Starting phenix.real_space_refine on Tue Jan 21 23:04:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.map" model { file = "/net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4m_42973/01_2025/8v4m_42973.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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 115 5.16 5 C 10984 2.51 5 N 2999 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17431 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3372 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3345 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3363 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 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: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3877 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 35, 'TRANS': 463} Chain breaks: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 14, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 119 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} 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} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.71, per 1000 atoms: 0.67 Number of scatterers: 17431 At special positions: 0 Unit cell: (130.725, 125.745, 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 115 16.00 P 12 15.00 Mg 4 11.99 O 3316 8.00 N 2999 7.00 C 10984 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 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 252 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 434 " 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 15 sheets defined 48.0% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.978A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 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 127 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.677A 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: 3.906A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.950A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.959A 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: 3.745A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.678A 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: 3.553A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.979A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.143A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.079A 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: 3.652A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.717A 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: 3.506A pdb=" N GLU B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.878A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.510A pdb=" N VAL B 175 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.747A 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: 4.273A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.730A 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: 3.895A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.843A 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: 3.531A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.598A pdb=" N ASN B 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.651A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.544A 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: 4.004A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 4.168A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.062A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.928A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 4.040A 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: 4.630A 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: 4.277A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.460A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.551A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) 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: 3.763A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.910A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.805A 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: 3.819A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.983A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.644A 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: 3.930A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.130A 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: 3.984A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.973A 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: 3.697A 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: 3.934A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 159 removed outlier: 3.678A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 removed outlier: 3.929A pdb=" N SER D 176 " --> pdb=" O PRO D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.613A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.659A 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: 3.853A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 removed outlier: 3.767A 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: 3.695A pdb=" N ASN D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.756A 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: 3.695A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.585A 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: 3.908A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.066A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 removed outlier: 7.408A pdb=" N ASP D 404 " --> pdb=" O GLU D 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 405 through 425 removed outlier: 3.841A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 104 removed outlier: 4.044A pdb=" N GLN E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 Processing helix chain 'E' and resid 256 through 270 removed outlier: 3.901A pdb=" N PHE E 260 " --> pdb=" O THR E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 282 Processing helix chain 'E' and resid 293 through 299 Processing helix chain 'E' and resid 310 through 314 removed outlier: 3.589A pdb=" N GLN E 314 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 340 removed outlier: 3.568A pdb=" N SER E 340 " --> pdb=" O HIS E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 467 removed outlier: 4.477A 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 484 Processing helix chain 'E' and resid 494 through 497 removed outlier: 3.660A pdb=" N GLY E 497 " --> pdb=" O SER E 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 494 through 497' Processing helix chain 'E' and resid 498 through 508 Processing helix chain 'E' and resid 551 through 570 removed outlier: 4.184A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 577 through 581 removed outlier: 3.660A pdb=" N LEU E 580 " --> pdb=" O ARG E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 601 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.943A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.552A 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 272 through 273 removed outlier: 3.552A 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: 