Starting phenix.real_space_refine on Thu Sep 18 15:02:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4k_42971/09_2025/8v4k_42971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4k_42971/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v4k_42971/09_2025/8v4k_42971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4k_42971/09_2025/8v4k_42971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v4k_42971/09_2025/8v4k_42971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4k_42971/09_2025/8v4k_42971.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'UNK:plan-1': 8, 'GLU:plan': 1} 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: {'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} 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: 4.64, per 1000 atoms: 0.26 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: 1.67 Conformation dependent library (CDL) restraints added in 818.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.66 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: 3.42 Time building geometry restraints manager: 2.17 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 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 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: 0.010 Normalize map: mean=0, sd=1: 8.950 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.340 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 215 TYR 0.052 0.002 TYR A 432 PHE 0.035 0.003 PHE C 255 TRP 0.048 0.003 TRP A 388 HIS 0.011 0.002 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00604 (17977) covalent geometry : angle 1.02712 (24435) hydrogen bonds : bond 0.16525 ( 795) hydrogen bonds : angle 7.44302 ( 2295) metal coordination : bond 0.01010 ( 2) Misc. bond : bond 0.05211 ( 1) link_TRANS : bond 0.00762 ( 1) link_TRANS : angle 0.88884 ( 3) *********************** 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 : 0.736 Fit side-chains revert: symmetry clash 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: 0.8211 (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: 0.7980 (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: 0.8072 (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: 0.7342 (pttt) REVERT: B 103 LYS cc_start: 0.8815 (tttt) cc_final: 0.7870 (ttpt) REVERT: B 108 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8440 (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: 0.8499 (mmmt) REVERT: B 203 ASP cc_start: 0.8266 (t0) cc_final: 0.7875 (t0) REVERT: B 205 GLU cc_start: 0.7955 (tt0) cc_final: 0.7742 (tt0) REVERT: B 252 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8636 (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: 0.7495 (mp0) REVERT: B 379 LYS cc_start: 0.8181 (mttp) cc_final: 0.7963 (mtmm) REVERT: B 383 GLU cc_start: 0.8336 (tp30) cc_final: 0.7981 (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: 0.7367 (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: 0.8239 (mm-30) REVERT: C 116 ASP cc_start: 0.7753 (p0) cc_final: 0.7283 (p0) REVERT: C 120 ASP cc_start: 0.7757 (t0) cc_final: 0.7268 (m-30) REVERT: C 123 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.6705 (tpp80) REVERT: C 211 ASP cc_start: 0.8078 (t70) cc_final: 0.7500 (t0) REVERT: C 280 LYS cc_start: 0.8615 (mttp) cc_final: 0.7631 (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: 0.7783 (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: 0.8361 (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: 0.6233 (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: 0.7684 (t0) REVERT: D 213 ARG cc_start: 0.8832 (ttp-110) cc_final: 0.8420 (ttp-110) 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: 0.8000 (pp30) REVERT: D 304 ASP cc_start: 0.8134 (t70) cc_final: 0.7748 (t0) 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: 0.7592 (mp0) REVERT: D 410 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 413 SER cc_start: 0.8329 (t) cc_final: 0.7573 (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: 0.8371 (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: 0.8603 (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: 0.7770 (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: 0.8205 (ttm) REVERT: E 451 ASP cc_start: 0.7474 (t0) cc_final: 0.6976 (t0) REVERT: E 549 ARG cc_start: 0.7988 (mtm110) cc_final: 0.7624 (mtm-85) REVERT: E 553 GLU cc_start: 0.7926 (mp0) cc_final: 0.7689 (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: 0.1964 time to fit residues: 127.7176 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 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 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 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 = 0.3313 r_free = 0.3313 target = 0.088238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078637 restraints weight = 35886.632| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.30 r_work: 0.2980 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2354 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= 0.143 Angle : 0.533 8.248 24438 Z= 0.283 Chirality : 0.043 0.155 2659 Planarity : 0.005 0.060 3193 Dihedral : 10.624 154.475 2525 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.13 % Allowed : 8.64 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.17), residues: 2207 helix: 0.05 (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 ARG 0.006 0.000 ARG B 306 TYR 0.013 0.001 TYR A 172 PHE 0.027 0.001 PHE A 255 TRP 0.015 0.002 TRP E 592 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00320 (17977) covalent geometry : angle 0.53336 (24435) hydrogen bonds : bond 0.04253 ( 795) hydrogen bonds : angle 4.86018 ( 2295) metal coordination : bond 0.00599 ( 2) Misc. bond : bond 0.00067 ( 1) link_TRANS : bond 0.00091 ( 1) link_TRANS : angle 0.23026 ( 3) *********************** 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 395 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 374 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8850 (mmmm) REVERT: A 123 ARG cc_start: 0.8354 (tpp-160) cc_final: 0.8103 (tpp-160) REVERT: A 203 MET cc_start: 0.8544 (mmt) cc_final: 0.8303 (mmm) REVERT: A 214 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8418 (mtm110) REVERT: A 218 ASP cc_start: 0.8296 (t0) cc_final: 0.7990 (t0) REVERT: A 221 ARG cc_start: 0.8328 (ptp-110) cc_final: 0.7894 (ptp-110) REVERT: A 284 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8300 (mm-30) REVERT: A 290 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7755 (mt-10) REVERT: A 414 GLU cc_start: 0.8710 (mp0) cc_final: 0.8231 (mp0) REVERT: A 415 GLU cc_start: 0.8702 (tt0) cc_final: 0.8050 (tp30) REVERT: A 423 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8343 (tp30) REVERT: A 424 ASP cc_start: 0.8652 (m-30) cc_final: 0.8165 (m-30) REVERT: B 53 GLU cc_start: 0.8398 (tt0) cc_final: 0.8042 (tp30) REVERT: B 58 LYS cc_start: 0.8458 (tttt) cc_final: 0.7736 (pttt) REVERT: B 103 LYS cc_start: 0.9043 (tttt) cc_final: 0.8138 (ttpt) REVERT: B 122 LYS cc_start: 0.9023 (tppp) cc_final: 0.8797 (ttmm) REVERT: B 129 CYS cc_start: 0.9003 (t) cc_final: 0.8714 (p) REVERT: B 205 GLU cc_start: 0.8370 (tt0) cc_final: 0.7968 (tt0) REVERT: B 209 ASP cc_start: 0.8379 (t70) cc_final: 0.7850 (t0) REVERT: B 213 ARG cc_start: 0.8384 (ptp-110) cc_final: 0.7943 (ptp90) REVERT: B 278 SER cc_start: 0.9059 (m) cc_final: 0.8479 (t) REVERT: B 295 ASP cc_start: 0.8483 (t70) cc_final: 0.8282 (t0) REVERT: B 325 GLU cc_start: 0.8243 (tp30) cc_final: 0.7926 (tp30) REVERT: B 328 GLU cc_start: 0.7705 (pt0) cc_final: 0.7233 (pp20) REVERT: B 392 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8825 (mtmm) REVERT: B 410 GLU cc_start: 0.7921 (pp20) cc_final: 0.7676 (pp20) REVERT: C 76 ASP cc_start: 0.8832 (m-30) cc_final: 0.8437 (m-30) REVERT: C 116 ASP cc_start: 0.8319 (p0) cc_final: 0.7999 (p0) REVERT: C 120 ASP cc_start: 0.8425 (t0) cc_final: 0.8042 (m-30) REVERT: C 123 ARG cc_start: 0.7892 (tpp-160) cc_final: 0.7317 (tpp80) REVERT: C 154 MET cc_start: 0.8995 (mmm) cc_final: 0.8524 (mtp) REVERT: C 158 SER cc_start: 0.8847 (t) cc_final: 0.8585 (p) REVERT: C 196 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 211 ASP cc_start: 0.8370 (t70) cc_final: 0.7835 (t0) REVERT: