 2.99 - 3.63: 26511 3.63 - 4.26: 42519 4.26 - 4.90: 71736 Nonbonded interactions: 148785 Sorted by model distance: nonbonded pdb=" OE1 GLU B 435 " pdb="ZN ZN B 503 " model vdw 1.719 2.230 nonbonded pdb=" OE2 GLU E 255 " pdb="ZN ZN B 503 " model vdw 2.131 2.230 nonbonded pdb=" OE1 GLU E 255 " pdb="ZN ZN B 503 " model vdw 2.152 2.230 nonbonded pdb="MG MG C 501 " pdb=" O2B GTP C 502 " model vdw 2.238 2.170 nonbonded pdb=" O ASN D 226 " pdb=" OG SER D 230 " model vdw 2.318 3.040 ... (remaining 148780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 112 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB )) or resid 91 through 439 or resid 501 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 110 or (resid 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 through 281 or (resid 282 through 284 an \ d (name N or name CA or name C or name O or name CB )) or resid 285 through 287 \ or (resid 288 and (name N or name CA or name C or name O or name CB )) or resid \ 289 through 305 or (resid 306 and (name N or name CA or name C or name O or name \ CB )) or resid 307 through 327 or (resid 328 and (name N or name CA or name C o \ r name O or name CB )) or resid 329 through 360 or (resid 361 through 362 and (n \ ame N or name CA or name C or name O or name CB )) or resid 363 through 389 or ( \ resid 390 and (name N or name CA or name C or name O or name CB )) or resid 391 \ through 428)) selection = (chain 'D' and (resid 1 through 278 or (resid 279 and (name N or name CA or name \ C or name O or name CB )) or resid 280 through 319 or (resid 320 and (name N or \ name CA or name C or name O or name CB )) or resid 321 through 428)) } 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: 6.510 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 45.000 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 17981 Z= 0.315 Angle : 1.027 12.859 24438 Z= 0.558 Chirality : 0.061 0.407 2659 Planarity : 0.008 0.089 3193 Dihedral : 14.274 140.086 6547 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.05 % Allowed : 2.15 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2207 helix: -1.88 (0.13), residues: 890 sheet: 0.56 (0.28), residues: 340 loop : -1.29 (0.17), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 388 HIS 0.011 0.002 HIS B 190 PHE 0.035 0.003 PHE C 255 TYR 0.052 0.002 TYR A 432 ARG 0.010 0.001 ARG A 215 Details of bonding type rmsd link_TRANS : bond 0.00762 ( 1) link_TRANS : angle 0.88884 ( 3) hydrogen bonds : bond 0.16525 ( 795) hydrogen bonds : angle 7.44302 ( 2295) metal coordination : bond 0.01010 ( 2) covalent geometry : bond 0.00604 (17977) covalent geometry : angle 1.02712 (24435) Misc. bond : bond 0.05211 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8521 (mtm180) cc_final: 0.8268 (ptt-90) REVERT: A 96 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8324 (mmmm) REVERT: A 98 ASP cc_start: 0.8324 (p0) cc_final: 0.8103 (p0) REVERT: A 123 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7760 (tpp80) REVERT: A 196 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8545 (mp0) REVERT: A 241 SER cc_start: 0.8794 (m) cc_final: 0.8563 (p) REVERT: A 284 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7979 (mm-30) REVERT: A 290 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7638 (mt-10) REVERT: A 304 LYS cc_start: 0.8660 (tptp) cc_final: 0.8372 (tptp) REVERT: A 390 ARG cc_start: 0.7792 (mtm180) cc_final: 0.7502 (mtt90) REVERT: A 423 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7976 (tm-30) REVERT: A 438 ASP cc_start: 0.8302 (m-30) cc_final: 0.7988 (p0) REVERT: B 19 LYS cc_start: 0.9036 (tptm) cc_final: 0.8812 (tppt) REVERT: B 37 HIS cc_start: 0.8428 (m-70) cc_final: 0.8073 (m-70) REVERT: B 53 GLU cc_start: 0.8379 (tt0) cc_final: 0.7828 (tp30) REVERT: B 58 LYS cc_start: 0.8015 (tttt) cc_final: 0.7341 (pttt) REVERT: B 103 LYS cc_start: 0.8815 (tttt) cc_final: 0.7866 (ttpt) REVERT: B 108 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8438 (mp0) REVERT: B 129 CYS cc_start: 0.8728 (t) cc_final: 0.7849 (t) REVERT: B 174 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8497 (mmmt) REVERT: B 203 ASP cc_start: 0.8266 (t0) cc_final: 0.7873 (t0) REVERT: B 205 GLU cc_start: 0.7955 (tt0) cc_final: 0.7740 (tt0) REVERT: B 252 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8637 (ttpt) REVERT: B 257 MET cc_start: 0.8375 (mmm) cc_final: 0.8151 (mmm) REVERT: B 278 SER cc_start: 0.8697 (m) cc_final: 0.8178 (t) REVERT: B 293 MET cc_start: 0.8391 (mtm) cc_final: 0.8125 (mtp) REVERT: B 324 LYS cc_start: 0.8051 (tptm) cc_final: 0.7745 (tptm) REVERT: B 328 GLU cc_start: 0.7170 (pt0) cc_final: 0.6896 (pt0) REVERT: B 376 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7503 (mp0) REVERT: B 379 LYS cc_start: 0.8181 (mttp) cc_final: 0.7956 (mtmm) REVERT: B 383 GLU cc_start: 0.8336 (tp30) cc_final: 0.7980 (tp30) REVERT: B 391 ARG cc_start: 0.8829 (mmm160) cc_final: 0.6775 (ptm160) REVERT: B 412 GLU cc_start: 0.7890 (tp30) cc_final: 0.7366 (tp30) REVERT: B 414 ASN cc_start: 0.8326 (m-40) cc_final: 0.8042 (t0) REVERT: B 424 GLN cc_start: 0.8447 (tt0) cc_final: 0.8247 (tt0) REVERT: C 2 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.8063 (mtm180) REVERT: C 60 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8170 (ttmm) REVERT: C 90 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8238 (mm-30) REVERT: C 120 ASP cc_start: 0.7757 (t0) cc_final: 0.7517 (t0) REVERT: C 123 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.6702 (tpp80) REVERT: C 211 ASP cc_start: 0.8078 (t70) cc_final: 0.7499 (t0) REVERT: C 280 LYS cc_start: 0.8615 (mttp) cc_final: 0.7467 (mmtt) REVERT: C 290 GLU cc_start: 0.8296 (mp0) cc_final: 0.7980 (mp0) REVERT: C 322 ASP cc_start: 0.8369 (t0) cc_final: 0.8129 (t0) REVERT: C 326 LYS cc_start: 0.8714 (ptmm) cc_final: 0.7654 (mmtt) REVERT: C 338 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8649 (mmtt) REVERT: C 386 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8147 (mp0) REVERT: C 390 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7782 (mtm-85) REVERT: C 397 LEU cc_start: 0.9277 (mt) cc_final: 0.9066 (mt) REVERT: C 433 GLU cc_start: 0.8512 (pt0) cc_final: 0.7914 (pp20) REVERT: C 434 GLU cc_start: 0.8480 (pp20) cc_final: 0.8198 (pp20) REVERT: D 19 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8606 (tppt) REVERT: D 22 GLU cc_start: 0.8502 (tt0) cc_final: 0.8287 (tm-30) REVERT: D 41 ASP cc_start: 0.8673 (m-30) cc_final: 0.8275 (p0) REVERT: D 45 GLU cc_start: 0.8490 (tt0) cc_final: 0.8229 (tm-30) REVERT: D 58 LYS cc_start: 0.8162 (tttt) cc_final: 0.7737 (tttm) REVERT: D 94 GLN cc_start: 0.8624 (mm110) cc_final: 0.8360 (mm-40) REVERT: D 103 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8484 (ttmm) REVERT: D 108 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8346 (mp0) REVERT: D 157 GLU cc_start: 0.6896 (pp20) cc_final: 0.6232 (pp20) REVERT: D 174 LYS cc_start: 0.8413 (mmtm) cc_final: 0.8193 (mmtm) REVERT: D 203 ASP cc_start: 0.8259 (t0) cc_final: 0.7828 (t70) REVERT: D 209 ASP cc_start: 0.8440 (t0) cc_final: 0.7866 (t0) REVERT: D 213 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8061 (mtp180) REVERT: D 252 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8526 (ttpt) REVERT: D 291 GLN cc_start: 0.8333 (pp30) cc_final: 0.7999 (pp30) REVERT: D 304 ASP cc_start: 0.8134 (t70) cc_final: 0.7749 (t0) REVERT: D 321 MET cc_start: 0.7882 (ptp) cc_final: 0.7647 (ptp) REVERT: D 324 LYS cc_start: 0.8993 (tptp) cc_final: 0.8784 (tptp) REVERT: D 376 GLU cc_start: 0.8224 (mp0) cc_final: 0.7700 (mp0) REVERT: D 383 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8324 (tm-30) REVERT: D 407 GLU cc_start: 0.8149 (mp0) cc_final: 0.7591 (mp0) REVERT: D 410 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 413 SER cc_start: 0.8329 (t) cc_final: 0.7572 (p) REVERT: D 417 ASP cc_start: 0.8095 (m-30) cc_final: 0.7658 (m-30) REVERT: D 421 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8185 (mt-10) REVERT: E 3 LEU cc_start: 0.7376 (mt) cc_final: 0.7064 (mt) REVERT: E 13 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8370 (ttp80) REVERT: E 21 HIS cc_start: 0.8818 (t70) cc_final: 0.8312 (t-170) REVERT: E 68 GLU cc_start: 0.8812 (tt0) cc_final: 0.8604 (tt0) REVERT: E 69 ASN cc_start: 0.8631 (m-40) cc_final: 0.8317 (m110) REVERT: E 96 ASN cc_start: 0.8088 (m110) cc_final: 0.7769 (m110) REVERT: E 116 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7788 (ttm-80) REVERT: E 118 ARG cc_start: 0.8588 (ttt180) cc_final: 0.8245 (ttm-80) REVERT: E 165 GLN cc_start: 0.7838 (mm110) cc_final: 0.7569 (mm110) REVERT: E 172 ASP cc_start: 0.8131 (t0) cc_final: 0.7824 (t0) REVERT: E 173 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8017 (mm-40) REVERT: E 230 ASP cc_start: 0.7031 (t0) cc_final: 0.6548 (t0) REVERT: E 248 SER cc_start: 0.8122 (m) cc_final: 0.7520 (p) REVERT: E 307 ARG cc_start: 0.8375 (mtp-110) cc_final: 0.8031 (mtp-110) REVERT: E 314 GLN cc_start: 0.8142 (mm-40) cc_final: 0.7817 (mm-40) REVERT: E 444 MET cc_start: 0.8751 (mtm) cc_final: 0.8206 (ttm) REVERT: E 451 ASP cc_start: 0.7474 (t0) cc_final: 0.6976 (t0) REVERT: E 523 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7840 (ttm-80) REVERT: E 549 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7702 (mtm110) REVERT: E 553 GLU cc_start: 0.7926 (mp0) cc_final: 0.7690 (mp0) REVERT: E 598 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7015 (ttm170) outliers start: 1 outliers final: 0 residues processed: 471 average time/residue: 0.3927 time to fit residues: 255.8305 Evaluate side-chains 366 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.3980 chunk 167 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 200 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 133 GLN A 216 ASN A 356 ASN B 291 GLN B 416 ASN C 176 GLN C 309 HIS C 356 ASN D 137 HIS D 292 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN E 214 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.088218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078590 restraints weight = 36025.134| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.31 r_work: 0.2981 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17981 Z= 0.142 Angle : 0.534 7.988 24438 Z= 0.283 Chirality : 0.043 0.158 2659 Planarity : 0.005 0.061 3193 Dihedral : 10.628 154.406 2525 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.18 % Allowed : 8.53 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: -0.47 (0.17), residues: 2207 helix: -0.02 (0.16), residues: 914 sheet: 0.33 (0.28), residues: 361 loop : -0.74 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 592 HIS 0.006 0.001 HIS A 197 PHE 0.026 0.001 PHE A 255 TYR 0.013 0.001 TYR A 172 ARG 0.006 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 1) link_TRANS : angle 0.23933 ( 3) hydrogen bonds : bond 0.04429 ( 795) hydrogen bonds : angle 4.89414 ( 2295) metal coordination : bond 0.00590 ( 2) covalent geometry : bond 0.00317 (17977) covalent geometry : angle 0.53402 (24435) Misc. bond : bond 0.00091 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 372 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8858 (mmmm) REVERT: A 123 ARG cc_start: 0.8359 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: A 203 MET cc_start: 0.8559 (mmt) cc_final: 0.8305 (mmm) REVERT: A 214 ARG cc_start: 0.8641 (mtp-110) cc_final: 0.8430 (mtm110) REVERT: A 218 ASP cc_start: 0.8287 (t0) cc_final: 0.8007 (t0) REVERT: A 221 ARG cc_start: 0.8324 (ptp-110) cc_final: 0.7891 (ptp-110) REVERT: A 290 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7757 (mt-10) REVERT: A 415 GLU cc_start: 0.8697 (tt0) cc_final: 0.8047 (tp30) REVERT: A 423 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8338 (tp30) REVERT: A 424 ASP cc_start: 0.8648 (m-30) cc_final: 0.8160 (m-30) REVERT: B 53 GLU cc_start: 0.8395 (tt0) cc_final: 0.8041 (tp30) REVERT: B 58 LYS cc_start: 0.8462 (tttt) cc_final: 0.7741 (pttt) REVERT: B 103 LYS cc_start: 0.9038 (tttt) cc_final: 0.8148 (ttpt) REVERT: B 122 LYS cc_start: 0.9025 (tppp) cc_final: 0.8794 (ttmm) REVERT: B 129 CYS cc_start: 0.8965 (t) cc_final: 0.8673 (p) REVERT: B 205 GLU cc_start: 0.8386 (tt0) cc_final: 0.8160 (tt0) REVERT: B 209 ASP cc_start: 0.8380 (t70) cc_final: 0.7859 (t0) REVERT: B 213 ARG cc_start: 0.8388 (ptp-110) cc_final: 0.7947 (ptp90) REVERT: B 278 SER cc_start: 0.9056 (m) cc_final: 0.8475 (t) REVERT: B 325 GLU cc_start: 0.8250 (tp30) cc_final: 0.7929 (tp30) REVERT: B 328 GLU cc_start: 0.7706 (pt0) cc_final: 0.7236 (pp20) REVERT: B 392 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8826 (mtmm) REVERT: B 410 GLU cc_start: 0.7927 (pp20) cc_final: 0.7679 (pp20) REVERT: C 76 ASP cc_start: 0.8823 (m-30) cc_final: 0.8440 (m-30) REVERT: C 116 ASP cc_start: 0.8255 (p0) cc_final: 0.8017 (p0) REVERT: C 120 ASP cc_start: 0.8447 (t0) cc_final: 0.8044 (m-30) REVERT: C 123 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7321 (tpp80) REVERT: C 154 MET cc_start: 0.9003 (mmm) cc_final: 0.8523 (mtp) REVERT: C 158 SER cc_start: 0.8850 (t) cc_final: 0.8575 (p) REVERT: C 196 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 211 ASP cc_start: 0.8364 (t70) cc_final: 0.7827 (t0) REVERT: C 214 ARG cc_start: 0.8694 (ptm-80) cc_final: 0.8059 (ttp80) REVERT: C 280 LYS cc_start: 0.8613 (mttp) cc_final: 0.8072 (mmtt) REVERT: C 290 GLU cc_start: 0.8362 (mp0) cc_final: 0.8066 (mp0) REVERT: C 338 LYS cc_start: 0.8954 (mtpp) cc_final: 0.8692 (mmtm) REVERT: C 390 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7976 (mtm-85) REVERT: C 423 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7488 (pp20) REVERT: C 433 GLU cc_start: 0.8570 (pt0) cc_final: 0.8234 (pp20) REVERT: C 434 GLU cc_start: 0.8500 (pp20) cc_final: 0.8208 (pp20) REVERT: D 22 GLU cc_start: 0.8720 (tt0) cc_final: 0.8429 (tm-30) REVERT: D 26 ASP cc_start: 0.8138 (t0) cc_final: 0.7852 (t0) REVERT: D 41 ASP cc_start: 0.8658 (m-30) cc_final: 0.8422 (p0) REVERT: D 58 LYS cc_start: 0.8737 (tttt) cc_final: 0.8217 (tttm) REVERT: D 94 GLN cc_start: 0.8780 (mm110) cc_final: 0.8495 (mm-40) REVERT: D 203 ASP cc_start: 0.8405 (t0) cc_final: 0.8131 (t70) REVERT: D 205 GLU cc_start: 0.8592 (tt0) cc_final: 0.8080 (tp30) REVERT: D 209 ASP cc_start: 0.8641 (t0) cc_final: 0.8419 (t0) REVERT: D 291 GLN cc_start: 0.8401 (pp30) cc_final: 0.8126 (pp30) REVERT: D 304 ASP cc_start: 0.8341 (t70) cc_final: 0.7982 (t0) REVERT: D 335 ASN cc_start: 0.8241 (m-40) cc_final: 0.7897 (m-40) REVERT: D 383 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8582 (tm-30) REVERT: D 410 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8047 (mm-30) REVERT: D 412 GLU cc_start: 0.8519 (tp30) cc_final: 0.8265 (tp30) REVERT: D 413 SER cc_start: 0.8737 (t) cc_final: 0.7840 (p) REVERT: D 417 ASP cc_start: 0.8278 (m-30) cc_final: 0.7819 (m-30) REVERT: D 421 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8268 (mt-10) REVERT: E 3 LEU cc_start: 0.8032 (mt) cc_final: 0.7742 (mt) REVERT: E 13 ARG cc_start: 0.8766 (ttp-170) cc_final: 0.8542 (ttp80) REVERT: E 68 GLU cc_start: 0.8849 (tt0) cc_final: 0.8610 (tt0) REVERT: E 95 MET cc_start: 0.8886 (ttm) cc_final: 0.8529 (ttp) REVERT: E 116 ARG cc_start: 0.8550 (ttm170) cc_final: 0.8328 (ttm-80) REVERT: E 118 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8408 (mmm-85) REVERT: E 165 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8163 (mm110) REVERT: E 172 ASP cc_start: 0.8718 (t0) cc_final: 0.8470 (t0) REVERT: E 173 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8453 (mm-40) REVERT: E 248 SER cc_start: 0.8456 (m) cc_final: 0.8064 (p) REVERT: E 307 ARG cc_start: 0.8886 (mtp-110) cc_final: 0.8583 (mtp-110) REVERT: E 444 MET cc_start: 0.8968 (mtm) cc_final: 0.8644 (mtm) REVERT: E 451 ASP cc_start: 0.7938 (t0) cc_final: 0.7656 (t0) REVERT: E 501 VAL cc_start: 0.8343 (t) cc_final: 0.8038 (m) REVERT: E 569 MET cc_start: 0.8526 (mmt) cc_final: 0.8229 (mmt) outliers start: 22 outliers final: 10 residues processed: 382 average time/residue: 0.3896 time to fit residues: 210.4558 Evaluate side-chains 361 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 350 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 196 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 122 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 21 HIS E 134 GLN E 526 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.086783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077247 restraints weight = 35948.445| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.30 r_work: 0.2963 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17981 Z= 0.123 Angle : 0.512 8.300 24438 Z= 0.265 Chirality : 0.043 0.158 2659 Planarity : 0.004 0.051 3193 Dihedral : 10.297 170.081 2525 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.29 % Allowed : 10.14 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.20 (0.18), residues: 2207 helix: 0.82 (0.17), residues: 929 sheet: 0.30 (0.29), residues: 342 loop : -0.54 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 592 HIS 0.008 0.001 HIS B 190 PHE 0.014 0.001 PHE E 128 TYR 0.011 0.001 TYR E 102 ARG 0.007 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00033 ( 1) link_TRANS : angle 0.06032 ( 3) hydrogen bonds : bond 0.03783 ( 795) hydrogen bonds : angle 4.53282 ( 2295) metal coordination : bond 0.00456 ( 2) covalent geometry : bond 0.00282 (17977) covalent geometry : angle 0.51171 (24435) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 362 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8643 (ptp90) cc_final: 0.8353 (ptt-90) REVERT: A 85 GLN cc_start: 0.8998 (mm110) cc_final: 0.8713 (tp40) REVERT: A 123 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.8114 (tpp-160) REVERT: A 218 ASP cc_start: 0.8459 (t0) cc_final: 0.8047 (t0) REVERT: A 221 ARG cc_start: 0.8584 (ptp-110) cc_final: 0.8283 (ptp90) REVERT: A 251 ASP cc_start: 0.7952 (p0) cc_final: 0.7508 (p0) REVERT: A 414 GLU cc_start: 0.8693 (mp0) cc_final: 0.8363 (mp0) REVERT: A 415 GLU cc_start: 0.8713 (tt0) cc_final: 0.8217 (tp30) REVERT: A 417 GLU cc_start: 0.7626 (mp0) cc_final: 0.7424 (mp0) REVERT: A 420 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 58 LYS cc_start: 0.8548 (tttt) cc_final: 0.7805 (pttt) REVERT: B 103 LYS cc_start: 0.9070 (tttt) cc_final: 0.8546 (ttpt) REVERT: B 108 GLU cc_start: 0.8019 (mp0) cc_final: 0.7814 (mp0) REVERT: B 122 LYS cc_start: 0.8955 (tppp) cc_final: 0.8712 (ttmm) REVERT: B 154 LYS cc_start: 0.9095 (mttm) cc_final: 0.8709 (mttp) REVERT: B 174 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8712 (mmmt) REVERT: B 205 GLU cc_start: 0.8440 (tt0) cc_final: 0.8044 (tt0) REVERT: B 209 ASP cc_start: 0.8351 (t70) cc_final: 0.7940 (t0) REVERT: B 213 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8075 (ptp90) REVERT: B 278 SER cc_start: 0.9017 (m) cc_final: 0.8446 (t) REVERT: B 379 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8453 (mtpp) REVERT: B 392 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: B 410 GLU cc_start: 0.8035 (pp20) cc_final: 0.7684 (pp20) REVERT: B 414 ASN cc_start: 0.8283 (t0) cc_final: 0.8020 (t0) REVERT: C 120 ASP cc_start: 0.8412 (t0) cc_final: 0.8108 (t0) REVERT: C 123 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7301 (tpp80) REVERT: C 158 SER cc_start: 0.8887 (t) cc_final: 0.8640 (p) REVERT: C 196 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7727 (tm-30) REVERT: C 203 MET cc_start: 0.8852 (tpp) cc_final: 0.8517 (mmm) REVERT: C 211 ASP cc_start: 0.8383 (t70) cc_final: 0.7724 (t0) REVERT: C 215 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8579 (ttp80) REVERT: C 284 GLU cc_start: 0.8394 (mp0) cc_final: 0.8002 (mp0) REVERT: C 290 GLU cc_start: 0.8518 (mp0) cc_final: 0.8226 (mp0) REVERT: C 297 GLU cc_start: 0.8247 (tp30) cc_final: 0.7995 (tp30) REVERT: C 338 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8714 (tptp) REVERT: C 386 GLU cc_start: 0.8241 (mp0) cc_final: 0.7945 (mp0) REVERT: C 390 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7968 (mtm-85) REVERT: C 425 MET cc_start: 0.8662 (mmm) cc_final: 0.7879 (tpp) REVERT: D 22 GLU cc_start: 0.8774 (tt0) cc_final: 0.8476 (tm-30) REVERT: D 26 ASP cc_start: 0.8235 (t0) cc_final: 0.7848 (t0) REVERT: D 57 ASN cc_start: 0.8088 (t0) cc_final: 0.7308 (t0) REVERT: D 58 LYS cc_start: 0.8800 (tttt) cc_final: 0.8519 (tttm) REVERT: D 69 GLU cc_start: 0.8558 (pp20) cc_final: 0.8294 (pm20) REVERT: D 108 GLU cc_start: 0.8298 (mp0) cc_final: 0.7831 (mp0) REVERT: D 190 HIS cc_start: 0.8535 (t-170) cc_final: 0.8160 (t-170) REVERT: D 203 ASP cc_start: 0.8438 (t0) cc_final: 0.8108 (t70) REVERT: D 205 GLU cc_start: 0.8652 (tt0) cc_final: 0.8269 (tp30) REVERT: D 209 ASP cc_start: 0.8775 (t0) cc_final: 0.7747 (t0) REVERT: D 213 ARG cc_start: 0.8841 (ttp-110) cc_final: 0.8560 (ttm110) REVERT: D 257 MET cc_start: 0.8363 (mmm) cc_final: 0.7913 (mmm) REVERT: D 291 GLN cc_start: 0.8442 (pp30) cc_final: 0.8184 (pp30) REVERT: D 304 ASP cc_start: 0.8518 (t70) cc_final: 0.7955 (t0) REVERT: D 321 MET cc_start: 0.8691 (ptp) cc_final: 0.8393 (ptp) REVERT: D 325 GLU cc_start: 0.8934 (tp30) cc_final: 0.8353 (tp30) REVERT: D 335 ASN cc_start: 0.8395 (m-40) cc_final: 0.8025 (m-40) REVERT: D 383 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8613 (tm-30) REVERT: D 410 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8007 (mt-10) REVERT: D 412 GLU cc_start: 0.8556 (tp30) cc_final: 0.8207 (tp30) REVERT: D 413 SER cc_start: 0.8748 (t) cc_final: 0.7902 (p) REVERT: D 417 ASP cc_start: 0.8274 (m-30) cc_final: 0.7823 (m-30) REVERT: D 421 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8257 (mt-10) REVERT: E 3 LEU cc_start: 0.8073 (mt) cc_final: 0.7779 (mt) REVERT: E 13 ARG cc_start: 0.8830 (ttp-170) cc_final: 0.8594 (ttp80) REVERT: E 68 GLU cc_start: 0.8890 (tt0) cc_final: 0.8688 (tt0) REVERT: E 118 ARG cc_start: 0.8563 (ttt180) cc_final: 0.7541 (mmm-85) REVERT: E 120 GLU cc_start: 0.8468 (pt0) cc_final: 0.8171 (mp0) REVERT: E 134 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7397 (mm110) REVERT: E 165 GLN cc_start: 0.8689 (mm-40) cc_final: 0.8412 (mm110) REVERT: E 172 ASP cc_start: 0.8614 (t0) cc_final: 0.8375 (t0) REVERT: E 248 SER cc_start: 0.8529 (m) cc_final: 0.8128 (p) REVERT: E 305 ASP cc_start: 0.8102 (p0) cc_final: 0.7861 (p0) REVERT: E 307 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8577 (mtp-110) REVERT: E 424 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8075 (tt0) REVERT: E 444 MET cc_start: 0.8955 (mtm) cc_final: 0.8586 (mtm) REVERT: E 451 ASP cc_start: 0.7935 (t0) cc_final: 0.7705 (t0) REVERT: E 523 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.8218 (ttm-80) REVERT: E 549 ARG cc_start: 0.8342 (mtm110) cc_final: 0.8133 (mtm-85) REVERT: E 569 MET cc_start: 0.8436 (mmt) cc_final: 0.8227 (mmt) REVERT: E 582 GLU cc_start: 0.8250 (tp30) cc_final: 0.8047 (tp30) outliers start: 24 outliers final: 14 residues processed: 375 average time/residue: 0.3956 time to fit residues: 205.4787 Evaluate side-chains 361 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 345 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 96 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 186 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 214 optimal weight: 0.4980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 280 GLN C 309 HIS D 384 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.085617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076166 restraints weight = 35755.933| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.26 r_work: 0.2956 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17981 Z= 0.121 Angle : 0.514 8.974 24438 Z= 0.263 Chirality : 0.042 0.160 2659 Planarity : 0.004 0.042 3193 Dihedral : 10.062 170.474 2525 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.45 % Allowed : 11.05 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.49 (0.18), residues: 2207 helix: 1.19 (0.17), residues: 931 sheet: 0.32 (0.29), residues: 335 loop : -0.48 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 PHE 0.013 0.001 PHE E 128 TYR 0.011 0.001 TYR E 102 ARG 0.007 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00013 ( 1) link_TRANS : angle 0.06257 ( 3) hydrogen bonds : bond 0.03548 ( 795) hydrogen bonds : angle 4.38801 ( 2295) metal coordination : bond 0.00463 ( 2) covalent geometry : bond 0.00282 (17977) covalent geometry : angle 0.51375 (24435) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 352 time to evaluate : 3.489 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8579 (ptp90) cc_final: 0.8324 (ptt-90) REVERT: A 50 ASN cc_start: 0.9030 (t0) cc_final: 0.8546 (t0) REVERT: A 85 GLN cc_start: 0.8955 (mm110) cc_final: 0.8615 (tp40) REVERT: A 154 MET cc_start: 0.9336 (mmm) cc_final: 0.9116 (mmm) REVERT: A 158 SER cc_start: 0.9355 (t) cc_final: 0.9033 (p) REVERT: A 214 ARG cc_start: 0.8675 (mtp-110) cc_final: 0.8394 (mtm110) REVERT: A 215 ARG cc_start: 0.8910 (mtm110) cc_final: 0.8675 (mtm110) REVERT: A 218 ASP cc_start: 0.8488 (t0) cc_final: 0.8035 (t0) REVERT: A 251 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7608 (p0) REVERT: A 290 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8069 (mt-10) REVERT: A 304 LYS cc_start: 0.8959 (tptp) cc_final: 0.8714 (tptt) REVERT: A 414 GLU cc_start: 0.8734 (mp0) cc_final: 0.8075 (mp0) REVERT: B 58 LYS cc_start: 0.8586 (tttt) cc_final: 0.7892 (pttt) REVERT: B 94 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8444 (mp10) REVERT: B 103 LYS cc_start: 0.9145 (tttt) cc_final: 0.8309 (ttpt) REVERT: B 122 LYS cc_start: 0.8945 (tppp) cc_final: 0.8660 (ttmm) REVERT: B 174 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8683 (mmmt) REVERT: B 190 HIS cc_start: 0.7844 (t-170) cc_final: 0.7390 (t-170) REVERT: B 205 GLU cc_start: 0.8383 (tt0) cc_final: 0.7985 (tt0) REVERT: B 209 ASP cc_start: 0.8348 (t70) cc_final: 0.7869 (t0) REVERT: B 213 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.8075 (ptp90) REVERT: B 278 SER cc_start: 0.8855 (m) cc_final: 0.8423 (t) REVERT: B 321 MET cc_start: 0.8540 (ptp) cc_final: 0.8148 (ptp) REVERT: B 325 GLU cc_start: 0.8111 (tp30) cc_final: 0.7863 (tp30) REVERT: B 376 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8313 (mt-10) REVERT: B 379 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8464 (mtpp) REVERT: B 392 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8967 (mtmm) REVERT: B 410 GLU cc_start: 0.8048 (pp20) cc_final: 0.7712 (pp20) REVERT: B 414 ASN cc_start: 0.8214 (t0) cc_final: 0.7797 (t0) REVERT: B 417 ASP cc_start: 0.8272 (m-30) cc_final: 0.8042 (m-30) REVERT: C 84 ARG cc_start: 0.8723 (ttp-110) cc_final: 0.8404 (ptp90) REVERT: C 120 ASP cc_start: 0.8440 (t0) cc_final: 0.8135 (t0) REVERT: C 123 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7317 (tpp80) REVERT: C 158 SER cc_start: 0.8899 (t) cc_final: 0.8690 (t) REVERT: C 196 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7770 (tm-30) REVERT: C 211 ASP cc_start: 0.8410 (t70) cc_final: 0.7765 (t0) REVERT: C 215 ARG cc_start: 0.8800 (ttp80) cc_final: 0.8512 (ttp80) REVERT: C 284 GLU cc_start: 0.8328 (mp0) cc_final: 0.7901 (mp0) REVERT: C 290 GLU cc_start: 0.8610 (mp0) cc_final: 0.8267 (mp0) REVERT: C 297 GLU cc_start: 0.8306 (tp30) cc_final: 0.8058 (tp30) REVERT: C 338 LYS cc_start: 0.8921 (mtpp) cc_final: 0.8714 (tptp) REVERT: C 386 GLU cc_start: 0.7986 (mp0) cc_final: 0.7675 (mp0) REVERT: C 390 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7987 (mtm-85) REVERT: C 425 MET cc_start: 0.8656 (mmm) cc_final: 0.8437 (tpt) REVERT: C 433 GLU cc_start: 0.8721 (pt0) cc_final: 0.8262 (pp20) REVERT: D 22 GLU cc_start: 0.8754 (tt0) cc_final: 0.8499 (tm-30) REVERT: D 26 ASP cc_start: 0.8299 (t0) cc_final: 0.7825 (t0) REVERT: D 57 ASN cc_start: 0.8174 (t0) cc_final: 0.7649 (t0) REVERT: D 58 LYS cc_start: 0.8783 (tttt) cc_final: 0.8540 (tttm) REVERT: D 69 GLU cc_start: 0.8616 (pp20) cc_final: 0.8370 (pm20) REVERT: D 108 GLU cc_start: 0.8154 (mp0) cc_final: 0.7885 (mp0) REVERT: D 203 ASP cc_start: 0.8414 (t0) cc_final: 0.8146 (t70) REVERT: D 205 GLU cc_start: 0.8628 (tt0) cc_final: 0.8349 (tp30) REVERT: D 209 ASP cc_start: 0.8868 (t0) cc_final: 0.8182 (t0) REVERT: D 213 ARG cc_start: 0.8833 (ttp-110) cc_final: 0.8450 (mtm-85) REVERT: D 257 MET cc_start: 0.8322 (mmm) cc_final: 0.7923 (mmm) REVERT: D 300 MET cc_start: 0.9113 (mtm) cc_final: 0.8894 (mtm) REVERT: D 325 GLU cc_start: 0.8790 (tp30) cc_final: 0.8488 (tp30) REVERT: D 383 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8606 (tm-30) REVERT: D 410 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8089 (mt-10) REVERT: D 412 GLU cc_start: 0.8543 (tp30) cc_final: 0.8226 (tp30) REVERT: D 413 SER cc_start: 0.8816 (t) cc_final: 0.7964 (p) REVERT: D 414 ASN cc_start: 0.8163 (p0) cc_final: 0.7740 (p0) REVERT: D 417 ASP cc_start: 0.8320 (m-30) cc_final: 0.7875 (m-30) REVERT: D 421 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 424 GLN cc_start: 0.8919 (tt0) cc_final: 0.8661 (tm-30) REVERT: E 3 LEU cc_start: 0.8083 (mt) cc_final: 0.7783 (mt) REVERT: E 13 ARG cc_start: 0.8804 (ttp-170) cc_final: 0.8583 (ttp80) REVERT: E 68 GLU cc_start: 0.8860 (tt0) cc_final: 0.8642 (tt0) REVERT: E 118 ARG cc_start: 0.8531 (ttt180) cc_final: 0.7565 (mmm-85) REVERT: E 120 GLU cc_start: 0.8490 (pt0) cc_final: 0.8276 (mp0) REVERT: E 134 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7406 (mm110) REVERT: E 165 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8418 (mm110) REVERT: E 169 ASN cc_start: 0.8370 (t0) cc_final: 0.8120 (t0) REVERT: E 226 GLN cc_start: 0.8304 (tt0) cc_final: 0.8098 (tt0) REVERT: E 248 SER cc_start: 0.8501 (m) cc_final: 0.8108 (p) REVERT: E 305 ASP cc_start: 0.8161 (p0) cc_final: 0.7932 (p0) REVERT: E 307 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.8414 (mtp85) REVERT: E 424 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: E 444 MET cc_start: 0.8949 (mtm) cc_final: 0.8518 (mtt) REVERT: E 451 ASP cc_start: 0.7901 (t0) cc_final: 0.7616 (t0) REVERT: E 523 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8209 (ttm-80) REVERT: E 549 ARG cc_start: 0.8352 (mtm110) cc_final: 0.8125 (mtm-85) REVERT: E 582 GLU cc_start: 0.8191 (tp30) cc_final: 0.7975 (tp30) outliers start: 27 outliers final: 15 residues processed: 365 average time/residue: 0.5333 time to fit residues: 270.9788 Evaluate side-chains 371 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 170 GLN Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 595 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 123 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 180 optimal weight: 0.0570 chunk 173 optimal weight: 0.0050 chunk 175 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 overall best weight: 0.4912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 280 GLN B 291 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.076196 restraints weight = 36121.178| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.27 r_work: 0.2953 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17981 Z= 0.114 Angle : 0.514 9.523 24438 Z= 0.262 Chirality : 0.042 0.159 2659 Planarity : 0.004 0.041 3193 Dihedral : 9.899 170.637 2525 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 11.59 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.63 (0.18), residues: 2207 helix: 1.39 (0.17), residues: 928 sheet: 0.21 (0.29), residues: 341 loop : -0.42 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 592 HIS 0.004 0.001 HIS A 197 PHE 0.017 0.001 PHE E 128 TYR 0.010 0.001 TYR A 357 ARG 0.007 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.05385 ( 3) hydrogen bonds : bond 0.03398 ( 795) hydrogen bonds : angle 4.27357 ( 2295) metal coordination : bond 0.00358 ( 2) covalent geometry : bond 0.00265 (17977) covalent geometry : angle 0.51445 (24435) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 355 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8328 (ptt-90) REVERT: A 50 ASN cc_start: 0.9046 (t0) cc_final: 0.8551 (t0) REVERT: A 158 SER cc_start: 0.9363 (t) cc_final: 0.9083 (p) REVERT: A 203 MET cc_start: 0.8588 (mmm) cc_final: 0.8381 (mmm) REVERT: A 214 ARG cc_start: 0.8743 (mtp-110) cc_final: 0.8263 (ttp80) REVERT: A 215 ARG cc_start: 0.8888 (mtm110) cc_final: 0.8495 (mtm110) REVERT: A 218 ASP cc_start: 0.8575 (t0) cc_final: 0.8033 (t0) REVERT: A 251 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7333 (p0) REVERT: A 284 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8143 (mp0) REVERT: A 290 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8076 (mt-10) REVERT: A 414 GLU cc_start: 0.8695 (mp0) cc_final: 0.8389 (mp0) REVERT: A 417 GLU cc_start: 0.7742 (mp0) cc_final: 0.7218 (mp0) REVERT: A 420 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7708 (tp30) REVERT: B 58 LYS cc_start: 0.8671 (tttt) cc_final: 0.7944 (pttt) REVERT: B 94 GLN cc_start: 0.8695 (mm-40) cc_final: 0.8425 (mp10) REVERT: B 122 LYS cc_start: 0.8947 (tppp) cc_final: 0.8724 (ttmm) REVERT: B 174 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8457 (mmmt) REVERT: B 205 GLU cc_start: 0.8412 (tt0) cc_final: 0.7989 (tt0) REVERT: B 209 ASP cc_start: 0.8350 (t70) cc_final: 0.7857 (t0) REVERT: B 213 ARG cc_start: 0.8475 (ptp-110) cc_final: 0.8124 (ptp90) REVERT: B 257 MET cc_start: 0.8016 (mmm) cc_final: 0.7670 (mmm) REVERT: B 278 SER cc_start: 0.8789 (m) cc_final: 0.8397 (t) REVERT: B 321 MET cc_start: 0.8582 (ptp) cc_final: 0.8331 (ptp) REVERT: B 325 GLU cc_start: 0.8065 (tp30) cc_final: 0.7562 (tt0) REVERT: B 328 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7089 (pp20) REVERT: B 332 ASN cc_start: 0.8367 (m-40) cc_final: 0.7986 (m-40) REVERT: B 376 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8275 (mp0) REVERT: B 379 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8507 (mtpp) REVERT: B 392 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (mmmm) REVERT: B 403 MET cc_start: 0.8350 (mtm) cc_final: 0.8138 (ttm) REVERT: B 410 GLU cc_start: 0.8073 (pp20) cc_final: 0.7779 (pp20) REVERT: B 414 ASN cc_start: 0.8300 (t0) cc_final: 0.7939 (t0) REVERT: B 417 ASP cc_start: 0.8281 (m-30) cc_final: 0.8015 (m-30) REVERT: C 84 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8451 (ptp90) REVERT: C 120 ASP cc_start: 0.8429 (t0) cc_final: 0.8134 (t0) REVERT: C 123 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7354 (tpp80) REVERT: C 158 SER cc_start: 0.8894 (t) cc_final: 0.8678 (t) REVERT: C 196 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7735 (tm-30) REVERT: C 211 ASP cc_start: 0.8442 (t70) cc_final: 0.7806 (t0) REVERT: C 215 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8511 (ttp80) REVERT: C 265 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8855 (mm) REVERT: C 284 GLU cc_start: 0.8333 (mp0) cc_final: 0.7901 (mp0) REVERT: C 290 GLU cc_start: 0.8621 (mp0) cc_final: 0.8175 (mp0) REVERT: C 297 GLU cc_start: 0.8324 (tp30) cc_final: 0.8073 (tp30) REVERT: C 338 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8730 (tptp) REVERT: C 386 GLU cc_start: 0.8000 (mp0) cc_final: 0.7682 (mp0) REVERT: C 390 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7969 (mtm-85) REVERT: C 433 GLU cc_start: 0.8716 (pt0) cc_final: 0.8235 (pp20) REVERT: D 22 GLU cc_start: 0.8718 (tt0) cc_final: 0.8503 (tm-30) REVERT: D 26 ASP cc_start: 0.8375 (t0) cc_final: 0.7977 (t0) REVERT: D 57 ASN cc_start: 0.8237 (t0) cc_final: 0.7793 (t0) REVERT: D 69 GLU cc_start: 0.8633 (pp20) cc_final: 0.8405 (pm20) REVERT: D 108 GLU cc_start: 0.8127 (mp0) cc_final: 0.7860 (mp0) REVERT: D 190 HIS cc_start: 0.8551 (t-170) cc_final: 0.8130 (t-170) REVERT: D 203 ASP cc_start: 0.8442 (t0) cc_final: 0.8168 (t70) REVERT: D 209 ASP cc_start: 0.8919 (t0) cc_final: 0.8401 (t0) REVERT: D 213 ARG cc_start: 0.8865 (ttp-110) cc_final: 0.8575 (mtm-85) REVERT: D 257 MET cc_start: 0.8302 (mmm) cc_final: 0.7935 (mtp) REVERT: D 300 MET cc_start: 0.9149 (mtm) cc_final: 0.8939 (mtm) REVERT: D 321 MET cc_start: 0.8639 (ptp) cc_final: 0.8426 (ptp) REVERT: D 324 LYS cc_start: 0.9246 (tptp) cc_final: 0.9043 (tptp) REVERT: D 325 GLU cc_start: 0.8753 (tp30) cc_final: 0.8453 (tp30) REVERT: D 383 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8627 (tm-30) REVERT: D 410 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 412 GLU cc_start: 0.8562 (tp30) cc_final: 0.8235 (tp30) REVERT: D 413 SER cc_start: 0.8817 (t) cc_final: 0.7924 (p) REVERT: D 417 ASP cc_start: 0.8324 (m-30) cc_final: 0.7962 (m-30) REVERT: E 3 LEU cc_start: 0.8047 (mt) cc_final: 0.7778 (mt) REVERT: E 13 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8617 (ttp80) REVERT: E 68 GLU cc_start: 0.8876 (tt0) cc_final: 0.8654 (tt0) REVERT: E 134 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7410 (mm110) REVERT: E 165 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8409 (mm110) REVERT: E 169 ASN cc_start: 0.8384 (t0) cc_final: 0.8142 (t0) REVERT: E 248 SER cc_start: 0.8497 (m) cc_final: 0.8123 (p) REVERT: E 305 ASP cc_start: 0.8139 (p0) cc_final: 0.7841 (p0) REVERT: E 307 ARG cc_start: 0.8743 (mtp-110) cc_final: 0.8401 (mtp85) REVERT: E 424 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: E 444 MET cc_start: 0.8932 (mtm) cc_final: 0.8488 (mtt) REVERT: E 451 ASP cc_start: 0.7917 (t0) cc_final: 0.7619 (t0) REVERT: E 514 THR cc_start: 0.9210 (m) cc_final: 0.8663 (p) REVERT: E 523 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8245 (ttm-80) REVERT: E 549 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8079 (mtm-85) REVERT: E 582 GLU cc_start: 0.8246 (tp30) cc_final: 0.8016 (tp30) outliers start: 34 outliers final: 19 residues processed: 369 average time/residue: 0.4828 time to fit residues: 250.0591 Evaluate side-chains 366 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 342 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 23 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.0980 chunk 163 optimal weight: 0.4980 chunk 220 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 190 optimal weight: 0.2980 chunk 194 optimal weight: 0.7980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 216 ASN B 37 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 216 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.086161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.076755 restraints weight = 35834.891| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.27 r_work: 0.2968 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17981 Z= 0.101 Angle : 0.504 9.950 24438 Z= 0.256 Chirality : 0.041 0.137 2659 Planarity : 0.004 0.039 3193 Dihedral : 9.682 169.411 2525 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.72 % Allowed : 12.66 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.73 (0.18), residues: 2207 helix: 1.49 (0.17), residues: 936 sheet: 0.24 (0.29), residues: 348 loop : -0.39 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 PHE 0.020 0.001 PHE E 128 TYR 0.007 0.001 TYR D 59 ARG 0.007 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.03263 ( 3) hydrogen bonds : bond 0.03176 ( 795) hydrogen bonds : angle 4.18328 ( 2295) metal coordination : bond 0.00218 ( 2) covalent geometry : bond 0.00232 (17977) covalent geometry : angle 0.50386 (24435) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 346 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8575 (ptp90) cc_final: 0.8325 (ptt-90) REVERT: A 50 ASN cc_start: 0.9057 (t0) cc_final: 0.8556 (t0) REVERT: A 158 SER cc_start: 0.9368 (t) cc_final: 0.9089 (p) REVERT: A 172 TYR cc_start: 0.9053 (t80) cc_final: 0.8835 (t80) REVERT: A 215 ARG cc_start: 0.8908 (mtm110) cc_final: 0.8705 (mtm110) REVERT: A 218 ASP cc_start: 0.8619 (t0) cc_final: 0.8113 (t0) REVERT: A 251 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7564 (p0) REVERT: A 284 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8152 (mp0) REVERT: A 290 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8056 (mt-10) REVERT: A 357 TYR cc_start: 0.9008 (m-80) cc_final: 0.8775 (m-80) REVERT: A 386 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7761 (mm-30) REVERT: A 414 GLU cc_start: 0.8662 (mp0) cc_final: 0.8277 (mp0) REVERT: A 417 GLU cc_start: 0.7701 (mp0) cc_final: 0.7307 (mp0) REVERT: B 58 LYS cc_start: 0.8681 (tttt) cc_final: 0.7973 (pttt) REVERT: B 94 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8391 (mp10) REVERT: B 122 LYS cc_start: 0.8936 (tppp) cc_final: 0.8718 (ttmm) REVERT: B 154 LYS cc_start: 0.9094 (mttm) cc_final: 0.8758 (mttp) REVERT: B 190 HIS cc_start: 0.8124 (t-170) cc_final: 0.7786 (t-170) REVERT: B 209 ASP cc_start: 0.8355 (t70) cc_final: 0.7860 (t0) REVERT: B 213 ARG cc_start: 0.8479 (ptp-110) cc_final: 0.8117 (ptp90) REVERT: B 257 MET cc_start: 0.8021 (mmm) cc_final: 0.7670 (mmm) REVERT: B 278 SER cc_start: 0.8819 (m) cc_final: 0.8374 (t) REVERT: B 321 MET cc_start: 0.8584 (ptp) cc_final: 0.8316 (ptp) REVERT: B 376 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8298 (mt-10) REVERT: B 379 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8521 (mtpp) REVERT: B 392 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9033 (mmmm) REVERT: B 417 ASP cc_start: 0.8223 (m-30) cc_final: 0.7938 (m-30) REVERT: C 123 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7338 (tpp80) REVERT: C 196 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7755 (tm-30) REVERT: C 211 ASP cc_start: 0.8444 (t70) cc_final: 0.7761 (t0) REVERT: C 215 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8527 (ttp80) REVERT: C 265 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8869 (mm) REVERT: C 284 GLU cc_start: 0.8376 (mp0) cc_final: 0.7999 (mp0) REVERT: C 290 GLU cc_start: 0.8628 (mp0) cc_final: 0.8193 (mp0) REVERT: C 297 GLU cc_start: 0.8358 (tp30) cc_final: 0.8035 (tp30) REVERT: C 338 LYS cc_start: 0.9009 (mtpp) cc_final: 0.8783 (tptp) REVERT: C 386 GLU cc_start: 0.7918 (mp0) cc_final: 0.7673 (mp0) REVERT: C 390 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7941 (mtm-85) REVERT: C 423 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7792 (tp30) REVERT: C 433 GLU cc_start: 0.8702 (pt0) cc_final: 0.8225 (pp20) REVERT: D 22 GLU cc_start: 0.8716 (tt0) cc_final: 0.8511 (tm-30) REVERT: D 26 ASP cc_start: 0.8388 (t0) cc_final: 0.7983 (t0) REVERT: D 57 ASN cc_start: 0.8327 (t0) cc_final: 0.7745 (t0) REVERT: D 108 GLU cc_start: 0.8096 (mp0) cc_final: 0.7663 (mp0) REVERT: D 116 VAL cc_start: 0.9236 (t) cc_final: 0.8984 (p) REVERT: D 190 HIS cc_start: 0.8534 (t-170) cc_final: 0.8108 (t-170) REVERT: D 203 ASP cc_start: 0.8428 (t0) cc_final: 0.8088 (t70) REVERT: D 209 ASP cc_start: 0.8945 (t0) cc_final: 0.8395 (t0) REVERT: D 213 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8607 (mtm-85) REVERT: D 257 MET cc_start: 0.8295 (mmm) cc_final: 0.7995 (mtp) REVERT: D 324 LYS cc_start: 0.9247 (tptp) cc_final: 0.9011 (tptp) REVERT: D 325 GLU cc_start: 0.8728 (tp30) cc_final: 0.8433 (tp30) REVERT: D 383 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8637 (tm-30) REVERT: D 410 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 