8.179A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.628A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.661A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.021A 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: 7.948A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.436A 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 268 through 273 Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.096A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.564A 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: 3.532A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.654A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.604A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.587A pdb=" N ARG E 111 " --> pdb=" O PHE E 152 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR E 112 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 5.876A 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 23 removed outlier: 3.534A pdb=" N HIS E 21 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS E 89 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 189 through 198 removed outlier: 7.153A pdb=" N VAL E 205 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N SER E 212 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N PHE E 284 " --> pdb=" O SER E 212 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG E 243 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS E 287 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE E 245 " --> pdb=" O LYS E 287 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE E 289 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 247 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE E 244 " --> pdb=" O TYR E 429 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N VAL E 431 " --> pdb=" O ILE E 244 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE E 246 " --> pdb=" O VAL E 431 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU E 433 " --> pdb=" O PHE E 246 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER E 248 " --> pdb=" O LEU E 433 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N GLY E 435 " --> pdb=" O SER E 248 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 216 through 220 removed outlier: 5.916A pdb=" N ASP E 219 " --> pdb=" O ARG E 238 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 4.53 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: 2906 1.31 - 1.44: 4943 1.44 - 1.57: 9797 1.57 - 1.70: 20 1.70 - 1.82: 183 Bond restraints: 17849 Sorted by residual: bond pdb=" O3B G2P B 602 " pdb=" PG G2P B 602 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" O3B G2P D 502 " pdb=" PG G2P D 502 " ideal model delta sigma weight residual 1.716 1.612 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C PHE D 260 " pdb=" N PRO D 261 " ideal model delta sigma weight residual 1.334 1.390 -0.055 1.51e-02 4.39e+03 1.34e+01 bond pdb=" O5' G2P D 502 " pdb=" PA G2P D 502 " ideal model delta sigma weight residual 1.656 1.586 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O5' G2P B 602 " pdb=" PA G2P B 602 " ideal model delta sigma weight residual 1.656 1.588 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 23551 2.69 - 5.37: 633 5.37 - 8.06: 67 8.06 - 10.75: 20 10.75 - 13.44: 5 Bond angle restraints: 24276 Sorted by residual: angle pdb=" N PRO E 114 " pdb=" CA PRO E 114 " pdb=" C PRO E 114 " ideal model delta sigma weight residual 114.03 120.18 -6.15 1.23e+00 6.61e-01 2.50e+01 angle pdb=" N THR E 256 " pdb=" CA THR E 256 " pdb=" C THR E 256 " ideal model delta sigma weight residual 109.81 120.13 -10.32 2.21e+00 2.05e-01 2.18e+01 angle pdb=" C CYS E 532 " pdb=" N HIS E 533 " pdb=" CA HIS E 533 " ideal model delta sigma weight residual 122.82 129.27 -6.45 1.42e+00 4.96e-01 2.06e+01 angle pdb=" PA GTP A 502 " pdb=" O3A GTP A 502 " pdb=" PB GTP A 502 " ideal model delta sigma weight residual 120.50 133.94 -13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" C PHE B 260 " pdb=" CA PHE B 260 " pdb=" CB PHE B 260 " ideal model delta sigma weight residual 108.88 115.50 -6.62 1.50e+00 4.44e-01 1.95e+01 ... (remaining 24271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.04: 10249 28.04 - 56.09: 301 56.09 - 84.13: 35 84.13 - 112.18: 7 112.18 - 140.22: 8 Dihedral angle restraints: 10600 sinusoidal: 4152 harmonic: 6448 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 -35.63 140.22 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 -32.76 137.35 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2G GTP C 502 " pdb=" O3B GTP C 502 " pdb=" PG GTP C 502 " pdb=" PB GTP C 502 " ideal model delta sinusoidal sigma weight residual 177.30 40.97 136.33 1 2.00e+01 2.50e-03 4.14e+01 ... (remaining 10597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1919 0.059 - 0.118: 581 0.118 - 0.176: 125 0.176 - 0.235: 19 0.235 - 0.294: 7 Chirality restraints: 2651 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 2.80 -0.29 2.00e-01 2.50e+01 2.16e+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 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR E 256 " pdb=" N THR E 256 " pdb=" C THR E 256 " pdb=" CB THR E 256 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2648 not shown) Planarity restraints: 3170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 432 " -0.019 2.00e-02 2.50e+03 2.20e-02 9.65e+00 pdb=" CG TYR A 432 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR A 432 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 432 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 432 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 432 " -0.018 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=" C MET D 267 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO D 268 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 268 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 268 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 546 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO E 547 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 547 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 547 " -0.041 5.00e-02 4.00e+02 ... (remaining 3167 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 292 2.69 - 3.24: 15782 3.24 - 3.79: 28651 3.79 - 4.35: 38766 4.35 - 4.90: 64231 Nonbonded interactions: 147722 Sorted by model distance: nonbonded pdb=" OE1 GLU B 503 " pdb="ZN ZN E 701 " model vdw 2.137 2.230 nonbonded pdb=" OE2 GLU E 255 " pdb="ZN ZN E 701 " model vdw 2.164 2.230 nonbonded pdb="MG MG A 501 " pdb=" O2B GTP A 502 " model vdw 2.210 2.170 nonbonded pdb=" OG SER A 178 " pdb=" OE1 GLU A 183 " model vdw 2.324 3.040 nonbonded pdb=" O ASN D 226 " pdb=" OG SER D 230 " model vdw 2.325 3.040 ... (remaining 147717 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 325 or (resid 326 and (name N or \ name CA or name C or name O or name CB )) or resid 327 through 413 or (resid 41 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 415 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or re \ sid 431 through 439 or resid 501 through 502)) selection = (chain 'C' and (resid 1 through 45 or (resid 46 and (name N or name CA or name C \ or name O or name CB )) or resid 47 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 439 or resid 501 throu \ gh 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 327 or (resid 328 and (name N or name CA or name C or name O or name \ CB )) or resid 329 through 360 or (resid 361 through 362 and (name N or name CA \ or name C or name O or name CB )) or resid 363 through 389 or (resid 390 and (n \ ame N or name CA or name C or name O or name CB )) or resid 391 through 428 or r \ esid 601 through 602)) 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 428 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.110 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: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.130 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 0.105 17849 Z= 0.395 Angle : 1.034 13.435 24276 Z= 0.567 Chirality : 0.060 0.294 2651 Planarity : 0.009 0.106 3170 Dihedral : 14.316 140.220 6460 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2205 helix: -1.73 (0.13), residues: 882 sheet: 0.30 (0.29), residues: 326 loop : -1.23 (0.17), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 346 HIS 0.010 0.002 HIS A 197 PHE 0.036 0.003 PHE C 255 TYR 0.048 0.003 TYR A 432 ARG 0.015 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7657 (ptt-90) REVERT: A 47 ASP cc_start: 0.7249 (p0) cc_final: 0.6720 (p0) REVERT: A 50 ASN cc_start: 0.7862 (t0) cc_final: 0.7219 (t0) REVERT: A 114 ILE cc_start: 0.7936 (pt) cc_final: 0.7716 (pt) REVERT: A 124 LYS cc_start: 0.8301 (mttt) cc_final: 0.7923 (ttmm) REVERT: A 128 GLN cc_start: 0.7646 (pt0) cc_final: 0.7310 (tm-30) REVERT: A 155 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 158 SER cc_start: 0.8568 (t) cc_final: 0.8251 (t) REVERT: A 196 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7977 (mt-10) REVERT: A 209 ILE cc_start: 0.7197 (mt) cc_final: 0.6882 (mt) REVERT: A 227 LEU cc_start: 0.7890 (mp) cc_final: 0.7676 (mt) REVERT: A 241 SER cc_start: 0.8650 (m) cc_final: 0.8186 (p) REVERT: A 254 GLU cc_start: 0.7187 (tt0) cc_final: 0.6426 (mm-30) REVERT: A 284 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7062 (mm-30) REVERT: A 322 ASP cc_start: 0.7533 (t0) cc_final: 0.7196 (t70) REVERT: A 414 GLU cc_start: 0.8362 (mp0) cc_final: 0.7980 (mp0) REVERT: A 415 GLU cc_start: 0.7757 (tt0) cc_final: 0.7316 (tm-30) REVERT: A 423 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 424 ASP cc_start: 0.8047 (m-30) cc_final: 0.7635 (t0) REVERT: B 3 GLU cc_start: 0.8100 (mp0) cc_final: 0.7241 (mp0) REVERT: B 19 LYS cc_start: 0.8315 (tptm) cc_final: 0.8066 (tptt) REVERT: B 41 ASP cc_start: 0.8342 (m-30) cc_final: 0.7863 (p0) REVERT: B 45 GLU cc_start: 0.7858 (pt0) cc_final: 0.7589 (pt0) REVERT: B 48 ASN cc_start: 0.8386 (p0) cc_final: 0.7950 (p0) REVERT: B 53 GLU cc_start: 0.7734 (tt0) cc_final: 0.7458 (tt0) REVERT: B 58 LYS cc_start: 0.7221 (tttt) cc_final: 0.6645 (pttt) REVERT: B 88 ASP cc_start: 0.8491 (t0) cc_final: 0.8149 (t0) REVERT: B 103 LYS cc_start: 0.8595 (tttt) cc_final: 0.8069 (mtpp) REVERT: B 181 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7719 (tt0) REVERT: B 201 CYS cc_start: 0.8603 (m) cc_final: 0.8354 (m) REVERT: B 212 PHE cc_start: 0.7868 (m-10) cc_final: 0.7545 (m-10) REVERT: B 213 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7324 (ttp-110) REVERT: B 216 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8342 (mmmm) REVERT: B 252 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8452 (ttpt) REVERT: B 278 SER cc_start: 0.8534 (m) cc_final: 0.7803 (p) REVERT: B 282 ARG cc_start: 0.7575 (ttt-90) cc_final: 0.7206 (ptm-80) REVERT: B 288 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7310 (tm-30) REVERT: B 300 MET cc_start: 0.8108 (mtm) cc_final: 0.7902 (mtm) REVERT: B 324 LYS cc_start: 0.7911 (tptm) cc_final: 0.7678 (tptp) REVERT: B 350 LYS cc_start: 0.8638 (tptt) cc_final: 0.8253 (tptm) REVERT: B 356 ILE cc_start: 0.8624 (mm) cc_final: 0.8312 (mp) REVERT: B 362 LYS cc_start: 0.8261 (tptp) cc_final: 0.7833 (tptp) REVERT: B 383 GLU cc_start: 0.7990 (tp30) cc_final: 0.7669 (tp30) REVERT: B 425 TYR cc_start: 0.8478 (m-80) cc_final: 0.7717 (m-80) REVERT: C 2 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7606 (mtm180) REVERT: C 22 GLU cc_start: 0.8215 (tt0) cc_final: 0.7978 (tt0) REVERT: C 47 ASP cc_start: 0.7944 (p0) cc_final: 0.7511 (t0) REVERT: C 60 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7728 (ttmm) REVERT: C 91 GLN cc_start: 0.8401 (mt0) cc_final: 0.8158 (mt0) REVERT: C 97 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7666 (tt0) REVERT: C 123 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7295 (tpp80) REVERT: C 124 LYS cc_start: 0.8286 (mtpp) cc_final: 0.8069 (ttmm) REVERT: C 154 MET cc_start: 0.8163 (mmm) cc_final: 0.7921 (mtt) REVERT: C 168 GLU cc_start: 0.8347 (pp20) cc_final: 0.8114 (pp20) REVERT: C 207 GLU cc_start: 0.7040 (tt0) cc_final: 0.5732 (tm-30) REVERT: C 218 ASP cc_start: 0.8147 (m-30) cc_final: 0.7414 (t0) REVERT: C 219 ILE cc_start: 0.8283 (mm) cc_final: 0.8010 (mp) REVERT: C 254 GLU cc_start: 0.7081 (tt0) cc_final: 0.6535 (mm-30) REVERT: C 280 LYS cc_start: 0.8607 (mttp) cc_final: 0.7369 (mmtt) REVERT: C 287 SER cc_start: 0.8042 (t) cc_final: 0.7840 (p) REVERT: C 304 LYS cc_start: 0.7771 (tppp) cc_final: 0.5933 (tttp) REVERT: C 308 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7046 (tmt-80) REVERT: C 322 ASP cc_start: 0.8179 (t0) cc_final: 0.7734 (t0) REVERT: C 338 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8473 (mtpp) REVERT: C 349 THR cc_start: 0.8369 (p) cc_final: 0.8130 (p) REVERT: C 352 LYS cc_start: 0.8382 (tptm) cc_final: 0.6773 (tppt) REVERT: C 411 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8080 (mm-30) REVERT: C 413 MET cc_start: 0.8050 (mtp) cc_final: 0.7797 (ttm) REVERT: C 420 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6950 (mp0) REVERT: C 433 GLU cc_start: 0.7695 (pt0) cc_final: 0.7478 (tp30) REVERT: D 19 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8090 (tptm) REVERT: D 44 LEU cc_start: 0.8300 (tp) cc_final: 0.7991 (tm) REVERT: D 45 GLU cc_start: 0.8320 (tt0) cc_final: 0.7684 (tm-30) REVERT: D 69 GLU cc_start: 0.7348 (pp20) cc_final: 0.6665 (pm20) REVERT: D 81 PHE cc_start: 0.8123 (m-80) cc_final: 0.6328 (m-80) REVERT: D 88 ASP cc_start: 0.8256 (t70) cc_final: 0.7875 (t0) REVERT: D 103 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8217 (mtpp) REVERT: D 118 ASP cc_start: 0.7930 (m-30) cc_final: 0.7648 (m-30) REVERT: D 121 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7383 (ptp-110) REVERT: D 122 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7797 (ttmm) REVERT: D 129 CYS cc_start: 0.8126 (t) cc_final: 0.7790 (t) REVERT: D 201 CYS cc_start: 0.8741 (m) cc_final: 0.8349 (m) REVERT: D 203 ASP cc_start: 0.7873 (t0) cc_final: 0.7410 (t70) REVERT: D 216 LYS cc_start: 0.8967 (mmtm) cc_final: 0.8597 (mmmm) REVERT: D 252 LYS cc_start: 0.8580 (ttpt) cc_final: 0.8244 (ttpt) REVERT: D 262 ARG cc_start: 0.8093 (mtp180) cc_final: 0.7729 (ttm110) REVERT: D 289 LEU cc_start: 0.7721 (mp) cc_final: 0.7339 (mt) REVERT: D 299 MET cc_start: 0.7773 (mmp) cc_final: 0.7551 (mpp) REVERT: D 300 MET cc_start: 0.8012 (mtm) cc_final: 0.7742 (mtm) REVERT: D 304 ASP cc_start: 0.7408 (t70) cc_final: 0.6959 (t0) REVERT: D 325 GLU cc_start: 0.8258 (tp30) cc_final: 0.7618 (tm-30) REVERT: D 376 GLU cc_start: 0.7767 (mp0) cc_final: 0.7128 (mp0) REVERT: D 383 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7661 (tm-30) REVERT: D 391 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7229 (mtm180) REVERT: D 404 ASP cc_start: 0.8316 (m-30) cc_final: 0.7886 (t0) REVERT: D 407 GLU cc_start: 0.7785 (mp0) cc_final: 0.7119 (mp0) REVERT: D 410 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7390 (mm-30) REVERT: D 413 SER cc_start: 0.7908 (t) cc_final: 0.7660 (p) REVERT: D 421 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7795 (mt-10) REVERT: E 11 SER cc_start: 0.7418 (t) cc_final: 0.7010 (p) REVERT: E 15 ASP cc_start: 0.8304 (t0) cc_final: 0.7843 (t0) REVERT: E 53 GLU cc_start: 0.7052 (tp30) cc_final: 0.6825 (tp30) REVERT: E 68 GLU cc_start: 0.7904 (tt0) cc_final: 0.7578 (tm-30) REVERT: E 71 ASN cc_start: 0.8468 (m110) cc_final: 0.7890 (m-40) REVERT: E 87 LEU cc_start: 0.7350 (tt) cc_final: 0.7115 (pp) REVERT: E 111 ARG cc_start: 0.6292 (ptt180) cc_final: 0.6044 (ptt-90) REVERT: E 262 PHE cc_start: 0.7618 (t80) cc_final: 0.7358 (t80) REVERT: E 289 ILE cc_start: 0.7270 (mt) cc_final: 0.7022 (tt) REVERT: E 294 PRO cc_start: 0.8209 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: E 295 ASP cc_start: 0.7473 (p0) cc_final: 0.5606 (p0) REVERT: E 330 LYS cc_start: 0.7502 (mtpt) cc_final: 0.7250 (mtpt) REVERT: E 341 ARG cc_start: 0.7006 (mtm-85) cc_final: 0.6409 (mtt-85) REVERT: E 434 HIS cc_start: 0.7932 (m-70) cc_final: 0.7504 (m170) REVERT: E 436 HIS cc_start: 0.7772 (t-90) cc_final: 0.7308 (t-90) REVERT: E 459 MET cc_start: 0.7948 (mtm) cc_final: 0.7263 (mtm) REVERT: E 504 TYR cc_start: 0.8077 (t80) cc_final: 0.7871 (t80) REVERT: E 534 ASP cc_start: 0.7349 (p0) cc_final: 0.6836 (p0) REVERT: E 584 SER cc_start: 0.7298 (m) cc_final: 0.6790 (t) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 1.5437 time to fit residues: 1009.0618 Evaluate side-chains 454 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.2980 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 35 GLN A 91 GLN A 133 GLN A 356 ASN B 11 GLN B 190 HIS B 292 GLN B 416 ASN C 91 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN D 292 GLN D 332 ASN D 334 GLN D 416 ASN E 71 ASN ** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN E 557 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.093531 restraints weight = 30883.439| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.05 r_work: 0.3279 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17849 Z= 0.228 Angle : 0.597 10.595 24276 Z= 0.311 Chirality : 0.045 0.162 2651 Planarity : 0.005 0.062 3170 Dihedral : 10.811 143.172 2517 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.61 % Allowed : 13.83 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2205 helix: 0.13 (0.16), residues: 912 sheet: 0.12 (0.28), residues: 342 loop : -0.77 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 21 HIS 0.007 0.001 HIS E 339 PHE 0.021 0.002 PHE A 255 TYR 0.012 0.001 TYR D 340 ARG 0.010 0.001 ARG E 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 484 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8216 (mtm180) cc_final: 0.7953 (ptp90) REVERT: A 50 ASN cc_start: 0.8319 (t0) cc_final: 0.7745 (t0) REVERT: A 83 TYR cc_start: 0.8415 (m-80) cc_final: 0.8075 (m-80) REVERT: A 123 ARG cc_start: 0.7913 (tpp-160) cc_final: 0.7542 (tpp80) REVERT: A 124 LYS cc_start: 0.8638 (mttt) cc_final: 0.8277 (ttmm) REVERT: A 254 GLU cc_start: 0.7864 (tt0) cc_final: 0.7264 (mm-30) REVERT: A 280 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8738 (ptmt) REVERT: A 284 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 322 ASP cc_start: 0.8089 (t0) cc_final: 0.7775 (t70) REVERT: A 414 GLU cc_start: 0.8518 (mp0) cc_final: 0.8083 (mp0) REVERT: A 415 GLU cc_start: 0.8188 (tt0) cc_final: 0.7800 (tm-30) REVERT: A 423 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8058 (mm-30) REVERT: A 433 GLU cc_start: 0.8052 (tp30) cc_final: 0.7632 (tp30) REVERT: B 19 LYS cc_start: 0.8626 (tptm) cc_final: 0.8299 (tptt) REVERT: B 22 GLU cc_start: 0.8412 (tp30) cc_final: 0.8173 (mt-10) REVERT: B 42 LEU cc_start: 0.8685 (mt) cc_final: 0.8118 (mm) REVERT: B 48 ASN cc_start: 0.8752 (p0) cc_final: 0.8284 (p0) REVERT: B 58 LYS cc_start: 0.7730 (tttt) cc_final: 0.7328 (pttt) REVERT: B 81 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7174 (m-80) REVERT: B 88 ASP cc_start: 0.8293 (t0) cc_final: 0.8072 (t0) REVERT: B 103 LYS cc_start: 0.8736 (tttt) cc_final: 0.8304 (mtpp) REVERT: B 121 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: B 122 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7993 (ttmm) REVERT: B 147 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8524 (ttt) REVERT: B 158 GLU cc_start: 0.8386 (tp30) cc_final: 0.8066 (tt0) REVERT: B 205 GLU cc_start: 0.8236 (tt0) cc_final: 0.7885 (mt-10) REVERT: B 252 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8616 (ttpt) REVERT: B 257 MET cc_start: 0.8465 (mmm) cc_final: 0.8166 (mmm) REVERT: B 278 SER cc_start: 0.8944 (m) cc_final: 0.8349 (p) REVERT: B 282 ARG cc_start: 0.7695 (ttt-90) cc_final: 0.6881 (ptm-80) REVERT: B 299 MET cc_start: 0.7973 (mmp) cc_final: 0.7716 (tpp) REVERT: B 304 ASP cc_start: 0.7035 (t70) cc_final: 0.6699 (t70) REVERT: B 350 LYS cc_start: 0.8884 (tptt) cc_final: 0.8513 (tptm) REVERT: B 362 LYS cc_start: 0.8587 (tptp) cc_final: 0.8255 (tptp) REVERT: B 363 MET cc_start: 0.8400 (mtm) cc_final: 0.7358 (mtm) REVERT: B 364 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8583 (t) REVERT: B 391 ARG cc_start: 0.7971 (mmm160) cc_final: 0.6275 (mtm180) REVERT: B 404 ASP cc_start: 0.8027 (m-30) cc_final: 0.7618 (m-30) REVERT: B 407 GLU cc_start: 0.7425 (mp0) cc_final: 0.7093 (mp0) REVERT: B 421 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: B 425 TYR cc_start: 0.8739 (m-80) cc_final: 0.8464 (m-80) REVERT: C 2 ARG cc_start: 0.8386 (mtm180) cc_final: 0.8180 (mtm180) REVERT: C 3 GLU cc_start: 0.8414 (mp0) cc_final: 0.8027 (mt-10) REVERT: C 36 MET cc_start: 0.8813 (ttp) cc_final: 0.8540 (ttp) REVERT: C 47 ASP cc_start: 0.8470 (p0) cc_final: 0.7825 (t0) REVERT: C 50 ASN cc_start: 0.8677 (t0) cc_final: 0.7963 (t160) REVERT: C 203 MET cc_start: 0.8528 (tpp) cc_final: 0.8228 (mmm) REVERT: C 218 ASP cc_start: 0.8219 (m-30) cc_final: 0.7739 (t0) REVERT: C 287 SER cc_start: 0.8680 (t) cc_final: 0.8446 (p) REVERT: C 308 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7628 (tmm160) REVERT: C 322 ASP cc_start: 0.8316 (t0) cc_final: 0.7971 (t0) REVERT: C 337 THR cc_start: 0.8653 (m) cc_final: 0.8280 (p) REVERT: C 349 THR cc_start: 0.8347 (p) cc_final: 0.8129 (p) REVERT: C 392 ASP cc_start: 0.7884 (m-30) cc_final: 0.7619 (m-30) REVERT: C 415 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7609 (tp30) REVERT: D 19 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8102 (tppt) REVERT: D 44 LEU cc_start: 0.8570 (tp) cc_final: 0.8327 (tm) REVERT: D 45 GLU cc_start: 