C 214 ARG cc_start: 0.8697 (ptm-80) cc_final: 0.8058 (ttp80) REVERT: C 280 LYS cc_start: 0.8562 (mttp) cc_final: 0.7913 (mmtt) REVERT: C 290 GLU cc_start: 0.8361 (mp0) cc_final: 0.8062 (mp0) REVERT: C 297 GLU cc_start: 0.8166 (tp30) cc_final: 0.7897 (tp30) REVERT: C 338 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8689 (mmtm) REVERT: C 390 ARG cc_start: 0.8259 (mtm180) cc_final: 0.7979 (mtm-85) REVERT: C 423 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7497 (pp20) REVERT: C 433 GLU cc_start: 0.8570 (pt0) cc_final: 0.8235 (pp20) REVERT: C 434 GLU cc_start: 0.8508 (pp20) cc_final: 0.8218 (pp20) REVERT: D 22 GLU cc_start: 0.8718 (tt0) cc_final: 0.8431 (tm-30) REVERT: D 26 ASP cc_start: 0.8142 (t0) cc_final: 0.7868 (t0) REVERT: D 41 ASP cc_start: 0.8658 (m-30) cc_final: 0.8420 (p0) REVERT: D 58 LYS cc_start: 0.8742 (tttt) cc_final: 0.8227 (tttm) REVERT: D 94 GLN cc_start: 0.8770 (mm110) cc_final: 0.8485 (mm-40) REVERT: D 190 HIS cc_start: 0.8477 (t70) cc_final: 0.8212 (t-170) REVERT: D 203 ASP cc_start: 0.8396 (t0) cc_final: 0.8082 (t70) REVERT: D 209 ASP cc_start: 0.8654 (t0) cc_final: 0.8450 (t0) REVERT: D 291 GLN cc_start: 0.8407 (pp30) cc_final: 0.8132 (pp30) REVERT: D 304 ASP cc_start: 0.8334 (t70) cc_final: 0.7980 (t0) REVERT: D 335 ASN cc_start: 0.8234 (m-40) cc_final: 0.7889 (m-40) REVERT: D 383 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8568 (tm-30) REVERT: D 410 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8109 (mm-30) REVERT: D 412 GLU cc_start: 0.8520 (tp30) cc_final: 0.8267 (tp30) REVERT: D 413 SER cc_start: 0.8736 (t) cc_final: 0.7840 (p) REVERT: D 414 ASN cc_start: 0.8099 (p0) cc_final: 0.7168 (p0) REVERT: D 417 ASP cc_start: 0.8280 (m-30) cc_final: 0.7817 (m-30) REVERT: D 421 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8258 (mt-10) REVERT: E 3 LEU cc_start: 0.8034 (mt) cc_final: 0.7739 (mt) REVERT: E 13 ARG cc_start: 0.8774 (ttp-170) cc_final: 0.8548 (ttp80) REVERT: E 68 GLU cc_start: 0.8843 (tt0) cc_final: 0.8599 (tt0) REVERT: E 95 MET cc_start: 0.8878 (ttm) cc_final: 0.8510 (ttp) REVERT: E 116 ARG cc_start: 0.8551 (ttm170) cc_final: 0.8326 (ttm-80) REVERT: E 118 ARG cc_start: 0.8645 (ttt180) cc_final: 0.8414 (mmm-85) REVERT: E 165 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8162 (mm110) REVERT: E 172 ASP cc_start: 0.8715 (t0) cc_final: 0.8470 (t0) REVERT: E 173 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8441 (mm-40) REVERT: E 248 SER cc_start: 0.8470 (m) cc_final: 0.8080 (p) REVERT: E 307 ARG cc_start: 0.8888 (mtp-110) cc_final: 0.8586 (mtp-110) REVERT: E 444 MET cc_start: 0.8965 (mtm) cc_final: 0.8641 (mtm) REVERT: E 451 ASP cc_start: 0.7931 (t0) cc_final: 0.7648 (t0) REVERT: E 501 VAL cc_start: 0.8322 (t) cc_final: 0.8011 (m) REVERT: E 523 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: E 569 MET cc_start: 0.8520 (mmt) cc_final: 0.8195 (mmt) outliers start: 21 outliers final: 10 residues processed: 384 average time/residue: 0.1899 time to fit residues: 102.2114 Evaluate side-chains 350 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 339 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 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 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 219 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 195 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076088 restraints weight = 36178.982| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.27 r_work: 0.2945 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17981 Z= 0.140 Angle : 0.528 8.176 24438 Z= 0.273 Chirality : 0.043 0.164 2659 Planarity : 0.004 0.051 3193 Dihedral : 10.354 173.518 2525 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 10.41 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.18), residues: 2207 helix: 0.82 (0.17), residues: 936 sheet: 0.28 (0.29), residues: 342 loop : -0.54 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 306 TYR 0.013 0.001 TYR E 102 PHE 0.013 0.001 PHE E 128 TRP 0.013 0.001 TRP E 592 HIS 0.009 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00323 (17977) covalent geometry : angle 0.52781 (24435) hydrogen bonds : bond 0.03908 ( 795) hydrogen bonds : angle 4.54102 ( 2295) metal coordination : bond 0.00541 ( 2) Misc. bond : bond 0.00063 ( 1) link_TRANS : bond 0.00036 ( 1) link_TRANS : angle 0.07579 ( 3) *********************** 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 381 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 358 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8568 (ptp90) cc_final: 0.8286 (ptt-90) REVERT: A 50 ASN cc_start: 0.9008 (t0) cc_final: 0.8539 (t0) REVERT: A 85 GLN cc_start: 0.8993 (mm110) cc_final: 0.8669 (tp40) REVERT: A 123 ARG cc_start: 0.8349 (tpp-160) cc_final: 0.8125 (tpp-160) REVERT: A 158 SER cc_start: 0.9353 (t) cc_final: 0.9028 (p) REVERT: A 218 ASP cc_start: 0.8508 (t0) cc_final: 0.8052 (t0) REVERT: A 251 ASP cc_start: 0.8030 (p0) cc_final: 0.7321 (p0) REVERT: A 284 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 414 GLU cc_start: 0.8672 (mp0) cc_final: 0.8390 (mp0) REVERT: A 415 GLU cc_start: 0.8744 (tt0) cc_final: 0.8275 (tp30) REVERT: B 58 LYS cc_start: 0.8633 (tttt) cc_final: 0.7841 (pttt) REVERT: B 103 LYS cc_start: 0.9156 (tttt) cc_final: 0.8415 (tttm) REVERT: B 108 GLU cc_start: 0.7996 (mp0) cc_final: 0.7791 (mp0) REVERT: B 122 LYS cc_start: 0.8985 (tppp) cc_final: 0.8734 (ttmm) REVERT: B 154 LYS cc_start: 0.9154 (mttm) cc_final: 0.8728 (mttp) REVERT: B 157 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7900 (pt0) REVERT: B 164 MET cc_start: 0.8906 (tpp) cc_final: 0.8589 (tpt) REVERT: B 205 GLU cc_start: 0.8404 (tt0) cc_final: 0.8021 (tt0) REVERT: B 209 ASP cc_start: 0.8374 (t70) cc_final: 0.7930 (t0) REVERT: B 213 ARG cc_start: 0.8433 (ptp-110) cc_final: 0.8084 (ptp90) REVERT: B 278 SER cc_start: 0.8997 (m) cc_final: 0.8447 (t) REVERT: B 328 GLU cc_start: 0.7854 (pt0) cc_final: 0.7499 (pt0) REVERT: B 332 ASN cc_start: 0.8360 (m-40) cc_final: 0.8096 (m-40) REVERT: B 376 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8286 (mt-10) REVERT: B 379 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8450 (mtpp) REVERT: B 392 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8958 (mtmm) REVERT: B 410 GLU cc_start: 0.8100 (pp20) cc_final: 0.7736 (pp20) REVERT: B 414 ASN cc_start: 0.8319 (t0) cc_final: 0.8019 (t0) REVERT: C 84 ARG cc_start: 0.8710 (ttp-110) cc_final: 0.7846 (ptp90) REVERT: C 112 LYS cc_start: 0.8314 (pttp) cc_final: 0.7970 (pttp) REVERT: C 120 ASP cc_start: 0.8410 (t0) cc_final: 0.8097 (t0) REVERT: C 123 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7351 (tpp80) REVERT: C 158 SER cc_start: 0.8917 (t) cc_final: 0.8709 (t) REVERT: C 196 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7667 (tm-30) REVERT: C 203 MET cc_start: 0.8883 (tpp) cc_final: 0.8602 (mmm) REVERT: C 211 ASP cc_start: 0.8405 (t70) cc_final: 0.7756 (t0) REVERT: C 215 ARG cc_start: 0.8825 (ttp80) cc_final: 0.8590 (ttp80) REVERT: C 280 LYS cc_start: 0.8648 (mttp) cc_final: 0.7741 (mmtt) REVERT: C 284 GLU cc_start: 0.8375 (mp0) cc_final: 0.7959 (mp0) REVERT: C 290 GLU cc_start: 0.8556 (mp0) cc_final: 0.8262 (mp0) REVERT: C 297 GLU cc_start: 0.8277 (tp30) cc_final: 0.8038 (tp30) REVERT: C 386 GLU cc_start: 0.8238 (mp0) cc_final: 0.7973 (mp0) REVERT: C 425 MET cc_start: 0.8678 (mmm) cc_final: 0.8185 (tpt) REVERT: D 22 GLU cc_start: 0.8788 (tt0) cc_final: 0.8477 (tm-30) REVERT: D 26 ASP cc_start: 0.8287 (t0) cc_final: 0.7862 (t0) REVERT: D 57 ASN cc_start: 0.8131 (t0) cc_final: 0.7361 (t0) REVERT: D 58 LYS cc_start: 0.8797 (tttt) cc_final: 0.8576 (tttm) REVERT: D 69 GLU cc_start: 0.8616 (pp20) cc_final: 0.8330 (pm20) REVERT: D 108 GLU cc_start: 0.8341 (mp0) cc_final: 0.8050 (mp0) REVERT: D 203 ASP cc_start: 0.8440 (t0) cc_final: 0.8125 (t70) REVERT: D 205 GLU cc_start: 0.8568 (tt0) cc_final: 0.8306 (tp30) REVERT: D 209 ASP cc_start: 0.8870 (t0) cc_final: 0.7800 (t0) REVERT: D 213 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8500 (ttp-110) REVERT: D 257 MET cc_start: 0.8349 (mmm) cc_final: 0.7917 (mmm) REVERT: D 291 GLN cc_start: 0.8442 (pp30) cc_final: 0.8196 (pp30) REVERT: D 321 