412 GLU cc_start: 0.8536 (tp30) cc_final: 0.8217 (tp30) REVERT: D 413 SER cc_start: 0.8820 (t) cc_final: 0.7925 (p) REVERT: D 417 ASP cc_start: 0.8347 (m-30) cc_final: 0.7977 (m-30) REVERT: E 13 ARG cc_start: 0.8823 (ttp-170) cc_final: 0.8601 (ttp80) REVERT: E 68 GLU cc_start: 0.8867 (tt0) cc_final: 0.8626 (tt0) REVERT: E 134 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7398 (mm110) REVERT: E 165 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8403 (mm110) REVERT: E 169 ASN cc_start: 0.8389 (t0) cc_final: 0.8162 (t0) REVERT: E 173 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8587 (mm-40) REVERT: E 248 SER cc_start: 0.8492 (m) cc_final: 0.8097 (p) REVERT: E 305 ASP cc_start: 0.8122 (p0) cc_final: 0.7828 (p0) REVERT: E 307 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.8283 (mtp-110) REVERT: E 424 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: E 444 MET cc_start: 0.8911 (mtm) cc_final: 0.8496 (mtt) REVERT: E 451 ASP cc_start: 0.7926 (t0) cc_final: 0.7647 (t0) REVERT: E 514 THR cc_start: 0.9201 (m) cc_final: 0.8652 (p) REVERT: E 523 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: E 549 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8015 (mtm-85) REVERT: E 582 GLU cc_start: 0.8288 (tp30) cc_final: 0.8075 (tp30) outliers start: 32 outliers final: 21 residues processed: 359 average time/residue: 0.3901 time to fit residues: 194.0626 Evaluate side-chains 357 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 332 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 170 GLN Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 134 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 216 ASN B 37 HIS B 190 HIS B 291 GLN B 298 ASN B 416 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN D 332 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 182 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074009 restraints weight = 35787.936| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.26 r_work: 0.2908 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17981 Z= 0.166 Angle : 0.555 9.461 24438 Z= 0.284 Chirality : 0.044 0.205 2659 Planarity : 0.004 0.041 3193 Dihedral : 9.969 176.693 2525 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.93 % Allowed : 12.93 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.68 (0.18), residues: 2207 helix: 1.45 (0.17), residues: 933 sheet: 0.24 (0.29), residues: 337 loop : -0.43 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 592 HIS 0.018 0.001 HIS B 190 PHE 0.022 0.001 PHE E 128 TYR 0.015 0.001 TYR E 102 ARG 0.008 0.001 ARG C 84 Details of bonding type rmsd link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.10885 ( 3) hydrogen bonds : bond 0.03816 ( 795) hydrogen bonds : angle 4.32715 ( 2295) metal coordination : bond 0.00746 ( 2) covalent geometry : bond 0.00387 (17977) covalent geometry : angle 0.55551 (24435) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8599 (ptp90) cc_final: 0.8390 (ptt-90) REVERT: A 158 SER cc_start: 0.9407 (t) cc_final: 0.9171 (p) REVERT: A 214 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8414 (mtm110) REVERT: A 218 ASP cc_start: 0.8711 (t0) cc_final: 0.8169 (t0) REVERT: A 221 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8243 (mtt90) REVERT: A 251 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7495 (p0) REVERT: A 290 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8046 (mt-10) REVERT: A 357 TYR cc_start: 0.9104 (m-80) cc_final: 0.8809 (m-80) REVERT: A 414 GLU cc_start: 0.8639 (mp0) cc_final: 0.8356 (mp0) REVERT: B 58 LYS cc_start: 0.8615 (tttt) cc_final: 0.7904 (pttt) REVERT: B 94 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8435 (mp10) REVERT: B 122 LYS cc_start: 0.8938 (tppp) cc_final: 0.8664 (ttmm) REVERT: B 205 GLU cc_start: 0.8458 (tt0) cc_final: 0.8004 (tt0) REVERT: B 213 ARG cc_start: 0.8492 (ptp-110) cc_final: 0.8078 (mtm110) REVERT: B 278 SER cc_start: 0.8826 (m) cc_final: 0.8422 (t) REVERT: B 327 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8019 (t0) REVERT: B 376 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8427 (mt-10) REVERT: B 379 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8568 (mtpp) REVERT: B 392 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9095 (mtmm) REVERT: B 410 GLU cc_start: 0.8019 (pp20) cc_final: 0.7748 (pp20) REVERT: B 417 ASP cc_start: 0.8250 (m-30) cc_final: 0.7943 (m-30) REVERT: C 123 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.7310 (tpp80) REVERT: C 196 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7696 (tm-30) REVERT: C 211 ASP cc_start: 0.8503 (t70) cc_final: 0.7856 (t0) REVERT: C 215 ARG cc_start: 0.8809 (ttp80) cc_final: 0.8484 (ttp80) REVERT: C 284 GLU cc_start: 0.8249 (mp0) cc_final: 0.7776 (mp0) REVERT: C 290 GLU cc_start: 0.8660 (mp0) cc_final: 0.8256 (mp0) REVERT: C 338 LYS cc_start: 0.8973 (mtpp) cc_final: 0.8740 (tptp) REVERT: C 386 GLU cc_start: 0.8012 (mp0) cc_final: 0.7612 (mp0) REVERT: C 397 LEU cc_start: 0.9348 (mt) cc_final: 0.9136 (mt) REVERT: C 433 GLU cc_start: 0.8832 (pt0) cc_final: 0.8336 (pp20) REVERT: D 26 ASP cc_start: 0.8621 (t0) cc_final: 0.8242 (t0) REVERT: D 57 ASN cc_start: 0.8298 (t0) cc_final: 0.7905 (t0) REVERT: D 190 HIS cc_start: 0.8583 (t-170) cc_final: 0.8129 (t-170) REVERT: D 203 ASP cc_start: 0.8469 (t0) cc_final: 0.8111 (t70) REVERT: D 209 ASP cc_start: 0.8988 (t0) cc_final: 0.8693 (t0) REVERT: D 325 GLU cc_start: 0.8832 (tp30) cc_final: 0.8554 (tp30) REVERT: D 383 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8671 (tm-30) REVERT: D 410 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8281 (mt-10) REVERT: D 412 GLU cc_start: 0.8638 (tp30) cc_final: 0.8313 (tp30) REVERT: D 417 ASP cc_start: 0.8588 (m-30) cc_final: 0.8181 (m-30) REVERT: E 13 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8701 (ttp80) REVERT: E 68 GLU cc_start: 0.8875 (tt0) cc_final: 0.8655 (tt0) REVERT: E 165 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8333 (mm-40) REVERT: E 169 ASN cc_start: 0.8403 (t0) cc_final: 0.8182 (t0) REVERT: E 173 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8561 (mm-40) REVERT: E 248 SER cc_start: 0.8548 (m) cc_final: 0.8145 (p) REVERT: E 305 ASP cc_start: 0.8199 (p0) cc_final: 0.7918 (p0) REVERT: E 307 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8350 (mtp-110) REVERT: E 444 MET cc_start: 0.8932 (mtm) cc_final: 0.8393 (mtt) REVERT: E 451 ASP cc_start: 0.7989 (t0) cc_final: 0.7677 (t0) REVERT: E 523 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8299 (ttm-80) REVERT: E 549 ARG cc_start: 0.8322 (mtm110) cc_final: 0.8046 (mtm-85) REVERT: E 582 GLU cc_start: 0.8251 (tp30) cc_final: 0.8006 (tp30) outliers start: 36 outliers final: 17 residues processed: 354 average time/residue: 0.5471 time to fit residues: 268.9061 Evaluate side-chains 348 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 328 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 54 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 180 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 181 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 37 HIS B 280 GLN C 91 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.075667 restraints weight = 35456.909| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.26 r_work: 0.2948 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17981 Z= 0.114 Angle : 0.545 9.712 24438 Z= 0.279 Chirality : 0.042 0.183 2659 Planarity : 0.004 0.058 3193 Dihedral : 9.844 174.570 2525 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.29 % Allowed : 14.22 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.80 (0.18), residues: 2207 helix: 1.57 (0.18), residues: 930 sheet: 0.52 (0.30), residues: 319 loop : -0.45 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.004 0.001 HIS B 190 PHE 0.022 0.001 PHE E 128 TYR 0.011 0.001 TYR A 172 ARG 0.013 0.001 ARG C 390 Details of bonding type rmsd link_TRANS : bond 0.00011 ( 1) link_TRANS : angle 0.04990 ( 3) hydrogen bonds : bond 0.03282 ( 795) hydrogen bonds : angle 4.23791 ( 2295) metal coordination : bond 0.00317 ( 2) covalent geometry : bond 0.00267 (17977) covalent geometry : angle 0.54460 (24435) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 331 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 SER cc_start: 0.9337 (t) cc_final: 0.9134 (p) REVERT: A 214 ARG cc_start: 0.8751 (mtp-110) cc_final: 0.8454 (ttp80) REVERT: A 218 ASP cc_start: 0.8685 (t0) cc_final: 0.8158 (t0) REVERT: A 221 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.8181 (mtt90) REVERT: A 251 