0.8162 (tt0) cc_final: 0.7909 (tm-30) REVERT: D 58 LYS cc_start: 0.8674 (tttt) cc_final: 0.8279 (mtpp) REVERT: D 88 ASP cc_start: 0.8138 (t70) cc_final: 0.7800 (t0) REVERT: D 118 ASP cc_start: 0.8041 (m-30) cc_final: 0.7723 (m-30) REVERT: D 121 ARG cc_start: 0.8309 (ttm110) cc_final: 0.7830 (ptp-110) REVERT: D 122 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8342 (ttmm) REVERT: D 203 ASP cc_start: 0.8085 (t0) cc_final: 0.7808 (t70) REVERT: D 213 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: D 233 MET cc_start: 0.8527 (ttm) cc_final: 0.8227 (mtp) REVERT: D 257 MET cc_start: 0.8355 (mmm) cc_final: 0.8012 (mtp) REVERT: D 304 ASP cc_start: 0.7735 (t70) cc_final: 0.6871 (t0) REVERT: D 309 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8134 (mtp85) REVERT: D 325 GLU cc_start: 0.8431 (tp30) cc_final: 0.7993 (tp30) REVERT: D 329 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7093 (mm-40) REVERT: D 376 GLU cc_start: 0.7712 (mp0) cc_final: 0.7060 (mp0) REVERT: D 383 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7981 (tm-30) REVERT: D 391 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7315 (mtm180) REVERT: D 407 GLU cc_start: 0.8064 (mp0) cc_final: 0.7731 (mp0) REVERT: D 410 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7865 (mm-30) REVERT: E 11 SER cc_start: 0.8541 (t) cc_final: 0.8297 (p) REVERT: E 94 ASN cc_start: 0.7693 (t0) cc_final: 0.6873 (t0) REVERT: E 120 GLU cc_start: 0.8104 (tt0) cc_final: 0.7892 (tt0) REVERT: E 169 ASN cc_start: 0.7453 (m-40) cc_final: 0.6800 (m-40) REVERT: E 206 ASP cc_start: 0.8532 (p0) cc_final: 0.8330 (p0) REVERT: E 314 GLN cc_start: 0.7338 (mp10) cc_final: 0.6996 (mp10) REVERT: E 327 TYR cc_start: 0.7943 (t80) cc_final: 0.7293 (t80) REVERT: E 456 VAL cc_start: 0.9051 (t) cc_final: 0.8820 (p) REVERT: E 459 MET cc_start: 0.8121 (mtm) cc_final: 0.7826 (mtm) REVERT: E 584 SER cc_start: 0.7522 (m) cc_final: 0.7197 (t) REVERT: E 590 ARG cc_start: 0.8550 (ttm110) cc_final: 0.7993 (ttm170) outliers start: 48 outliers final: 14 residues processed: 502 average time/residue: 1.6291 time to fit residues: 898.6662 Evaluate side-chains 436 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 417 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 178 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN B 256 ASN B 292 GLN B 334 GLN B 416 ASN C 28 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 104 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087560 restraints weight = 30171.563| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.01 r_work: 0.3167 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 17849 Z= 0.310 Angle : 0.624 9.427 24276 Z= 0.324 Chirality : 0.047 0.195 2651 Planarity : 0.005 0.050 3170 Dihedral : 10.949 165.716 2517 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.10 % Allowed : 15.46 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2205 helix: 0.85 (0.17), residues: 905 sheet: 0.35 (0.30), residues: 330 loop : -0.71 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 21 HIS 0.007 0.001 HIS D 137 PHE 0.026 0.002 PHE C 49 TYR 0.039 0.002 TYR E 191 ARG 0.014 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 458 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7704 (p0) cc_final: 0.7503 (t70) REVERT: A 50 ASN cc_start: 0.8410 (t0) cc_final: 0.7762 (t0) REVERT: A 76 ASP cc_start: 0.8390 (m-30) cc_final: 0.7682 (m-30) REVERT: A 123 ARG cc_start: 0.7950 (tpp-160) cc_final: 0.7653 (tpp80) REVERT: A 124 LYS cc_start: 0.8646 (mttt) cc_final: 0.8253 (ttmm) REVERT: A 203 MET cc_start: 0.8395 (tpp) cc_final: 0.8130 (mmm) REVERT: A 230 LEU cc_start: 0.8765 (mp) cc_final: 0.8558 (mm) REVERT: A 254 GLU cc_start: 0.8140 (tt0) cc_final: 0.7666 (mm-30) REVERT: A 284 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 297 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7408 (tp30) REVERT: A 322 ASP cc_start: 0.8239 (t0) cc_final: 0.7802 (t70) REVERT: A 413 MET cc_start: 0.8562 (ttm) cc_final: 0.7588 (ttp) REVERT: A 414 GLU cc_start: 0.8509 (mp0) cc_final: 0.7809 (mp0) REVERT: A 415 GLU cc_start: 0.8228 (tt0) cc_final: 0.7956 (tm-30) REVERT: A 417 GLU cc_start: 0.7451 (tt0) cc_final: 0.7152 (pp20) REVERT: A 420 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7721 (mt-10) REVERT: A 423 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 433 GLU cc_start: 0.8337 (tp30) cc_final: 0.7839 (tp30) REVERT: B 19 LYS cc_start: 0.8596 (tptm) cc_final: 0.8378 (tptt) REVERT: B 22 GLU cc_start: 0.8542 (tp30) cc_final: 0.7603 (mm-30) REVERT: B 42 LEU cc_start: 0.8687 (mt) cc_final: 0.8208 (mm) REVERT: B 48 ASN cc_start: 0.8760 (p0) cc_final: 0.8393 (p0) REVERT: B 58 LYS cc_start: 0.8198 (tttt) cc_final: 0.7844 (pttt) REVERT: B 81 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: B 88 ASP cc_start: 0.8324 (t0) cc_final: 0.7998 (t0) REVERT: B 103 LYS cc_start: 0.8924 (tttt) cc_final: 0.8447 (mtpp) REVERT: B 122 LYS cc_start: 0.8488 (ttpt) cc_final: 0.8269 (ttpt) REVERT: B 157 GLU cc_start: 0.8548 (tp30) cc_final: 0.8058 (tm-30) REVERT: B 205 GLU cc_start: 0.8338 (tt0) cc_final: 0.7997 (mt-10) REVERT: B 278 SER cc_start: 0.8961 (m) cc_final: 0.8403 (p) REVERT: B 299 MET cc_start: 0.8564 (mmp) cc_final: 0.8230 (tpp) REVERT: B 350 LYS cc_start: 0.8894 (tptt) cc_final: 0.8610 (tptm) REVERT: B 362 LYS cc_start: 0.8577 (tptp) cc_final: 0.8120 (tptp) REVERT: B 363 MET cc_start: 0.8631 (mtm) cc_final: 0.7818 (mtp) REVERT: B 380 ARG cc_start: 0.8302 (ptp90) cc_final: 0.8098 (ptp-170) REVERT: B 391 ARG cc_start: 0.8222 (mmm160) cc_final: 0.6548 (mtm180) REVERT: B 403 MET cc_start: 0.8333 (mtp) cc_final: 0.8091 (mtm) REVERT: B 421 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: B 425 TYR cc_start: 0.8806 (m-80) cc_final: 0.8565 (m-80) REVERT: C 2 ARG cc_start: 0.8410 (mtm180) cc_final: 0.8129 (mtm180) REVERT: C 47 ASP cc_start: 0.8495 (p0) cc_final: 0.7852 (t0) REVERT: C 50 ASN cc_start: 0.8722 (t0) cc_final: 0.7764 (t0) REVERT: C 71 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: C 77 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8142 (mp0) REVERT: C 203 MET cc_start: 0.8624 (tpp) cc_final: 0.8387 (mmm) REVERT: C 207 GLU cc_start: 0.7471 (tt0) cc_final: 0.7204 (mt-10) REVERT: C 218 ASP cc_start: 0.8253 (m-30) cc_final: 0.7782 (t0) REVERT: C 221 ARG cc_start: 0.8291 (pmm-80) cc_final: 0.8047 (pmm-80) REVERT: C 254 GLU cc_start: 0.4645 (tp30) cc_final: 0.2393 (mm-30) REVERT: C 284 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 287 SER cc_start: 0.8820 (t) cc_final: 0.8521 (p) REVERT: C 290 GLU cc_start: 0.7955 (mp0) cc_final: 0.7591 (mp0) REVERT: C 308 ARG cc_start: 0.8305 (mtm180) cc_final: 0.7347 (tmt-80) REVERT: C 322 ASP cc_start: 0.8419 (t0) cc_final: 0.8101 (t0) REVERT: C 337 THR cc_start: 0.8733 (m) cc_final: 0.8328 (p) REVERT: C 349 THR cc_start: 0.8375 (p) cc_final: 0.8170 (p) REVERT: C 377 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8175 (tmm) REVERT: C 386 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8048 (mp0) REVERT: C 392 ASP cc_start: 0.8085 (m-30) cc_final: 0.7808 (m-30) REVERT: C 415 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7814 (tp30) REVERT: C 433 GLU cc_start: 0.7832 (tp30) cc_final: 0.7500 (tp30) REVERT: D 19 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8164 (tppt) REVERT: D 45 GLU cc_start: 0.8377 (tt0) cc_final: 0.8067 (tm-30) REVERT: D 57 ASN cc_start: 0.8422 (m-40) cc_final: 0.8204 (m-40) REVERT: D 88 ASP cc_start: 0.8325 (t70) cc_final: 0.7942 (t0) REVERT: D 118 ASP cc_start: 0.8166 (m-30) cc_final: 0.7782 (m-30) REVERT: D 121 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7957 (ptp-110) REVERT: D 122 LYS cc_start: 0.8865 (ttpt) cc_final: 0.8565 (ttmm) REVERT: D 154 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8669 (mptp) REVERT: D 203 ASP cc_start: 0.8203 (t0) cc_final: 0.7886 (t70) REVERT: D 213 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8343 (ptp-110) REVERT: D 233 MET cc_start: 0.8919 (ttm) cc_final: 0.8699 (mtp) REVERT: D 257 MET cc_start: 0.8320 (mmm) cc_final: 0.8104 (mtp) REVERT: D 291 GLN cc_start: 0.8698 (tt0) cc_final: 0.8496 (tt0) REVERT: D 304 ASP cc_start: 0.7968 (t70) cc_final: 0.7240 (t0) REVERT: D 306 ARG cc_start: 0.8248 (mtm180) cc_final: 0.7796 (mtm180) REVERT: D 309 ARG cc_start: 0.8487 (mtp85) cc_final: 0.8159 (mtp85) REVERT: D 324 LYS cc_start: 0.9075 (tptm) cc_final: 0.8836 (tppt) REVERT: D 325 GLU cc_start: 0.8449 (tp30) cc_final: 0.8020 (tp30) REVERT: D 377 LEU cc_start: 0.8609 (mt) cc_final: 0.8302 (mp) REVERT: D 391 ARG cc_start: 0.8337 (mmm160) cc_final: 0.7580 (mtm180) REVERT: D 404 ASP cc_start: 0.8224 (t0) cc_final: 0.7431 (t0) REVERT: D 407 GLU cc_start: 0.7975 (mp0) cc_final: 0.7343 (mp0) REVERT: D 410 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7757 (mm-30) REVERT: E 9 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7551 (mt) REVERT: E 67 PHE cc_start: 0.8375 (m-10) cc_final: 0.7319 (m-10) REVERT: E 94 ASN cc_start: 0.8145 (t0) cc_final: 0.7695 (t0) REVERT: E 120 GLU cc_start: 0.8033 (tt0) cc_final: 0.7824 (tt0) REVERT: E 169 ASN cc_start: 0.7962 (m-40) cc_final: 0.7688 (m-40) REVERT: E 307 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7133 (mmm-85) REVERT: E 314 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: E 327 TYR cc_start: 0.8341 (t80) cc_final: 0.7843 (t80) REVERT: E 483 ASN cc_start: 0.7564 (t0) cc_final: 0.6941 (t0) REVERT: E 556 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6958 (mm-30) REVERT: E 584 SER cc_start: 0.7605 (m) cc_final: 0.7364 (t) outliers start: 57 outliers final: 17 residues processed: 483 average time/residue: 1.5315 time to fit residues: 812.7430 Evaluate side-chains 440 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 416 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 71 GLU 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 C residue 377 MET Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 121 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.0040 chunk 200 optimal weight: 0.4980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 416 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088291 restraints weight = 29963.195| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.01 r_work: 0.3179 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17849 Z= 0.214 Angle : 0.583 9.775 24276 Z= 0.299 Chirality : 0.044 0.165 2651 Planarity : 0.005 0.047 3170 Dihedral : 10.799 171.140 2517 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.45 % Allowed : 17.75 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2205 helix: 1.15 (0.17), residues: 913 sheet: 0.21 (0.29), residues: 341 loop : -0.62 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 21 HIS 0.005 0.001 HIS A 197 PHE 0.017 0.001 PHE C 49 TYR 0.018 0.001 TYR E 52 ARG 0.012 0.001 ARG E 598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 441 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8445 (t0) cc_final: 0.7819 (t0) REVERT: A 83 TYR cc_start: 0.8343 (m-80) cc_final: 0.8087 (m-80) REVERT: A 123 ARG cc_start: 0.7959 (tpp-160) cc_final: 0.7664 (tpp80) REVERT: A 124 LYS cc_start: 0.8609 (mttt) cc_final: 0.8244 (ttmm) REVERT: A 203 MET cc_start: 0.8388 (tpp) cc_final: 0.8118 (mmm) REVERT: A 252 LEU cc_start: 0.8076 (mp) cc_final: 0.7778 (mt) REVERT: A 254 GLU cc_start: 0.8188 (tt0) cc_final: 0.7705 (mm-30) REVERT: A 280 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8904 (ptpp) REVERT: A 284 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 297 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7494 (tp30) REVERT: A 322 ASP cc_start: 0.8225 (t0) cc_final: 0.7829 (t70) REVERT: A 358 GLN cc_start: 0.9140 (tp40) cc_final: 0.8904 (mm-40) REVERT: A 414 GLU cc_start: 0.8481 (mp0) cc_final: 0.8054 (mp0) REVERT: A 415 GLU cc_start: 0.8228 (tt0) cc_final: 0.7975 (tm-30) REVERT: A 423 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 433 GLU cc_start: 0.8341 (tp30) cc_final: 0.7818 (tp30) REVERT: B 19 LYS cc_start: 0.8568 (tptm) cc_final: 0.8361 (tptt) REVERT: B 48 ASN cc_start: 0.8761 (p0) cc_final: 0.8398 (p0) REVERT: B 58 LYS cc_start: 0.8164 (tttt) cc_final: 0.7803 (pttt) REVERT: B 81 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: B 88 ASP cc_start: 0.8299 (t0) cc_final: 0.7948 (t0) REVERT: B 103 LYS cc_start: 0.8932 (tttt) cc_final: 0.8420 (tttt) REVERT: B 122 LYS cc_start: 0.8489 (ttpt) cc_final: 0.8276 (ttpt) REVERT: B 154 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8562 (mttm) REVERT: B 157 GLU cc_start: 0.8549 (tp30) cc_final: 0.8073 (tm-30) REVERT: B 158 GLU cc_start: 0.8559 (tp30) cc_final: 0.8268 (tp30) REVERT: B 205 GLU cc_start: 0.8350 (tt0) cc_final: 0.7998 (mt-10) REVERT: B 209 ASP cc_start: 0.8316 (t0) cc_final: 0.8089 (t0) REVERT: B 213 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8299 (ttp-110) REVERT: B 267 MET cc_start: 0.8657 (mtp) cc_final: 0.8447 (mtm) REVERT: B 278 SER cc_start: 0.8933 (m) cc_final: 0.8708 (m) REVERT: B 282 ARG cc_start: 0.7931 (ptm160) cc_final: 0.7534 (ptm160) REVERT: B 327 ASP cc_start: 0.7695 (m-30) cc_final: 0.7470 (m-30) REVERT: B 350 LYS cc_start: 0.8898 (tptt) cc_final: 0.8621 (tptm) REVERT: B 362 LYS cc_start: 0.8585 (tptp) cc_final: 0.8152 (tptp) REVERT: B 363 MET cc_start: 0.8633 (mtm) cc_final: 0.7979 (mtp) REVERT: B 379 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8361 (mtpm) REVERT: B 391 ARG cc_start: 0.8201 (mmm160) cc_final: 0.6607 (mtm180) REVERT: B 410 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 421 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: C 2 ARG cc_start: 0.8401 (mtm180) cc_final: 0.8143 (mtm180) REVERT: C 47 ASP cc_start: 0.8484 (p0) cc_final: 0.7866 (t0) REVERT: C 50 ASN cc_start: 0.8677 (t0) cc_final: 0.7780 (t0) REVERT: C 77 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8291 (mt-10) REVERT: C 123 ARG cc_start: 0.8258 (tpp80) cc_final: 0.8053 (tpp80) REVERT: C 203 MET cc_start: 0.8653 (tpp) cc_final: 0.8397 (mmm) REVERT: C 207 GLU cc_start: 0.7516 (tt0) cc_final: 0.7239 (mt-10) REVERT: C 218 ASP cc_start: 0.8324 (m-30) cc_final: 0.7811 (t0) REVERT: C 221 ARG cc_start: 0.8321 (pmm-80) cc_final: 0.8067 (pmm-80) REVERT: C 254 GLU cc_start: 0.4451 (tp30) cc_final: 0.2527 (mm-30) REVERT: C 284 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 