MET cc_start: 0.8768 (ptp) cc_final: 0.8557 (ptp) REVERT: D 325 GLU cc_start: 0.8923 (tp30) cc_final: 0.8377 (tp30) REVERT: D 335 ASN cc_start: 0.8411 (m-40) cc_final: 0.8045 (m-40) REVERT: D 383 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8604 (tm-30) REVERT: D 410 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8285 (mm-30) REVERT: D 412 GLU cc_start: 0.8617 (tp30) cc_final: 0.8267 (tp30) REVERT: D 413 SER cc_start: 0.8816 (t) cc_final: 0.7954 (p) REVERT: D 417 ASP cc_start: 0.8367 (m-30) cc_final: 0.7898 (m-30) REVERT: D 421 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8108 (mt-10) REVERT: D 424 GLN cc_start: 0.8921 (tt0) cc_final: 0.8579 (tm-30) REVERT: E 3 LEU cc_start: 0.8075 (mt) cc_final: 0.7803 (mt) REVERT: E 13 ARG cc_start: 0.8786 (ttp-170) cc_final: 0.8563 (ttp80) REVERT: E 118 ARG cc_start: 0.8490 (ttt180) cc_final: 0.7527 (mmm-85) REVERT: E 120 GLU cc_start: 0.8481 (pt0) cc_final: 0.8209 (mp0) REVERT: E 134 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7417 (mm110) REVERT: E 165 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8426 (mm110) REVERT: E 172 ASP cc_start: 0.8644 (t0) cc_final: 0.8401 (t0) REVERT: E 248 SER cc_start: 0.8525 (m) cc_final: 0.8139 (p) REVERT: E 305 ASP cc_start: 0.8125 (p0) cc_final: 0.7880 (p0) REVERT: E 307 ARG cc_start: 0.8705 (mtp-110) cc_final: 0.8373 (mtp-110) REVERT: E 424 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: E 444 MET cc_start: 0.8960 (mtm) cc_final: 0.8595 (mtm) REVERT: E 451 ASP cc_start: 0.7935 (t0) cc_final: 0.7732 (t0) REVERT: E 523 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8125 (ttm-80) REVERT: E 582 GLU cc_start: 0.8240 (tp30) cc_final: 0.8014 (tp30) outliers start: 23 outliers final: 12 residues processed: 371 average time/residue: 0.1954 time to fit residues: 100.8065 Evaluate side-chains 353 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 339 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 200 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 133 GLN C 309 HIS D 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075933 restraints weight = 36033.518| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.27 r_work: 0.2934 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17981 Z= 0.128 Angle : 0.522 11.036 24438 Z= 0.266 Chirality : 0.043 0.158 2659 Planarity : 0.004 0.043 3193 Dihedral : 10.159 176.481 2525 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.72 % Allowed : 10.73 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.18), residues: 2207 helix: 1.15 (0.17), residues: 932 sheet: 0.27 (0.29), residues: 337 loop : -0.49 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 306 TYR 0.012 0.001 TYR E 102 PHE 0.011 0.001 PHE A 255 TRP 0.017 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00300 (17977) covalent geometry : angle 0.52241 (24435) hydrogen bonds : bond 0.03611 ( 795) hydrogen bonds : angle 4.41651 ( 2295) metal coordination : bond 0.00480 ( 2) Misc. bond : bond 0.00062 ( 1) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.05880 ( 3) *********************** 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 387 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8576 (ptp90) cc_final: 0.8348 (ptt-90) REVERT: A 50 ASN cc_start: 0.9037 (t0) cc_final: 0.8556 (t0) REVERT: A 85 GLN cc_start: 0.8994 (mm110) cc_final: 0.8632 (tp40) REVERT: A 158 SER cc_start: 0.9380 (t) cc_final: 0.9074 (p) REVERT: A 214 ARG cc_start: 0.8726 (mtp-110) cc_final: 0.8444 (mtm110) REVERT: A 215 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8667 (mtm110) REVERT: A 218 ASP cc_start: 0.8578 (t0) cc_final: 0.8061 (t0) REVERT: A 284 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 290 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8096 (mt-10) REVERT: A 304 LYS cc_start: 0.8929 (tptp) cc_final: 0.8723 (tptt) REVERT: A 414 GLU cc_start: 0.8782 (mp0) cc_final: 0.8130 (mp0) REVERT: A 415 GLU cc_start: 0.8746 (tt0) cc_final: 0.8495 (tp30) REVERT: B 58 LYS cc_start: 0.8614 (tttt) cc_final: 0.7933 (pttt) REVERT: B 94 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8465 (mp10) REVERT: B 103 LYS cc_start: 0.9169 (tttt) cc_final: 0.8301 (ttpt) REVERT: B 108 GLU cc_start: 0.8367 (mp0) cc_final: 0.8166 (mp0) REVERT: B 122 LYS cc_start: 0.8950 (tppp) cc_final: 0.8668 (ttmm) REVERT: B 174 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8664 (mmmt) REVERT: B 205 GLU cc_start: 0.8411 (tt0) cc_final: 0.7993 (tt0) REVERT: B 209 ASP cc_start: 0.8310 (t70) cc_final: 0.7807 (t0) REVERT: B 213 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.8087 (ptp90) REVERT: B 278 SER cc_start: 0.8816 (m) cc_final: 0.8383 (t) REVERT: B 328 GLU cc_start: 0.7899 (pt0) cc_final: 0.7135 (pp20) REVERT: B 332 ASN cc_start: 0.8405 (m-40) cc_final: 0.8025 (m-40) REVERT: B 376 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8315 (mt-10) REVERT: B 379 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8498 (mtpp) REVERT: B 392 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9030 (mtmm) REVERT: B 410 GLU cc_start: 0.8065 (pp20) cc_final: 0.7709 (pp20) REVERT: B 414 ASN cc_start: 0.8348 (t0) cc_final: 0.8048 (t0) REVERT: B 417 ASP cc_start: 0.8322 (m-30) cc_final: 0.8084 (m-30) REVERT: C 76 ASP cc_start: 0.8805 (m-30) cc_final: 0.8430 (m-30) REVERT: C 84 ARG cc_start: 0.8756 (ttp-110) cc_final: 0.8439 (ptp90) REVERT: C 120 ASP cc_start: 0.8453 (t0) cc_final: 0.8060 (m-30) REVERT: C 123 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7395 (tpp80) REVERT: C 155 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: C 158 SER cc_start: 0.8907 (t) cc_final: 0.8699 (t) REVERT: C 196 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 203 MET cc_start: 0.8981 (tpp) cc_final: 0.8600 (mmm) REVERT: C 211 ASP cc_start: 0.8449 (t70) cc_final: 0.7802 (t0) REVERT: C 215 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8520 (ttp80) REVERT: C 280 LYS cc_start: 0.8765 (mttp) cc_final: 0.7732 (mmtt) REVERT: C 284 GLU cc_start: 0.8328 (mp0) cc_final: 0.7873 (mp0) REVERT: C 290 GLU cc_start: 0.8640 (mp0) cc_final: 0.8286 (mp0) REVERT: C 297 GLU cc_start: 0.8330 (tp30) cc_final: 0.8075 (tp30) REVERT: C 386 GLU cc_start: 0.8123 (mp0) cc_final: 0.7911 (mp0) REVERT: C 433 GLU cc_start: 0.8736 (pt0) cc_final: 0.8254 (pp20) REVERT: D 22 GLU cc_start: 0.8785 (tt0) cc_final: 0.8527 (tm-30) REVERT: D 26 ASP cc_start: 0.8407 (t0) cc_final: 0.7936 (t0) REVERT: D 57 ASN cc_start: 0.8260 (t0) cc_final: 0.7781 (t0) REVERT: D 58 LYS cc_start: 0.8803 (tttt) cc_final: 0.8573 (tttt) REVERT: D 69 GLU cc_start: 0.8668 (pp20) cc_final: 0.8396 (pm20) REVERT: D 108 GLU cc_start: 0.8219 (mp0) cc_final: 0.7825 (mp0) REVERT: D 190 HIS cc_start: 0.8541 (t-170) cc_final: 0.8173 (t-170) REVERT: D 203 ASP cc_start: 0.8437 (t0) cc_final: 0.8157 (t70) REVERT: D 205 GLU cc_start: 0.8637 (tt0) cc_final: 0.8420 (tp30) REVERT: D 209 ASP cc_start: 0.8940 (t0) cc_final: 0.8268 (t0) REVERT: D 212 PHE cc_start: 0.8709 (m-10) cc_final: 0.8435 (m-10) REVERT: D 213 ARG cc_start: 0.8905 (ttp-110) cc_final: 0.8457 (mtm-85) REVERT: D 257 MET cc_start: 0.8378 (mmm) cc_final: 0.7974 (mmm) REVERT: D 300 MET cc_start: 0.9225 (mtm) cc_final: 0.9005 (mtm) REVERT: D 325 GLU cc_start: 0.8806 (tp30) cc_final: 0.8494 (tp30) REVERT: D 383 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8629 (tm-30) REVERT: D 405 GLU cc_start: 0.8793 (tm-30) cc_final: 0.8570 (tm-30) REVERT: D 410 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 412 GLU cc_start: 0.8453 (tp30) cc_final: 0.8117 (tp30) REVERT: D 413 SER cc_start: 0.8790 (t) cc_final: 0.7949 (p) REVERT: D 417 ASP cc_start: 0.8440 (m-30) cc_final: 0.7988 (m-30) REVERT: D 421 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8286 (mt-10) REVERT: D 424 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: E 3 LEU cc_start: 0.8068 (mt) cc_final: 0.7766 (mt) REVERT: E 13 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8632 (ttp80) REVERT: E 68 GLU cc_start: 0.8892 (tt0) cc_final: 0.8655 (tt0) REVERT: E 134 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7459 (mm110) REVERT: E 165 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8432 (mm110) REVERT: E 169 ASN cc_start: 0.8398 (t0) cc_final: 0.8158 (t0) REVERT: E 172 ASP cc_start: 0.8623 (t0) cc_final: 0.8412 (t0) REVERT: E 226 GLN cc_start: 0.8341 (tt0) cc_final: 0.8125 (tt0) REVERT: E 248 SER cc_start: 0.8509 (m) cc_final: 0.8127 (p) REVERT: E 305 ASP cc_start: 0.8189 (p0) cc_final: 0.7952 (p0) REVERT: E 307 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8373 (mtp-110) REVERT: E 424 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: E 444 MET cc_start: 0.8947 (mtm) cc_final: 0.8416 (mtt) REVERT: E 451 ASP cc_start: 0.7905 (t0) cc_final: 0.7637 (t0) REVERT: E 523 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8183 (ttm-80) REVERT: E 582 GLU cc_start: 0.8229 (tp30) cc_final: 0.7989 (tp30) outliers start: 32 outliers final: 19 residues processed: 370 average time/residue: 0.2014 time to fit residues: 102.8237 Evaluate side-chains 370 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 347 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 163 LYS Chi-restraints excluded: chain A residue 177 VAL 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 155 GLU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 424 GLN 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 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 26 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 291 GLN B 298 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.073201 restraints weight = 35868.112| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.24 r_work: 0.2890 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17981 Z= 0.191 Angle : 0.562 9.181 24438 Z= 0.289 Chirality : 0.044 0.164 2659 Planarity : 0.004 0.046 3193 Dihedral : 10.301 179.049 2525 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.72 % Allowed : 11.86 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.18), residues: 2207 helix: 1.27 (0.17), residues: 928 sheet: 0.17 (0.29), residues: 338 loop : -0.48 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 306 TYR 0.018 0.001 TYR E 102 PHE 0.020 0.001 PHE E 128 TRP 0.017 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00442 (17977) covalent geometry : angle 0.56206 (24435) hydrogen bonds : bond 0.04104 ( 795) hydrogen bonds : angle 4.48153 ( 2295) metal coordination : bond 0.00895 ( 2) Misc. bond : bond 0.00100 ( 1) link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.09456 ( 3) *********************** 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 381 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 349 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8630 (ptp90) cc_final: 0.8394 (ptt-90) REVERT: A 85 GLN cc_start: 0.8999 (mm110) cc_final: 0.8646 (tp40) REVERT: A 158 SER cc_start: 0.9397 (t) cc_final: 0.9169 (p) REVERT: A 214 ARG cc_start: 0.8839 (mtp-110) cc_final: 0.8336 (ttp80) REVERT: A 215 ARG cc_start: 0.8922 (mtm110) cc_final: 0.8638 (mtm110) REVERT: A 218 ASP cc_start: 0.8696 (t0) cc_final: 0.8191 (t0) REVERT: A 357 TYR cc_start: 0.9151 (m-80) cc_final: 0.8873 (m-80) REVERT: A 414 GLU cc_start: 0.8669 (mp0) cc_final: 0.8249 (mp0) REVERT: A 417 GLU cc_start: 0.7919 (mp0) cc_final: 0.7392 (mp0) REVERT: A 420 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7706 (tp30) REVERT: A 424 ASP cc_start: 0.8861 (m-30) cc_final: 0.8320 (m-30) REVERT: B 58 LYS cc_start: 0.8716 (tttt) cc_final: 0.8011 (pttt) REVERT: B 94 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8396 (mp10) REVERT: B 103 LYS cc_start: 0.9275 (tttt) cc_final: 0.8415 (ttpt) REVERT: B 108 GLU cc_start: 0.8494 (mp0) cc_final: 0.8231 (mp0) REVERT: B 122 LYS cc_start: 0.8951 (tppp) cc_final: 0.8685 (ttmm) REVERT: B 174 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8568 (mmmt) REVERT: B 213 ARG cc_start: 0.8468 (ptp-110) cc_final: 0.8068 (mtm110) REVERT: B 257 MET cc_start: 0.8001 (mmm) cc_final: 0.7679 (mmm) REVERT: B 278 SER cc_start: 0.8798 (m) cc_final: 0.8374 (t) REVERT: B 328 GLU cc_start: 0.8060 (pt0) cc_final: 0.7781 (pt0) REVERT: B 362 LYS cc_start: 0.8983 (tppt) cc_final: 0.8733 (tppt) REVERT: B 376 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8342 (mt-10) REVERT: B 392 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9058 (mtmm) REVERT: B 403 MET cc_start: 0.8533 (mtm) cc_final: 0.8314 (ttm) REVERT: B 410 GLU cc_start: 0.8177 (pp20) cc_final: 0.7949 (pp20) REVERT: B 414 ASN cc_start: 0.8501 (t0) cc_final: 0.8163 (t0) REVERT: B 417 ASP cc_start: 0.8380 (m-30) cc_final: 0.8094 (m-30) REVERT: C 76 ASP cc_start: 0.8788 (m-30) cc_final: 0.8378 (m-30) REVERT: C 84 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8124 (ptp90) REVERT: C 120 ASP cc_start: 0.8437 (t0) cc_final: 0.8138 (t0) REVERT: C 123 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7586 (tpp80) REVERT: C 155 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: C 196 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7673 (tm-30) REVERT: C 211 ASP cc_start: 0.8478 (t70) cc_final: 0.7849 (t0) REVERT: C 215 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8519 (ttp80) REVERT: C 280 LYS cc_start: 0.8790 (mttp) cc_final: 0.7755 (mmtt) REVERT: C 284 GLU cc_start: 0.8239 (mp0) cc_final: 0.7737 (mp0) REVERT: C 290 GLU cc_start: 0.8635 (mp0) cc_final: 0.8219 (mp0) REVERT: C 386 GLU cc_start: 0.8184 (mp0) cc_final: 0.7803 (mp0) REVERT: C 417 GLU cc_start: 0.7653 (mp0) cc_final: 0.7329 (mp0) REVERT: C 425 MET cc_start: 0.8666 (tpt) cc_final: 0.8208 (tpp) REVERT: C 433 GLU cc_start: 0.8843 (pt0) cc_final: 0.8451 (tm-30) REVERT: D 26 ASP cc_start: 0.8649 (t0) cc_final: 0.8299 (t0) REVERT: D 57 ASN cc_start: 0.8340 (t0) cc_final: 0.7998 (t0) REVERT: D 69 GLU cc_start: 0.8585 (pp20) cc_final: 0.8360 (pm20) REVERT: D 108 GLU cc_start: 0.8168 (mp0) cc_final: 0.7922 (mp0) REVERT: D 203 ASP cc_start: 0.8472 (t0) cc_final: 0.8138 (t70) REVERT: D 209 ASP cc_start: 0.8988 (t0) cc_final: 0.8687 (t0) REVERT: D 257 MET cc_start: 0.8427 (mmm) cc_final: 0.8016 (mmm) REVERT: D 392 LYS cc_start: 0.9376 (tppt) cc_final: 0.9143 (ttmm) REVERT: D 412 GLU cc_start: 0.8589 (tp30) cc_final: 0.8254 (tp30) REVERT: D 421 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8567 (tt0) REVERT: E 3 LEU cc_start: 0.8085 (mt) cc_final: 0.7792 (mt) REVERT: E 165 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8332 (mm-40) REVERT: E 172 ASP cc_start: 0.8650 (t0) cc_final: 0.8425 (t0) REVERT: E 173 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8552 (mm-40) REVERT: E 248 SER cc_start: 0.8554 (m) cc_final: 0.8198 (p) REVERT: E 305 ASP cc_start: 0.8255 (p0) cc_final: 0.7975 (p0) REVERT: E 307 ARG cc_start: 0.8747 (mtp-110) cc_final: 0.8365 (mtp-110) REVERT: E 424 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: E 444 MET cc_start: 0.8947 (mtm) cc_final: 0.8419 (mtt) REVERT: E 451 ASP cc_start: 0.7931 (t0) cc_final: 0.7652 (t0) REVERT: E 523 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8251 (ttm-80) REVERT: E 582 GLU cc_start: 0.8317 (tp30) cc_final: 0.8078 (tp30) outliers start: 32 outliers final: 17 residues processed: 365 average time/residue: 0.2026 time to fit residues: 102.0259 Evaluate side-chains 359 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 255 PHE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 155 GLU 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 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 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 97 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 291 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 216 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.073980 restraints weight = 35633.106| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.26 r_work: 0.2905 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17981 Z= 0.142 Angle : 0.533 8.852 24438 Z= 0.273 Chirality : 0.043 0.191 2659 Planarity : 0.004 0.045 3193 Dihedral : 10.171 176.328 2525 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.61 % Allowed : 12.66 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 2207 helix: 1.37 (0.17), residues: 929 sheet: 0.10 (0.29), residues: 338 loop : -0.48 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 390 TYR 0.013 0.001 TYR E 102 PHE 0.020 0.001 PHE E 128 TRP 0.014 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00332 (17977) covalent geometry : angle 0.53257 (24435) hydrogen bonds : bond 0.03685 ( 795) hydrogen bonds : angle 4.40094 ( 2295) metal coordination : bond 0.00537 ( 2) Misc. bond : bond 0.00063 ( 1) link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.06213 ( 3) *********************** 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 369 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 339 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8616 (ptp90) cc_final: 0.8390 (ptt-90) REVERT: A 158 SER cc_start: 0.9352 (t) cc_final: 0.9147 (p) REVERT: A 214 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8324 (ttp80) REVERT: A 215 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8506 (mtm110) REVERT: A 218 ASP cc_start: 0.8688 (t0) cc_final: 0.8196 (t0) REVERT: A 304 LYS cc_start: 0.8852 (tptp) cc_final: 0.8589 (mmtt) REVERT: A 357 TYR cc_start: 0.9165 (m-80) cc_final: 0.8885 (m-80) REVERT: A 414 GLU cc_start: 0.8689 (mp0) cc_final: 0.8425 (mp0) REVERT: A 415 GLU cc_start: 0.8743 (tt0) cc_final: 0.8414 (tp30) REVERT: A 417 GLU cc_start: 0.7902 (mp0) cc_final: 0.7522 (mp0) REVERT: A 420 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7843 (tp30) REVERT: A 424 ASP cc_start: 0.8847 (m-30) cc_final: 0.8465 (m-30) REVERT: B 58 LYS cc_start: 0.8720 (tttt) cc_final: 0.8012 (pttt) REVERT: B 94 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8410 (mp10) REVERT: B 103 LYS cc_start: 0.9273 (tttt) cc_final: 0.8743 (ttpt) REVERT: B 108 GLU cc_start: 0.8482 (mp0) cc_final: 0.8247 (mp0) REVERT: B 122 LYS cc_start: 0.8932 (tppp) cc_final: 0.8666 (ttmm) REVERT: B 205 GLU cc_start: 0.8471 (tt0) cc_final: 0.8060 (tt0) REVERT: B 209 ASP cc_start: 0.8428 (t70) cc_final: 0.8081 (t0) REVERT: B 212 PHE cc_start: 0.8444 (m-10) cc_final: 0.8163 (m-10) REVERT: B 213 ARG cc_start: 0.8456 (ptp-110) cc_final: 0.8010 (mtm110) REVERT: B 278 SER cc_start: 0.8769 (m) cc_final: 0.8356 (t) REVERT: B 321 MET cc_start: 0.8636 (ptp) cc_final: 0.8357 (ptp) REVERT: B 327 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7987 (t0) REVERT: B 362 LYS cc_start: 0.9008 (tppt) cc_final: 0.8748 (tppt) REVERT: B 376 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8340 (mt-10) REVERT: B 392 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9100 (mmmm) REVERT: B 414 ASN cc_start: 0.8504 (t0) cc_final: 0.8168 (t0) REVERT: B 417 ASP cc_start: 0.8374 (m-30) cc_final: 0.8057 (m-30) REVERT: C 76 ASP cc_start: 0.8817 (m-30) cc_final: 0.8375 (m-30) REVERT: C 84 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8243 (ptp90) REVERT: C 123 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7576 (tpp80) REVERT: C 196 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 211 ASP cc_start: 0.8508 (t70) cc_final: 0.7794 (t0) REVERT: C 215 ARG cc_start: 0.8855 (ttp80) cc_final: 0.8577 (ttp80) REVERT: C 265 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8898 (mm) REVERT: C 280 LYS cc_start: 0.8778 (mttp) cc_final: 0.7773 (mmtt) REVERT: C 284 GLU cc_start: 0.8224 (mp0) cc_final: 0.7750 (mp0) REVERT: C 290 GLU cc_start: 0.8641 (mp0) cc_final: 0.8263 (mp0) REVERT: C 386 GLU cc_start: 0.8317 (mp0) cc_final: 0.8055 (mp0) REVERT: C 425 MET cc_start: 0.8688 (tpt) cc_final: 0.8180 (tpp) REVERT: C 433 GLU cc_start: 0.8813 (pt0) cc_final: 0.8440 (tm-30) REVERT: D 26 ASP cc_start: 0.8700 (t0) cc_final: 0.8306 (t0) REVERT: D 45 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8151 (tm-30) REVERT: D 57 ASN cc_start: 0.8324 (t0) cc_final: 0.7901 (t0) REVERT: D 108 GLU cc_start: 0.8138 (mp0) cc_final: 0.7891 (mp0) REVERT: D 203 ASP cc_start: 0.8478 (t0) cc_final: 0.8164 (t70) REVERT: D 209 ASP cc_start: 0.8997 (t0) cc_final: 0.8688 (t0) REVERT: D 212 PHE cc_start: 0.8886 (m-10) cc_final: 0.8556 (m-10) REVERT: D 257 MET cc_start: 0.8393 (mmm) cc_final: 0.8021 (mmm) REVERT: D 324 LYS cc_start: 0.9238 (tptp) cc_final: 0.8996 (tmtt) REVERT: D 392 LYS cc_start: 0.9357 (tppt) cc_final: 0.9113 (ttmm) REVERT: D 412 GLU cc_start: 0.8494 (tp30) cc_final: 0.8162 (tp30) REVERT: D 413 SER cc_start: 0.8798 (t) cc_final: 0.7953 (p) REVERT: D 417 ASP cc_start: 0.8588 (m-30) cc_final: 0.8207 (m-30) REVERT: E 3 LEU cc_start: 0.8134 (mt) cc_final: 0.7864 (mt) REVERT: E 165 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8428 (mm110) REVERT: E 172 ASP cc_start: 0.8610 (t0) cc_final: 0.8407 (t0) REVERT: E 173 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8549 (mm-40) REVERT: E 226 GLN cc_start: 0.8499 (tt0) cc_final: 0.8231 (tm-30) REVERT: E 248 SER cc_start: 0.8517 (m) cc_final: 0.8170 (p) REVERT: E 305 ASP cc_start: 0.8195 (p0) cc_final: 0.7902 (p0) REVERT: E 307 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8322 (mtp-110) REVERT: E 424 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: E 444 MET cc_start: 0.8937 (mtm) cc_final: 0.8385 (mtt) REVERT: E 451 ASP cc_start: 0.7991 (t0) cc_final: 0.7697 (t0) REVERT: E 523 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8260 (ttm-80) REVERT: E 582 GLU cc_start: 0.8259 (tp30) cc_final: 0.8041 (tp30) outliers start: 30 outliers final: 18 residues processed: 353 average time/residue: 0.1943 time to fit residues: 94.6305 Evaluate side-chains 360 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 338 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 B residue 392 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 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 170 GLN 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 189 optimal weight: 0.5980 chunk 199 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 142 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 HIS B 291 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN D 335 ASN D 384 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.074136 restraints weight = 35622.208| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.23 r_work: 0.2911 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17981 Z= 0.138 Angle : 0.539 8.289 24438 Z= 0.276 Chirality : 0.043 0.194 2659 Planarity : 0.004 0.043 3193 Dihedral : 10.166 174.206 2525 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.77 % Allowed : 13.04 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.18), residues: 2207 helix: 1.44 (0.17), residues: 935 sheet: 0.14 (0.29), residues: 342 loop : -0.48 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 306 TYR 0.013 0.001 TYR E 102 PHE 0.023 0.001 PHE E 128 TRP 0.013 0.001 TRP E 592 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00324 (17977) covalent geometry : angle 0.53884 (24435) hydrogen bonds : bond 0.03596 ( 795) hydrogen bonds : angle 4.34417 ( 2295) metal coordination : bond 0.00532 ( 2) Misc. bond : bond 0.00053 ( 1) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.07615 ( 3) *********************** 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 377 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 344 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8641 (ptp90) cc_final: 0.8431 (ptt-90) REVERT: A 55 GLU cc_start: 0.7753 (tp30) cc_final: 0.7425 (tp30) REVERT: A 127 ASP cc_start: 0.8385 (p0) cc_final: 0.8147 (p0) REVERT: A 158 SER cc_start: 0.9370 (t) cc_final: 0.9163 (p) REVERT: A 214 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8348 (ttp80) REVERT: A 215 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8486 (mtm110) REVERT: A 218 ASP cc_start: 0.8701 (t0) cc_final: 0.8180 (t0) REVERT: A 304 LYS cc_start: 0.8858 (tptp) cc_final: 0.8585 (mmtt) REVERT: A 357 TYR cc_start: 0.9174 (m-80) cc_final: 0.8891 (m-80) REVERT: A 414 GLU cc_start: 0.8665 (mp0) cc_final: 0.8405 (mp0) REVERT: A 417 GLU cc_start: 0.7905 (mp0) cc_final: 0.7551 (mp0) REVERT: A 420 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7862 (tp30) REVERT: A 424 ASP cc_start: 0.8849 (m-30) cc_final: 0.8497 (m-30) REVERT: B 58 LYS cc_start: 0.8708 (tttt) cc_final: 0.8004 (pttt) REVERT: B 94 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8406 (mp10) REVERT: B 103 LYS cc_start: 0.9265 (tttt) cc_final: 0.8223 (ttpt) REVERT: B 108 GLU cc_start: 0.8389 (mp0) cc_final: 0.8173 (mp0) REVERT: B 122 LYS cc_start: 0.8930 (tppp) cc_final: 0.8666 (ttmm) REVERT: B 205 GLU cc_start: 0.8498 (tt0) cc_final: 0.8079 (tt0) REVERT: B 209 ASP cc_start: 0.8434 (t70) cc_final: 0.8219 (t0) REVERT: B 212 PHE cc_start: 0.8432 (m-10) cc_final: 0.8119 (m-10) REVERT: B 278 SER cc_start: 0.8772 (m) cc_final: 0.8369 (t) REVERT: B 321 MET cc_start: 0.8693 (ptp) cc_final: 0.8314 (ptp) REVERT: B 327 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.8018 (t0) REVERT: B 362 LYS cc_start: 0.8978 (tppt) cc_final: 0.8704 (tppt) REVERT: B 376 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8339 (mt-10) REVERT: B 410 GLU cc_start: 0.8018 (pp20) cc_final: 0.7776 (pp20) REVERT: B 414 ASN cc_start: 0.8452 (t0) cc_final: 0.8079 (t0) REVERT: B 416 ASN cc_start: 0.8668 (m-40) cc_final: 0.8468 (m110) REVERT: B 417 ASP cc_start: 0.8371 (m-30) cc_final: 0.8054 (m-30) REVERT: C 76 ASP cc_start: 0.8809 (m-30) cc_final: 0.8317 (m-30) REVERT: C 84 ARG cc_start: 0.8843 (ttp-110) cc_final: 0.8331 (ptp90) REVERT: C 123 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.7591 (tpp80) REVERT: C 196 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7724 (tm-30) REVERT: C 211 ASP cc_start: 0.8537 (t70) cc_final: 0.7870 (t0) REVERT: C 215 ARG cc_start: 0.8836 (ttp80) cc_final: 0.8494 (ttp80) REVERT: C 265 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8914 (mm) REVERT: C 280 LYS cc_start: 0.8774 (mttp) cc_final: 0.7749 (mmtt) REVERT: C 284 GLU cc_start: 0.8203 (mp0) cc_final: 0.7735 (mp0) REVERT: C 290 GLU cc_start: 0.8613 (mp0) cc_final: 0.8270 (mp0) REVERT: C 297 GLU cc_start: 0.8194 (tp30) cc_final: 0.7826 (tp30) REVERT: C 386 GLU cc_start: 0.8127 (mp0) cc_final: 0.7892 (mp0) REVERT: C 425 MET cc_start: 0.8678 (tpt) cc_final: 0.8177 (tpp) REVERT: C 433 GLU cc_start: 0.8805 (pt0) cc_final: 0.8443 (tm-30) REVERT: D 26 ASP cc_start: 0.8686 (t0) cc_final: 0.8283 (t0) REVERT: D 45 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8146 (tm-30) REVERT: D 57 ASN cc_start: 0.8228 (t0) cc_final: 0.7908 (t0) REVERT: D 103 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8744 (mtmt) REVERT: D 108 GLU cc_start: 0.8094 (mp0) cc_final: 0.7807 (mp0) REVERT: D 203 ASP cc_start: 0.8481 (t0) cc_final: 0.8226 (t70) REVERT: D 209 ASP cc_start: 0.8977 (t0) cc_final: 0.8275 (t0) REVERT: D 213 ARG cc_start: 0.8888 (ttp-110) cc_final: 0.8454 (ttp-110) REVERT: D 257 MET cc_start: 0.8369 (mmm) cc_final: 0.8166 (mmm) REVERT: D 280 GLN cc_start: 0.8045 (pm20) cc_final: 0.7725 (pm20) REVERT: D 281 TYR cc_start: 0.8867 (m-10) cc_final: 0.8578 (m-10) REVERT: D 392 LYS cc_start: 0.9340 (tppt) cc_final: 0.9084 (ttmm) REVERT: D 410 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 412 GLU cc_start: 0.8467 (tp30) cc_final: 0.8187 (tp30) REVERT: E 3 LEU cc_start: 0.8110 (mt) cc_final: 0.7831 (mt) REVERT: E 165 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8426 (mm110) REVERT: E 173 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8542 (mm-40) REVERT: E 226 GLN cc_start: 0.8510 (tt0) cc_final: 0.8292 (tm-30) REVERT: E 248 SER cc_start: 0.8536 (m) cc_final: 0.8160 (p) REVERT: E 305 ASP cc_start: 0.8185 (p0) cc_final: 0.7908 (p0) REVERT: E 307 ARG cc_start: 0.8687 (mtp-110) cc_final: 0.8271 (mtp-110) REVERT: E 424 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: E 444 MET cc_start: 0.8938 (mtm) cc_final: 0.8397 (mtt) REVERT: E 451 ASP cc_start: 0.7986 (t0) cc_final: 0.7699 (t0) REVERT: E 523 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8295 (ttm-80) outliers start: 33 outliers final: 22 residues processed: 358 average time/residue: 0.1972 time to fit residues: 97.6143 Evaluate side-chains 353 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 328 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 255 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 331 LEU 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 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 170 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 170 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.081879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.072716 restraints weight = 35456.966| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.21 r_work: 0.2874 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17981 Z= 0.206 Angle : 0.585 8.173 24438 Z= 0.301 Chirality : 0.045 0.164 2659 Planarity : 0.004 0.044 3193 Dihedral : 10.418 172.284 2525 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.56 % Allowed : 13.36 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2207 helix: 1.38 (0.17), residues: 933 sheet: 0.12 (0.29), residues: 339 loop : -0.51 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 306 TYR 0.019 0.001 TYR E 102 PHE 0.023 0.001 PHE E 128 TRP 0.017 0.001 TRP E 592 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00479 (17977) covalent geometry : angle 0.58500 (24435) hydrogen bonds : bond 0.04116 ( 795) hydrogen bonds : angle 4.47031 ( 2295) metal coordination : bond 0.00987 ( 2) Misc. bond : bond 0.00086 ( 1) link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 0.13451 ( 3) *********************** 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 358 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7710 (tp30) cc_final: 0.7386 (tp30) REVERT: A 123 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7994 (tpp-160) REVERT: A 127 ASP cc_start: 0.8369 (p0) cc_final: 0.8146 (p0) REVERT: A 158 SER cc_start: 0.9419 (t) cc_final: 0.9128 (p) REVERT: A 214 ARG cc_start: 0.8893 (mtp-110) cc_final: 0.8388 (ttp80) REVERT: A 215 ARG cc_start: 0.8932 (mtm110) cc_final: 0.8446 (mtm110) REVERT: A 218 ASP cc_start: 0.8713 (t0) cc_final: 0.8237 (t0) REVERT: A 302 MET cc_start: 0.9126 (mtp) cc_final: 0.8751 (mtt) REVERT: A 304 LYS cc_start: 0.8833 (tptp) cc_final: 0.8567 (mmtt) REVERT: A 357 TYR cc_start: 0.9225 (m-80) cc_final: 0.8924 (m-80) REVERT: A 414 GLU cc_start: 0.8727 (mp0) cc_final: 0.8411 (mp0) REVERT: A 417 GLU cc_start: 0.7936 (mp0) cc_final: 0.7554 (mp0) REVERT: A 420 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7577 (tp30) REVERT: A 424 ASP cc_start: 0.8811 (m-30) cc_final: 0.8200 (m-30) REVERT: B 58 LYS cc_start: 0.8680 (tttt) cc_final: 0.8042 (pttt) REVERT: B 94 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8419 (mp10) REVERT: B 103 LYS cc_start: 0.9288 (tttt) cc_final: 0.8402 (ttpt) REVERT: B 108 GLU cc_start: 0.8578 (mp0) cc_final: 0.8315 (mp0) REVERT: B 122 LYS cc_start: 0.8942 (tppp) cc_final: 0.8686 (ttmm) REVERT: B 174 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8332 (mmmt) REVERT: B 209 ASP cc_start: 0.8474 (t70) cc_final: 0.8075 (t0) REVERT: B 218 THR cc_start: 0.9087 (p) cc_final: 0.8881 (t) REVERT: B 278 SER cc_start: 0.8779 (m) cc_final: 0.8315 (p) REVERT: B 321 MET cc_start: 0.8774 (ptp) cc_final: 0.8334 (ptp) REVERT: B 327 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 362 LYS cc_start: 0.8992 (tppt) cc_final: 0.8729 (tppt) REVERT: B 376 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8480 (mt-10) REVERT: B 390 ARG cc_start: 0.8880 (mtp-110) cc_final: 0.8673 (mtp85) REVERT: B 410 GLU cc_start: 0.8032 (pp20) cc_final: 0.7792 (pp20) REVERT: B 414 ASN cc_start: 0.8533 (t0) cc_final: 0.8142 (t0) REVERT: B 416 ASN cc_start: 0.8705 (m-40) cc_final: 0.8483 (m110) REVERT: B 417 ASP cc_start: 0.8538 (m-30) cc_final: 0.8183 (m-30) REVERT: C 50 ASN cc_start: 0.9107 (t0) cc_final: 0.8764 (t0) REVERT: C 76 ASP cc_start: 0.8748 (m-30) cc_final: 0.8347 (m-30) REVERT: C 120 ASP cc_start: 0.8518 (t0) cc_final: 0.8123 (m-30) REVERT: C 123 ARG cc_start: 0.8031 (tpp-160) cc_final: 0.7546 (tpp80) REVERT: C 196 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7678 (tm-30) REVERT: C 211 ASP cc_start: 0.8575 (t70) cc_final: 0.7867 (t0) REVERT: C 215 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8599 (ttp80) REVERT: C 265 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8961 (mm) REVERT: C 280 LYS cc_start: 0.8700 (mttp) cc_final: 0.7748 (mmtt) REVERT: C 284 GLU cc_start: 0.8179 (mp0) cc_final: 0.7696 (mp0) REVERT: C 290 GLU cc_start: 0.8641 (mp0) cc_final: 0.8305 (mp0) REVERT: C 297 GLU cc_start: 0.8265 (tp30) cc_final: 0.7855 (tp30) REVERT: C 386 GLU cc_start: 0.8193 (mp0) cc_final: 0.7939 (mp0) REVERT: C 425 MET cc_start: 0.8748 (tpt) cc_final: 