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7375 (p0) REVERT: A 290 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8007 (mt-10) REVERT: A 357 TYR cc_start: 0.9098 (m-80) cc_final: 0.8817 (m-80) REVERT: A 414 GLU cc_start: 0.8578 (mp0) cc_final: 0.8315 (mp0) REVERT: B 58 LYS cc_start: 0.8625 (tttt) cc_final: 0.7886 (pttt) REVERT: B 94 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8423 (mp10) REVERT: B 122 LYS cc_start: 0.8913 (tppp) cc_final: 0.8703 (ttmm) REVERT: B 205 GLU cc_start: 0.8432 (tt0) cc_final: 0.7942 (tt0) REVERT: B 209 ASP cc_start: 0.8350 (t70) cc_final: 0.8129 (t0) REVERT: B 212 PHE cc_start: 0.8401 (m-10) cc_final: 0.8116 (m-10) REVERT: B 278 SER cc_start: 0.8784 (m) cc_final: 0.8371 (t) REVERT: B 327 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7964 (t0) REVERT: B 376 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8387 (mt-10) REVERT: B 379 LYS cc_start: 0.8764 (mtpp) cc_final: 0.8562 (mtpp) REVERT: B 390 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8662 (mtp85) REVERT: B 410 GLU cc_start: 0.7848 (pp20) cc_final: 0.7598 (pp20) REVERT: B 412 GLU cc_start: 0.8591 (tt0) cc_final: 0.8163 (tt0) REVERT: B 417 ASP cc_start: 0.8278 (m-30) cc_final: 0.7951 (m-30) REVERT: C 123 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7300 (tpp80) REVERT: C 196 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 207 GLU cc_start: 0.8300 (tt0) cc_final: 0.8063 (mt-10) REVERT: C 211 ASP cc_start: 0.8471 (t70) cc_final: 0.7840 (t0) REVERT: C 215 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8534 (ttp80) REVERT: C 284 GLU cc_start: 0.8291 (mp0) cc_final: 0.7894 (mp0) REVERT: C 290 GLU cc_start: 0.8650 (mp0) cc_final: 0.8256 (mp0) REVERT: C 297 GLU cc_start: 0.8408 (tp30) cc_final: 0.8075 (tp30) REVERT: C 338 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8764 (tptp) REVERT: C 386 GLU cc_start: 0.8091 (mp0) cc_final: 0.7874 (mp0) REVERT: C 397 LEU cc_start: 0.9348 (mt) cc_final: 0.9130 (mt) REVERT: C 433 GLU cc_start: 0.8796 (pt0) cc_final: 0.8347 (pp20) REVERT: D 26 ASP cc_start: 0.8646 (t0) cc_final: 0.8225 (t0) REVERT: D 57 ASN cc_start: 0.8118 (t0) cc_final: 0.7794 (t0) REVERT: D 103 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8818 (ttmm) REVERT: D 190 HIS cc_start: 0.8545 (t-170) cc_final: 0.8084 (t-170) REVERT: D 203 ASP cc_start: 0.8447 (t0) cc_final: 0.8053 (t70) REVERT: D 209 ASP cc_start: 0.8999 (t0) cc_final: 0.8359 (t0) REVERT: D 213 ARG cc_start: 0.9009 (ttp-110) cc_final: 0.8594 (mtm-85) REVERT: D 325 GLU cc_start: 0.8772 (tp30) cc_final: 0.8483 (tp30) REVERT: D 376 GLU cc_start: 0.8117 (mp0) cc_final: 0.7805 (mp0) REVERT: D 383 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 410 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 412 GLU cc_start: 0.8619 (tp30) cc_final: 0.8321 (tp30) REVERT: D 413 SER cc_start: 0.8832 (t) cc_final: 0.8138 (p) REVERT: D 417 ASP cc_start: 0.8541 (m-30) cc_final: 0.8200 (m-30) REVERT: E 53 GLU cc_start: 0.7286 (tp30) cc_final: 0.7049 (tp30) REVERT: E 68 GLU cc_start: 0.8850 (tt0) cc_final: 0.8624 (tt0) REVERT: E 165 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8410 (mm110) REVERT: E 169 ASN cc_start: 0.8383 (t0) cc_final: 0.8167 (t0) REVERT: E 173 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8542 (mm-40) REVERT: E 248 SER cc_start: 0.8497 (m) cc_final: 0.8182 (p) REVERT: E 305 ASP cc_start: 0.8239 (p0) cc_final: 0.7911 (p0) REVERT: E 307 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8303 (mtp-110) REVERT: E 314 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8295 (mm-40) REVERT: E 424 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: E 444 MET cc_start: 0.8904 (mtm) cc_final: 0.8458 (mtt) REVERT: E 451 ASP cc_start: 0.7995 (t0) cc_final: 0.7689 (t0) REVERT: E 514 THR cc_start: 0.9197 (m) cc_final: 0.8664 (p) REVERT: E 523 ARG cc_start: 0.8600 (ttm-80) cc_final: 0.8292 (ttm-80) REVERT: E 549 ARG cc_start: 0.8317 (mtm110) cc_final: 0.8044 (mtm-85) REVERT: E 582 GLU cc_start: 0.8219 (tp30) cc_final: 0.8008 (tp30) outliers start: 24 outliers final: 15 residues processed: 340 average time/residue: 0.5474 time to fit residues: 262.9818 Evaluate side-chains 342 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 324 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 202 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 153 optimal weight: 0.0670 chunk 203 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 37 HIS B 280 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.074764 restraints weight = 35851.761| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.27 r_work: 0.2922 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17981 Z= 0.140 Angle : 0.555 9.413 24438 Z= 0.285 Chirality : 0.043 0.178 2659 Planarity : 0.004 0.044 3193 Dihedral : 9.978 176.152 2525 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.13 % Allowed : 14.27 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % 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: 0.79 (0.18), residues: 2207 helix: 1.56 (0.17), residues: 930 sheet: 0.49 (0.30), residues: 317 loop : -0.46 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 21 HIS 0.005 0.001 HIS E 533 PHE 0.023 0.001 PHE E 128 TYR 0.013 0.001 TYR E 102 ARG 0.010 0.001 ARG C 390 Details of bonding type rmsd link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 0.08528 ( 3) hydrogen bonds : bond 0.03526 ( 795) hydrogen bonds : angle 4.28446 ( 2295) metal coordination : bond 0.00579 ( 2) covalent geometry : bond 0.00330 (17977) covalent geometry : angle 0.55519 (24435) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 4.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7789 (tp30) cc_final: 0.7490 (tp30) REVERT: A 84 ARG cc_start: 0.8603 (ptp90) cc_final: 0.8245 (ptp90) REVERT: A 158 SER cc_start: 0.9370 (t) cc_final: 0.9160 (p) REVERT: A 214 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8396 (mtm110) REVERT: A 218 ASP cc_start: 0.8712 (t0) cc_final: 0.8152 (t0) REVERT: A 251 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7341 (p0) REVERT: A 284 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8021 (mp0) REVERT: A 290 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8087 (mt-10) REVERT: A 357 TYR cc_start: 0.9111 (m-80) cc_final: 0.8803 (m-80) REVERT: A 414 GLU cc_start: 0.8593 (mp0) cc_final: 0.8169 (mp0) REVERT: B 58 LYS cc_start: 0.8594 (tttt) cc_final: 0.7916 (pttt) REVERT: B 94 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8438 (mp10) REVERT: B 111 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8124 (mp0) REVERT: B 122 LYS cc_start: 0.8907 (tppp) cc_final: 0.8703 (ttmm) REVERT: B 209 ASP cc_start: 0.8481 (t70) cc_final: 0.8075 (t0) REVERT: B 212 PHE cc_start: 0.8421 (m-10) cc_final: 0.8178 (m-10) REVERT: B 213 ARG cc_start: 0.8508 (ptp-110) cc_final: 0.8044 (mtm110) REVERT: B 278 SER cc_start: 0.8783 (m) cc_final: 0.8375 (t) REVERT: B 376 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8283 (mp0) REVERT: B 390 ARG cc_start: 0.8882 (mtp-110) cc_final: 0.8681 (mtp85) REVERT: B 410 GLU cc_start: 0.7702 (pp20) cc_final: 0.7458 (pp20) REVERT: B 412 GLU cc_start: 0.8488 (tt0) cc_final: 0.8169 (tt0) REVERT: B 417 ASP cc_start: 0.8290 (m-30) cc_final: 0.7940 (m-30) REVERT: C 120 ASP cc_start: 0.8368 (t0) cc_final: 0.8136 (t0) REVERT: C 123 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7305 (tpp80) REVERT: C 196 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7753 (tm-30) REVERT: C 211 ASP cc_start: 0.8484 (t70) cc_final: 0.7851 (t0) REVERT: C 215 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8537 (ttp80) REVERT: C 280 LYS cc_start: 0.8736 (mttp) cc_final: 0.7704 (mmtt) REVERT: C 284 GLU cc_start: 0.8287 (mp0) cc_final: 0.7870 (mp0) REVERT: C 290 GLU cc_start: 0.8656 (mp0) cc_final: 0.8284 (mp0) REVERT: C 338 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8755 (tptp) REVERT: C 397 LEU cc_start: 0.9351 (mt) cc_final: 0.9138 (mt) REVERT: C 433 GLU cc_start: 0.8809 (pt0) cc_final: 0.8359 (pp20) REVERT: D 26 ASP cc_start: 0.8608 (t0) cc_final: 0.8219 (t0) REVERT: D 57 ASN cc_start: 0.8295 (t0) cc_final: 0.7970 (t0) REVERT: D 103 LYS cc_start: 0.9185 (mtpt) cc_final: 0.8796 (ttmm) REVERT: D 190 HIS cc_start: 0.8564 (t-170) cc_final: 0.8091 (t-170) REVERT: D 203 ASP cc_start: 0.8417 (t0) cc_final: 0.8077 (t0) REVERT: D 209 ASP cc_start: 0.8979 (t0) cc_final: 0.8506 (t0) REVERT: D 213 ARG cc_start: 0.9020 (ttp-110) cc_final: 0.8696 (mtm-85) REVERT: D 383 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8650 (tm-30) REVERT: D 407 