287 SER cc_start: 0.8821 (t) cc_final: 0.8466 (p) REVERT: C 290 GLU cc_start: 0.7964 (mp0) cc_final: 0.7567 (mp0) REVERT: C 297 GLU cc_start: 0.7814 (tp30) cc_final: 0.7544 (tp30) REVERT: C 308 ARG cc_start: 0.8316 (mtm180) cc_final: 0.7272 (tmt-80) REVERT: C 337 THR cc_start: 0.8721 (m) cc_final: 0.8302 (p) REVERT: C 377 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: C 392 ASP cc_start: 0.8074 (m-30) cc_final: 0.7780 (m-30) REVERT: C 415 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7761 (tp30) REVERT: C 417 GLU cc_start: 0.7599 (mp0) cc_final: 0.7316 (mp0) REVERT: C 420 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 433 GLU cc_start: 0.7850 (tp30) cc_final: 0.7573 (tp30) REVERT: D 19 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8156 (mmmt) REVERT: D 45 GLU cc_start: 0.8365 (tt0) cc_final: 0.8039 (tm-30) REVERT: D 118 ASP cc_start: 0.8132 (m-30) cc_final: 0.7702 (m-30) REVERT: D 121 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8009 (ptp-110) REVERT: D 122 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8582 (ttmm) REVERT: D 128 ASP cc_start: 0.8733 (t0) cc_final: 0.8367 (t0) REVERT: D 181 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8001 (mt-10) REVERT: D 203 ASP cc_start: 0.8222 (t0) cc_final: 0.7898 (t70) REVERT: D 213 ARG cc_start: 0.8642 (ttm-80) cc_final: 0.8435 (ttm-80) REVERT: D 233 MET cc_start: 0.8943 (ttm) cc_final: 0.8737 (mtp) REVERT: D 257 MET cc_start: 0.8279 (mmm) cc_final: 0.8020 (mtp) REVERT: D 304 ASP cc_start: 0.8132 (t70) cc_final: 0.7104 (t0) REVERT: D 306 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7738 (mtm180) REVERT: D 309 ARG cc_start: 0.8550 (mtp85) cc_final: 0.8182 (mtp85) REVERT: D 325 GLU cc_start: 0.8402 (tp30) cc_final: 0.7985 (tp30) REVERT: D 391 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7399 (mtm110) REVERT: D 410 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7674 (mm-30) REVERT: D 414 ASN cc_start: 0.8052 (m110) cc_final: 0.7701 (m-40) REVERT: D 425 TYR cc_start: 0.7611 (m-10) cc_final: 0.7387 (m-10) REVERT: E 53 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6725 (tm-30) REVERT: E 94 ASN cc_start: 0.8220 (t0) cc_final: 0.7810 (t0) REVERT: E 120 GLU cc_start: 0.8003 (tt0) cc_final: 0.7800 (tt0) REVERT: E 169 ASN cc_start: 0.7984 (m-40) cc_final: 0.7742 (m-40) REVERT: E 206 ASP cc_start: 0.8555 (p0) cc_final: 0.8335 (p0) REVERT: E 314 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: E 327 TYR cc_start: 0.8387 (t80) cc_final: 0.7886 (t80) REVERT: E 483 ASN cc_start: 0.7611 (t0) cc_final: 0.7058 (t0) REVERT: E 556 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6911 (mm-30) REVERT: E 584 SER cc_start: 0.7513 (m) cc_final: 0.7227 (t) REVERT: E 593 MET cc_start: 0.8313 (tpp) cc_final: 0.8049 (tpp) outliers start: 45 outliers final: 23 residues processed: 465 average time/residue: 1.5861 time to fit residues: 808.6846 Evaluate side-chains 442 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 412 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 81 PHE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 53 optimal weight: 0.6980 chunk 208 optimal weight: 0.0570 chunk 139 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 212 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.5114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 329 GLN B 414 ASN B 416 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 301 HIS E 599 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088290 restraints weight = 30421.895| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.04 r_work: 0.3177 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17849 Z= 0.198 Angle : 0.593 11.012 24276 Z= 0.299 Chirality : 0.044 0.206 2651 Planarity : 0.005 0.071 3170 Dihedral : 10.652 174.030 2517 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.10 % Allowed : 18.18 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.18), residues: 2205 helix: 1.29 (0.17), residues: 915 sheet: 0.24 (0.29), residues: 339 loop : -0.58 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 21 HIS 0.004 0.001 HIS A 197 PHE 0.021 0.001 PHE A 255 TYR 0.018 0.001 TYR E 52 ARG 0.014 0.001 ARG E 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 431 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8440 (t0) cc_final: 0.7823 (t0) REVERT: A 83 TYR cc_start: 0.8328 (m-80) cc_final: 0.8037 (m-80) REVERT: A 113 GLU cc_start: 0.7348 (mp0) cc_final: 0.6965 (mp0) REVERT: A 123 ARG cc_start: 0.7912 (tpp-160) cc_final: 0.7644 (tpp80) REVERT: A 124 LYS cc_start: 0.8621 (mttt) cc_final: 0.8244 (ttmm) REVERT: A 252 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7802 (mt) REVERT: A 254 GLU cc_start: 0.8223 (tt0) cc_final: 0.7749 (mm-30) REVERT: A 255 PHE cc_start: 0.8586 (p90) cc_final: 0.8277 (p90) REVERT: A 284 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 297 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7484 (tp30) REVERT: A 322 ASP cc_start: 0.8248 (t0) cc_final: 0.7851 (t70) REVERT: A 414 GLU cc_start: 0.8441 (mp0) cc_final: 0.8028 (mp0) REVERT: A 415 GLU cc_start: 0.8179 (tt0) cc_final: 0.7881 (tm-30) REVERT: A 423 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 433 GLU cc_start: 0.8185 (tp30) cc_final: 0.7681 (tp30) REVERT: B 48 ASN cc_start: 0.8777 (p0) cc_final: 0.8427 (p0) REVERT: B 58 LYS cc_start: 0.8189 (tttt) cc_final: 0.7786 (pttt) REVERT: B 88 ASP cc_start: 0.8318 (t0) cc_final: 0.7977 (t0) REVERT: B 103 LYS cc_start: 0.8853 (tttt) cc_final: 0.7909 (mtpm) REVERT: B 122 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8292 (ttpt) REVERT: B 154 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8550 (mttm) REVERT: B 157 GLU cc_start: 0.8540 (tp30) cc_final: 0.8101 (tm-30) REVERT: B 158 GLU cc_start: 0.8573 (tp30) cc_final: 0.8294 (tp30) REVERT: B 179 VAL cc_start: 0.8704 (m) cc_final: 0.8303 (t) REVERT: B 205 GLU cc_start: 0.8364 (tt0) cc_final: 0.7907 (mt-10) REVERT: B 282 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7624 (ptm160) REVERT: B 299 MET cc_start: 0.8562 (mmp) cc_final: 0.8178 (tpp) REVERT: B 324 LYS cc_start: 0.8863 (tptp) cc_final: 0.8615 (tppt) REVERT: B 327 ASP cc_start: 0.7737 (m-30) cc_final: 0.7514 (m-30) REVERT: B 340 TYR cc_start: 0.8025 (m-80) cc_final: 0.7692 (m-80) REVERT: B 362 LYS cc_start: 0.8608 (tptp) cc_final: 0.8278 (tptp) REVERT: B 363 MET cc_start: 0.8635 (mtm) cc_final: 0.7986 (mtp) REVERT: B 379 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8390 (mtpm) REVERT: B 391 ARG cc_start: 0.8235 (mmm160) cc_final: 0.6583 (mtm180) REVERT: B 410 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 421 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: C 2 ARG cc_start: 0.8396 (mtm180) cc_final: 0.8108 (mtm180) REVERT: C 47 ASP cc_start: 0.8419 (p0) cc_final: 0.7688 (t0) REVERT: C 50 ASN cc_start: 0.8696 (t0) cc_final: 0.7797 (t0) REVERT: C 77 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8129 (mp0) REVERT: C 90 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8045 (mm-30) REVERT: C 123 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7984 (tpp80) REVERT: C 207 GLU cc_start: 