0.8260 (tpp) REVERT: C 433 GLU cc_start: 0.8839 (pt0) cc_final: 0.8471 (tm-30) REVERT: D 22 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8417 (tp30) REVERT: D 45 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7910 (tm-30) REVERT: D 57 ASN cc_start: 0.8336 (t0) cc_final: 0.8050 (t0) REVERT: D 108 GLU cc_start: 0.8100 (mp0) cc_final: 0.7782 (mp0) REVERT: D 209 ASP cc_start: 0.8979 (t0) cc_final: 0.8514 (t0) REVERT: D 213 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8627 (mtm-85) REVERT: D 280 GLN cc_start: 0.8060 (pm20) cc_final: 0.7428 (pm20) REVERT: D 376 GLU cc_start: 0.8121 (mp0) cc_final: 0.7815 (mp0) REVERT: D 392 LYS cc_start: 0.9416 (tppt) cc_final: 0.9177 (ttmm) REVERT: D 410 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7757 (mm-30) REVERT: D 412 GLU cc_start: 0.8616 (tp30) cc_final: 0.8297 (tp30) REVERT: D 417 ASP cc_start: 0.8643 (m-30) cc_final: 0.8244 (m-30) REVERT: E 120 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: E 165 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8351 (mm-40) REVERT: E 248 SER cc_start: 0.8575 (m) cc_final: 0.8212 (p) REVERT: E 305 ASP cc_start: 0.8236 (p0) cc_final: 0.8013 (p0) REVERT: E 307 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8200 (mtp-110) REVERT: E 424 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: E 444 MET cc_start: 0.9017 (mtm) cc_final: 0.8502 (mtt) REVERT: E 451 ASP cc_start: 0.7996 (t0) cc_final: 0.7705 (t0) REVERT: E 481 GLU cc_start: 0.8172 (tp30) cc_final: 0.7927 (tp30) REVERT: E 523 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8254 (ttm-80) outliers start: 29 outliers final: 18 residues processed: 345 average time/residue: 0.1995 time to fit residues: 95.0562 Evaluate side-chains 358 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 336 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 328 GLU Chi-restraints excluded: chain B residue 331 LEU 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 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 424 GLU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 595 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 128 optimal weight: 0.7980 chunk 198 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 0.0770 chunk 34 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 111 optimal weight: 0.0670 chunk 204 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 overall best weight: 0.3154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 372 GLN B 37 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 HIS C 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075142 restraints weight = 35678.765| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.24 r_work: 0.2932 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4359 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= 0.111 Angle : 0.553 8.433 24438 Z= 0.283 Chirality : 0.042 0.205 2659 Planarity : 0.004 0.044 3193 Dihedral : 10.158 177.657 2525 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.39 % Allowed : 14.06 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 2207 helix: 1.54 (0.17), residues: 934 sheet: 0.18 (0.28), residues: 351 loop : -0.49 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 84 TYR 0.014 0.001 TYR E 485 PHE 0.025 0.001 PHE E 128 TRP 0.014 0.001 TRP C 21 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00257 (17977) covalent geometry : angle 0.55333 (24435) hydrogen bonds : bond 0.03278 ( 795) hydrogen bonds : angle 4.29158 ( 2295) metal coordination : bond 0.00187 ( 2) Misc. bond : bond 0.00013 ( 1) link_TRANS : bond 0.00009 ( 1) link_TRANS : angle 0.04680 ( 3) *********************** 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 373 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 347 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7754 (tp30) cc_final: 0.7462 (tp30) REVERT: A 127 ASP cc_start: 0.8366 (p0) cc_final: 0.8138 (p0) REVERT: A 158 SER cc_start: 0.9382 (t) cc_final: 0.9090 (p) REVERT: A 214 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8349 (ttp80) REVERT: A 215 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8511 (mtm110) REVERT: A 218 ASP cc_start: 0.8685 (t0) cc_final: 0.8222 (t0) REVERT: A 302 MET cc_start: 0.9038 (mtp) cc_final: 0.8643 (mtt) REVERT: A 357 TYR cc_start: 0.9178 (m-80) cc_final: 0.8874 (m-80) REVERT: A 414 GLU cc_start: 0.8738 (mp0) cc_final: 0.8445 (mp0) REVERT: A 417 GLU cc_start: 0.7970 (mp0) cc_final: 0.7610 (mp0) REVERT: A 420 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7765 (tp30) REVERT: A 424 ASP cc_start: 0.8784 (m-30) cc_final: 0.8246 (m-30) REVERT: B 26 ASP cc_start: 0.8807 (t0) cc_final: 0.8537 (m-30) REVERT: B 58 LYS cc_start: 0.8639 (tttt) cc_final: 0.7903 (pttt) REVERT: B 103 LYS cc_start: 0.9257 (tttt) cc_final: 0.8235 (ttpt) REVERT: B 108 GLU cc_start: 0.8328 (mp0) cc_final: 0.8113 (mp0) REVERT: B 174 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8258 (mmmt) REVERT: B 209 ASP cc_start: 0.8408 (t70) cc_final: 0.7401 (t0) REVERT: B 212 PHE cc_start: 0.8307 (m-10) cc_final: 0.8080 (m-10) REVERT: B 213 ARG cc_start: 0.8535 (ptp90) cc_final: 0.7910 (ptp90) REVERT: B 278 SER cc_start: 0.8733 (m) cc_final: 0.8279 (p) REVERT: B 321 MET cc_start: 0.8653 (ptp) cc_final: 0.8278 (ptp) REVERT: B 362 LYS cc_start: 0.8972 (tppt) cc_final: 0.8717 (tppt) REVERT: B 376 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8327 (mp0) REVERT: B 410 GLU cc_start: 0.7963 (pp20) cc_final: 0.7723 (pp20) REVERT: B 414 ASN cc_start: 0.8383 (t0) cc_final: 0.8043 (t0) REVERT: B 417 ASP cc_start: 0.8400 (m-30) cc_final: 0.8083 (m-30) REVERT: C 50 ASN cc_start: 0.9073 (t0) cc_final: 0.8719 (t0) REVERT: C 76 ASP cc_start: 0.8818 (m-30) cc_final: 0.8291 (m-30) REVERT: C 123 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7549 (tpp80) REVERT: C 196 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 211 ASP cc_start: 0.8561 (t70) cc_final: 0.7879 (t0) REVERT: C 215 ARG cc_start: 0.8834 (ttp80) cc_final: 0.8589 (ttp80) REVERT: C 280 LYS cc_start: 0.8746 (mttp) cc_final: 0.7736 (mmtt) REVERT: C 284 GLU cc_start: 0.8136 (mp0) cc_final: 0.7661 (mp0) REVERT: C 290 GLU cc_start: 0.8627 (mp0) cc_final: 0.8311 (mp0) REVERT: C 297 GLU cc_start: 0.8248 (tp30) cc_final: 0.7913 (tp30) REVERT: C 386 GLU cc_start: 0.7935 (mp0) cc_final: 0.7631 (mp0) REVERT: C 413 MET cc_start: 0.8527 (ttm) cc_final: 0.8169 (ttp) REVERT: C 417 GLU cc_start: 0.7719 (mp0) cc_final: 0.6829 (mp0) REVERT: C 425 MET cc_start: 0.8708 (tpt) cc_final: 0.8500 (tpt) REVERT: C 433 GLU cc_start: 0.8762 (pt0) cc_final: 0.8426 (tm-30) REVERT: D 22 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8327 (tp30) REVERT: D 26 ASP cc_start: 0.8680 (t0) cc_final: 0.8216 (t0) REVERT: D 45 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7857 (tm-30) REVERT: D 57 ASN cc_start: 0.8315 (t0) cc_final: 0.7977 (t0) REVERT: D 58 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8305 (tttm) REVERT: D 103 LYS cc_start: 0.9147 (mtpt) cc_final: 0.8907 (mtmt) REVERT: D 108 GLU cc_start: 0.8120 (mp0) cc_final: 0.7916 (mp0) REVERT: D 209 ASP cc_start: 0.8972 (t0) cc_final: 0.8277 (t0) REVERT: D 213 ARG cc_start: 0.8910 (ttp-110) cc_final: 0.8457 (ttp-110) REVERT: D 392 LYS cc_start: 0.9304 (tppt) cc_final: 0.9055 (ttmm) REVERT: D 407 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8021 (mt-10) REVERT: D 410 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 412 GLU cc_start: 0.8453 (tp30) cc_final: 0.8188 (tp30) REVERT: E 165 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8412 (mm110) REVERT: E 248 SER cc_start: 0.8471 (m) cc_final: 0.8196 (p) REVERT: E 305 ASP cc_start: 0.8117 (p0) cc_final: 0.7837 (p0) REVERT: E 307 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8315 (mtp-110) REVERT: E 424 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: E 444 MET cc_start: 0.8897 (mtm) cc_final: 0.8437 (mtt) REVERT: E 451 ASP cc_start: 0.8012 (t0) cc_final: 0.7729 (t0) REVERT: E 523 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8227 (ttm-80) REVERT: E 533 HIS cc_start: 0.7208 (t-170) cc_final: 0.6959 (t-170) outliers start: 26 outliers final: 15 residues processed: 358 average time/residue: 0.1938 time