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8113 (mt-10) REVERT: D 410 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8292 (mt-10) REVERT: D 412 GLU cc_start: 0.8641 (tp30) cc_final: 0.8344 (tp30) REVERT: D 417 ASP cc_start: 0.8566 (m-30) cc_final: 0.8217 (m-30) REVERT: E 53 GLU cc_start: 0.7318 (tp30) cc_final: 0.7086 (tp30) REVERT: E 68 GLU cc_start: 0.8875 (tt0) cc_final: 0.8653 (tt0) REVERT: E 165 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8436 (mm110) REVERT: E 169 ASN cc_start: 0.8386 (t0) cc_final: 0.8163 (t0) REVERT: E 173 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8550 (mm-40) REVERT: E 248 SER cc_start: 0.8507 (m) cc_final: 0.8108 (p) REVERT: E 305 ASP cc_start: 0.8134 (p0) cc_final: 0.7852 (p0) REVERT: E 307 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8318 (mtp-110) REVERT: E 424 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: E 444 MET cc_start: 0.8946 (mtm) cc_final: 0.8508 (mtt) REVERT: E 451 ASP cc_start: 0.7986 (t0) cc_final: 0.7688 (t0) REVERT: E 514 THR cc_start: 0.9220 (m) cc_final: 0.8702 (p) REVERT: E 523 ARG cc_start: 0.8652 (ttm-80) cc_final: 0.8319 (ttm-80) REVERT: E 549 ARG cc_start: 0.8313 (mtm110) cc_final: 0.8060 (mtm-85) outliers start: 21 outliers final: 17 residues processed: 331 average time/residue: 0.4828 time to fit residues: 228.2961 Evaluate side-chains 337 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 533 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 215 optimal weight: 0.0270 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 162 optimal weight: 0.0980 chunk 93 optimal weight: 0.2980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 216 ASN B 37 HIS B 280 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 35 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.076324 restraints weight = 35609.429| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.25 r_work: 0.2957 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17981 Z= 0.109 Angle : 0.546 10.045 24438 Z= 0.280 Chirality : 0.042 0.156 2659 Planarity : 0.004 0.040 3193 Dihedral : 9.784 171.465 2525 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.13 % Allowed : 14.48 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2207 helix: 1.55 (0.17), residues: 942 sheet: 0.50 (0.30), residues: 319 loop : -0.52 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 21 HIS 0.005 0.001 HIS E 533 PHE 0.024 0.001 PHE E 128 TYR 0.013 0.001 TYR B 59 ARG 0.008 0.000 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.04084 ( 3) hydrogen bonds : bond 0.03177 ( 795) hydrogen bonds : angle 4.22431 ( 2295) metal coordination : bond 0.00237 ( 2) covalent geometry : bond 0.00254 (17977) covalent geometry : angle 0.54598 (24435) Misc. bond : bond 0.00020 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4414 Ramachandran restraints generated. 2207 Oldfield, 0 Emsley, 2207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 328 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7832 (tp30) cc_final: 0.7579 (tp30) REVERT: A 84 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8271 (ptp90) REVERT: A 158 SER cc_start: 0.9354 (t) cc_final: 0.9148 (p) REVERT: A 214 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.8392 (mtm110) REVERT: A 218 ASP cc_start: 0.8693 (t0) cc_final: 0.8202 (t0) REVERT: A 251 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7366 (p0) REVERT: A 284 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7996 (mp0) REVERT: A 290 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8128 (mt-10) REVERT: A 357 TYR cc_start: 0.9102 (m-80) cc_final: 0.8805 (m-80) REVERT: A 414 GLU cc_start: 0.8586 (mp0) cc_final: 0.8162 (mp0) REVERT: B 53 GLU cc_start: 0.8249 (tp30) cc_final: 0.8019 (mm-30) REVERT: B 58 LYS cc_start: 0.8601 (tttt) cc_final: 0.7784 (pttt) REVERT: B 94 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8419 (mp10) REVERT: B 205 GLU cc_start: 0.8454 (tt0) cc_final: 0.8064 (tt0) REVERT: B 209 ASP cc_start: 0.8371 (t70) cc_final: 0.7904 (t0) REVERT: B 212 PHE cc_start: 0.8381 (m-10) cc_final: 0.8091 (m-10) REVERT: B 213 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8005 (mtm110) REVERT: B 278 SER cc_start: 0.8800 (m) cc_final: 0.8394 (t) REVERT: B 376 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8282 (mp0) REVERT: B 410 GLU cc_start: 0.7571 (pp20) cc_final: 0.7355 (pp20) REVERT: B 413 SER cc_start: 0.7693 (t) cc_final: 0.7462 (p) REVERT: C 120 ASP cc_start: 0.8380 (t0) cc_final: 0.8140 (t0) REVERT: C 123 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7312 (tpp80) REVERT: C 211 ASP cc_start: 0.8486 (t70) cc_final: 0.7831 (t0) REVERT: C 215 ARG cc_start: 0.8835 (ttp80) cc_final: 0.8513 (ttp80) REVERT: C 284 GLU cc_start: 0.8229 (mp0) cc_final: 0.7823 (mp0) REVERT: C 290 GLU cc_start: 0.8651 (mp0) cc_final: 0.8308 (mp0) REVERT: C 297 GLU cc_start: 0.8271 (tp30) cc_final: 0.7821 (tm-30) REVERT: C 338 LYS cc_start: 0.9012 (mtpp) cc_final: 0.8765 (tptp) REVERT: C 397 LEU cc_start: 0.9347 (mt) cc_final: 0.9127 (mt) REVERT: C 433 GLU cc_start: 0.8755 (pt0) cc_final: 0.8409 (tm-30) REVERT: D 26 ASP cc_start: 0.8555 (t0) cc_final: 0.8156 (t0) REVERT: D 57 ASN cc_start: 0.8320 (t0) cc_final: 0.8013 (t0) REVERT: D 103 LYS cc_start: 0.9183 (mtpt) cc_final: 0.8794 (ttmm) REVERT: D 190 HIS cc_start: 0.8540 (t-170) cc_final: 0.8091 (t-170) REVERT: D 203 ASP cc_start: 0.8363 (t0) cc_final: 0.8039 (t0) REVERT: D 209 ASP cc_start: 0.8999 (t0) cc_final: 0.8334 (t0) REVERT: D 213 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8569 (mtm-85) REVERT: D 325 GLU cc_start: 0.8728 (tp30) cc_final: 0.8485 (tp30) REVERT: D 383 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8617 (tm-30) REVERT: D 410 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8056 (mt-10) REVERT: D 412 GLU cc_start: 0.8606 (tp30) cc_final: 0.8324 (tp30) REVERT: D 413 SER cc_start: 0.8829 (t) cc_final: 0.8123 (p) REVERT: D 417 ASP cc_start: 0.8529 (m-30) cc_final: 0.8194 (m-30) REVERT: E 53 GLU cc_start: 0.7315 (tp30) cc_final: 0.7040 (tp30) REVERT: E 68 GLU cc_start: 0.8841 (tt0) cc_final: 0.8614 (tt0) REVERT: E 165 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8388 (mm110) REVERT: E 169 ASN cc_start: 0.8384 (t0) cc_final: 0.8161 (t0) REVERT: E 173 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8563 (mm-40) REVERT: E 248 SER cc_start: 0.8481 (m) cc_final: 0.8175 (p) REVERT: E 305 ASP cc_start: 0.8048 (p0) cc_final: 0.7681 (p0) REVERT: E 307 ARG cc_start: 0.8756 (mtp-110) cc_final: 0.8279 (mtp-110) REVERT: E 424 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: E 444 MET cc_start: 0.8918 (mtm) cc_final: 0.8474 (mtt) REVERT: E 451 ASP cc_start: 0.7974 (t0) cc_final: 0.7680 (t0) REVERT: E 514 THR cc_start: 0.9205 (m) cc_final: 0.8666 (p) REVERT: E 523 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: E 549 ARG cc_start: 0.8265 (mtm110) cc_final: 0.8055 (mtm-85) outliers start: 21 outliers final: 18 residues processed: 335 average time/residue: 0.4476 time to fit residues: 210.7854 Evaluate side-chains 337 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 317 time to evaluate : 3.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 424 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 533 HIS Chi-restraints excluded: chain E residue 595 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 8 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 191 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075294 restraints weight = 35634.837| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.28 r_work: 0.2932 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17981 Z= 0.136 Angle : 0.569 9.625 24438 Z= 0.292 Chirality : 0.043 0.245 2659 Planarity : 0.004 0.041 3193 Dihedral : 9.726 170.574 2525 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.13 % Allowed : 15.08 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2207 helix: 1.53 (0.17), residues: 942 sheet: 0.48 (0.30), residues: 329 loop : -0.50 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.005 0.001 HIS E 533 PHE 0.026 0.001 PHE E 128 TYR 0.012 0.001 TYR E 102 ARG 0.009 0.001 ARG B 306 Details of bonding type rmsd link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.07718 ( 3) hydrogen bonds : bond 0.03432 ( 795) hydrogen bonds : angle 4.27714 ( 2295) metal coordination : bond 0.00474 ( 2) covalent geometry : bond 0.00321 (17977) covalent geometry : angle 0.56925 (24435) Misc. bond : bond 0.00044 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11027.42 seconds wall clock time: 199 minutes 46.34 seconds (11986.34 seconds total)