to fit residues: 95.8560 Evaluate side-chains 351 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 335 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 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 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 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 171 optimal weight: 0.0770 chunk 7 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 GLN B 348 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** E 336 HIS ** 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 = 0.3231 r_free = 0.3231 target = 0.084023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074889 restraints weight = 35384.286| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.23 r_work: 0.2925 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17981 Z= 0.127 Angle : 0.564 10.801 24438 Z= 0.287 Chirality : 0.043 0.245 2659 Planarity : 0.004 0.045 3193 Dihedral : 9.819 178.036 2525 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.18 % Allowed : 14.59 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.18), residues: 2207 helix: 1.49 (0.17), residues: 946 sheet: 0.16 (0.28), residues: 353 loop : -0.53 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 84 TYR 0.013 0.001 TYR D 281 PHE 0.029 0.001 PHE E 128 TRP 0.012 0.001 TRP C 21 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00299 (17977) covalent geometry : angle 0.56390 (24435) hydrogen bonds : bond 0.03397 ( 795) hydrogen bonds : angle 4.26859 ( 2295) metal coordination : bond 0.00462 ( 2) Misc. bond : bond 0.00031 ( 1) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.04839 ( 3) ********************** 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 362 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 340 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 GLU cc_start: 0.7763 (tp30) cc_final: 0.7474 (tp30) REVERT: A 84 ARG cc_start: 0.8615 (ptp90) cc_final: 0.8259 (ptp90) REVERT: A 158 SER cc_start: 0.9399 (t) cc_final: 0.9102 (p) REVERT: A 211 ASP cc_start: 0.8175 (m-30) cc_final: 0.7950 (p0) REVERT: A 218 ASP cc_start: 0.8711 (t0) cc_final: 0.8250 (t0) REVERT: A 302 MET cc_start: 0.9028 (mtp) cc_final: 0.8636 (mtt) REVERT: A 357 TYR cc_start: 0.9179 (m-80) cc_final: 0.8883 (m-80) REVERT: A 414 GLU cc_start: 0.8762 (mp0) cc_final: 0.8452 (mp0) REVERT: A 417 GLU cc_start: 0.7961 (mp0) cc_final: 0.7623 (mp0) REVERT: A 420 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7853 (tp30) REVERT: A 424 ASP cc_start: 0.8776 (m-30) cc_final: 0.8387 (m-30) REVERT: A 434 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8174 (pp20) REVERT: B 26 ASP cc_start: 0.8697 (t0) cc_final: 0.8320 (m-30) REVERT: B 58 LYS cc_start: 0.8511 (tttt) cc_final: 0.7885 (ttpt) REVERT: B 103 LYS cc_start: 0.9254 (tttt) cc_final: 0.8219 (ttpt) REVERT: B 108 GLU cc_start: 0.8500 (mp0) cc_final: 0.8274 (mp0) REVERT: B 174 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8257 (mmmt) REVERT: B 209 ASP cc_start: 0.8421 (t70) cc_final: 0.7318 (t0) REVERT: B 212 PHE cc_start: 0.8322 (m-10) cc_final: 0.8017 (m-10) REVERT: B 213 ARG cc_start: 0.8572 (ptp90) cc_final: 0.7891 (ptp90) REVERT: B 278 SER cc_start: 0.8764 (m) cc_final: 0.8329 (t) REVERT: B 321 MET cc_start: 0.8704 (ptp) cc_final: 0.8381 (ptp) REVERT: B 362 LYS cc_start: 0.9005 (tppt) cc_final: 0.8754 (tppt) REVERT: B 376 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8335 (mp0) REVERT: B 383 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 410 GLU cc_start: 0.7970 (pp20) cc_final: 0.7738 (pp20) REVERT: B 414 ASN cc_start: 0.8384 (t0) cc_final: 0.8039 (t0) REVERT: B 417 ASP cc_start: 0.8405 (m-30) cc_final: 0.8073 (m-30) REVERT: C 50 ASN cc_start: 0.9104 (t0) cc_final: 0.8889 (t0) REVERT: C 76 ASP cc_start: 0.8765 (m-30) cc_final: 0.8303 (m-30) REVERT: C 120 ASP cc_start: 0.8519 (t0) cc_final: 0.8042 (m-30) REVERT: C 123 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.7572 (tpp80) REVERT: C 196 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7753 (tm-30) REVERT: C 211 ASP cc_start: 0.8566 (t70) cc_final: 0.7884 (t0) REVERT: C 215 ARG cc_start: 0.8854 (ttp80) cc_final: 0.8595 (ttp80) REVERT: C 280 LYS cc_start: 0.8776 (mttp) cc_final: 0.7788 (mmtt) REVERT: C 284 GLU cc_start: 0.8183 (mp0) cc_final: 0.7766 (mp0) REVERT: C 290 GLU cc_start: 0.8615 (mp0) cc_final: 0.8297 (mp0) REVERT: C 297 GLU cc_start: 0.8232 (tp30) cc_final: 0.7901 (tp30) REVERT: C 425 MET cc_start: 0.8723 (tpt) cc_final: 0.8222 (tpp) REVERT: C 433 GLU cc_start: 0.8761 (pt0) cc_final: 0.8421 (tm-30) REVERT: D 26 ASP cc_start: 0.8687 (t0) cc_final: 0.8240 (t0) REVERT: D 45 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 57 ASN cc_start: 0.8333 (t0) cc_final: 0.7975 (t0) REVERT: D 58 LYS cc_start: 0.8696 (ttmm) cc_final: 0.8294 (tttm) REVERT: D 103 LYS cc_start: 0.9154 (mtpt) cc_final: 0.8922 (mtmt) REVERT: D 108 GLU cc_start: 0.8096 (mp0) cc_final: 0.7894 (mp0) REVERT: D 209 ASP cc_start: 0.8969 (t0) cc_final: 0.8485 (t0) REVERT: D 213 ARG cc_start: 0.8909 (ttp-110) cc_final: 0.8525 (mtm-85) REVERT: D 257 MET cc_start: 0.8565 (mmm) cc_final: 0.8185 (mtp) REVERT: D 281 TYR cc_start: 0.8616 (m-80) cc_final: 0.8397 (m-80) REVERT: D 392 LYS cc_start: 0.9314 (tppt) cc_final: 0.9060 (ttmm) REVERT: D 407 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 410 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7622 (mm-30) REVERT: D 412 GLU cc_start: 0.8528 (tp30) cc_final: 0.8264 (tp30) REVERT: D 417 ASP cc_start: 0.8587 (m-30) cc_final: 0.8203 (m-30) REVERT: E 165 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8433 (mm110) REVERT: E 248 SER cc_start: 0.8484 (m) cc_final: 0.8206 (p) REVERT: E 295 ASP cc_start: 0.8483 (p0) cc_final: 0.8277 (p0) REVERT: E 305 ASP cc_start: 0.8097 (p0) cc_final: 0.7785 (p0) REVERT: E 307 ARG cc_start: 0.8703 (mtp-110) cc_final: 0.8261 (mtp-110) REVERT: E 424 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: E 444 MET cc_start: 0.8924 (mtm) cc_final: 0.8437 (mtt) REVERT: E 451 ASP cc_start: 0.7999 (t0) cc_final: 0.7694 (t0) REVERT: E 514 THR cc_start: 0.9215 (m) cc_final: 0.8706 (p) REVERT: E 523 ARG cc_start: 0.8621 (ttm-80) cc_final: 0.8229 (ttm-80) outliers start: 22 outliers final: 19 residues processed: 348 average time/residue: 0.1839 time to fit residues: 88.5929 Evaluate side-chains 351 residues out of total 1913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 331 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 230 LEU 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 1 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 328 GLU 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 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 424 GLU Chi-restraints excluded: chain E residue 528 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 93 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 114 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 0 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: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN E 336 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.073562 restraints weight = 35745.745| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.24 r_work: 0.2900 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17981 Z= 0.170 Angle : 0.602 10.910 24438 Z= 0.307 Chirality : 0.044 0.247 2659 Planarity : 0.005 0.100 3193 Dihedral : 9.728 172.820 2525 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.18 % Allowed : 15.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2207 helix: 1.42 (0.17), residues: 948 sheet: 0.29 (0.30), residues: 325 loop : -0.58 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 215 TYR 0.015 0.001 TYR E 102 PHE 0.030 0.001 PHE E 128 TRP 0.013 0.001 TRP E 592 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00400 (17977) covalent geometry : angle 0.60216 (24435) hydrogen bonds : bond 0.03721 ( 795) hydrogen bonds : angle 4.33298 ( 2295) metal coordination : bond 0.00760 ( 2) Misc. bond : bond 0.00063 ( 1) link_TRANS : bond 0.00004 ( 1) link_TRANS : angle 0.08195 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4987.65 seconds wall clock time: 86 minutes 21.47 seconds (5181.47 seconds total)