0.7519 (tt0) cc_final: 0.7250 (mt-10) REVERT: C 218 ASP cc_start: 0.8300 (m-30) cc_final: 0.7803 (t0) REVERT: C 254 GLU cc_start: 0.4482 (tp30) cc_final: 0.2521 (mm-30) REVERT: C 269 LEU cc_start: 0.8679 (mp) cc_final: 0.8439 (mp) REVERT: C 284 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7977 (mm-30) REVERT: C 290 GLU cc_start: 0.7969 (mp0) cc_final: 0.7597 (mp0) REVERT: C 297 GLU cc_start: 0.7857 (tp30) cc_final: 0.7559 (tp30) REVERT: C 308 ARG cc_start: 0.8367 (mtm180) cc_final: 0.7283 (tmt-80) REVERT: C 337 THR cc_start: 0.8726 (m) cc_final: 0.8309 (p) REVERT: C 349 THR cc_start: 0.8233 (p) cc_final: 0.8011 (p) REVERT: C 377 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8030 (tmm) REVERT: C 392 ASP cc_start: 0.8101 (m-30) cc_final: 0.7797 (m-30) REVERT: C 415 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7872 (tp30) REVERT: C 417 GLU cc_start: 0.7674 (mp0) cc_final: 0.7394 (mp0) REVERT: C 420 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7533 (mm-30) REVERT: C 433 GLU cc_start: 0.8073 (tp30) cc_final: 0.7743 (tp30) REVERT: D 19 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8215 (mmmt) REVERT: D 45 GLU cc_start: 0.8376 (tt0) cc_final: 0.8031 (tm-30) REVERT: D 121 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8026 (ptp-110) REVERT: D 122 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8614 (ttmm) REVERT: D 181 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 203 ASP cc_start: 0.8140 (t0) cc_final: 0.7847 (t70) REVERT: D 213 ARG cc_start: 0.8616 (ttm-80) cc_final: 0.8357 (ttm-80) REVERT: D 233 MET cc_start: 0.8968 (ttm) cc_final: 0.8758 (mtp) REVERT: D 257 MET cc_start: 0.8260 (mmm) cc_final: 0.7972 (mtp) REVERT: D 304 ASP cc_start: 0.7586 (t70) cc_final: 0.6681 (t0) REVERT: D 306 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7684 (mtm180) REVERT: D 309 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8174 (mtp85) REVERT: D 324 LYS cc_start: 0.9093 (tptm) cc_final: 0.8815 (tppt) REVERT: D 325 GLU cc_start: 0.8420 (tp30) cc_final: 0.8005 (tp30) REVERT: D 391 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7307 (mtm180) REVERT: D 404 ASP cc_start: 0.8195 (t0) cc_final: 0.7886 (t0) REVERT: D 407 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7675 (mm-30) REVERT: D 410 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7678 (mm-30) REVERT: D 414 ASN cc_start: 0.8034 (m110) cc_final: 0.7643 (m-40) REVERT: D 425 TYR cc_start: 0.7631 (m-10) cc_final: 0.7380 (m-10) REVERT: E 53 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6613 (tm-30) REVERT: E 94 ASN cc_start: 0.8190 (t0) cc_final: 0.7708 (t0) REVERT: E 120 GLU cc_start: 0.7968 (tt0) cc_final: 0.7762 (tt0) REVERT: E 169 ASN cc_start: 0.8034 (m-40) cc_final: 0.7743 (m-40) REVERT: E 206 ASP cc_start: 0.8543 (p0) cc_final: 0.8317 (p0) REVERT: E 314 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: E 327 TYR cc_start: 0.8422 (t80) cc_final: 0.7913 (t80) REVERT: E 483 ASN cc_start: 0.7469 (t0) cc_final: 0.7003 (t0) REVERT: E 556 GLU cc_start: 0.7262 (mm-30) cc_final: 0.7029 (mm-30) REVERT: E 584 SER cc_start: 0.7557 (m) cc_final: 0.7257 (t) outliers start: 57 outliers final: 26 residues processed: 465 average time/residue: 1.5399 time to fit residues: 786.4704 Evaluate side-chains 451 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 419 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 21 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 chunk 144 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 195 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 133 GLN A 266 HIS B 190 HIS B 335 ASN B 414 ASN B 416 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN E 533 HIS E 599 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.088019 restraints weight = 30082.614| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.01 r_work: 0.3174 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17849 Z= 0.207 Angle : 0.598 11.232 24276 Z= 0.303 Chirality : 0.044 0.209 2651 Planarity : 0.004 0.066 3170 Dihedral : 10.641 175.935 2517 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.94 % Allowed : 18.73 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2205 helix: 1.31 (0.17), residues: 917 sheet: 0.34 (0.29), residues: 343 loop : -0.52 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 21 HIS 0.005 0.001 HIS A 197 PHE 0.020 0.001 PHE A 255 TYR 0.019 0.001 TYR A 161 ARG 0.010 0.001 ARG E 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 423 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8496 (mpp-170) cc_final: 0.8210 (ptt90) REVERT: A 50 ASN cc_start: 0.8453 (t0) cc_final: 0.7802 (t0) REVERT: A 83 TYR cc_start: 0.8335 (m-80) cc_final: 0.8039 (m-80) REVERT: A 113 GLU cc_start: 0.7404 (mp0) cc_final: 0.7005 (mp0) REVERT: A 123 ARG cc_start: 0.7919 (tpp-160) cc_final: 0.7609 (tpp80) REVERT: A 124 LYS cc_start: 0.8616 (mttt) cc_final: 0.8241 (ttmm) REVERT: A 254 GLU cc_start: 0.8342 (tt0) cc_final: 0.7849 (mm-30) REVERT: A 255 PHE cc_start: 0.8585 (p90) cc_final: 0.8380 (p90) REVERT: A 284 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 297 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7475 (tp30) REVERT: A 322 ASP cc_start: 0.8255 (t0) cc_final: 0.7841 (t70) REVERT: A 358 GLN cc_start: 0.9130 (tp40) cc_final: 0.8909 (mm-40) REVERT: A 414 GLU cc_start: 0.8419 (mp0) cc_final: 0.8017 (mp0) REVERT: A 415 GLU cc_start: 0.8204 (tt0) cc_final: 0.7927 (tm-30) REVERT: A 423 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8071 (mm-30) REVERT: A 433 GLU cc_start: 0.8194 (tp30) cc_final: 0.7739 (tp30) REVERT: B 48 ASN cc_start: 0.8771 (p0) cc_final: 0.8445 (p0) REVERT: B 58 LYS cc_start: 0.8163 (tttt) cc_final: 0.7801 (pttt) REVERT: B 74 ASP cc_start: 0.8196 (t70) cc_final: 0.7950 (t0) REVERT: B 88 ASP cc_start: 0.8303 (t0) cc_final: 0.7969 (t0) REVERT: B 122 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8298 (ttpt) REVERT: B 157 GLU cc_start: 0.8576 (tp30) cc_final: 0.8135 (tm-30) REVERT: B 158 GLU cc_start: 0.8553 (tp30) cc_final: 0.8278 (tp30) REVERT: B 205 GLU cc_start: 0.8313 (tt0) cc_final: 0.7983 (mt-10) REVERT: B 213 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.7574 (mtm-85) REVERT: B 267 MET cc_start: 0.8652 (mtp) cc_final: 0.8399 (mtm) REVERT: B 306 ARG cc_start: 0.8533 (mpt-90) cc_final: 0.8056 (mpp-170) REVERT: B 324 LYS cc_start: 0.8871 (tptp) cc_final: 0.8619 (tppt) REVERT: B 327 ASP cc_start: 0.7754 (m-30) cc_final: 0.7536 (m-30) REVERT: B 340 TYR cc_start: 0.8033 (m-80) cc_final: 0.7609 (m-80) REVERT: B 350 LYS cc_start: 0.8916 (tptt) cc_final: 0.8657 (tptm) REVERT: B 362 LYS cc_start: 0.8562 (tptp) cc_final: 0.8231 (tptp) REVERT: B 363 MET cc_start: 0.8679 (mtm) cc_final: 0.8024 (mtp) REVERT: B 391 ARG cc_start: 0.8264 (mmm160) cc_final: 0.6554 (mtm110) REVERT: B 410 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7451 (mm-30) REVERT: C 2 ARG cc_start: 0.8398 (mtm180) cc_final: 0.8108 (mtm180) REVERT: C 47 ASP cc_start: 0.8414 (p0) cc_final: 0.7694 (t0) REVERT: C 50 ASN cc_start: 0.8694 (t0) cc_final: 0.7811 (t0) REVERT: C 71 GLU cc_start: 0.7682 (tt0) cc_final: 0.7335 (pt0) REVERT: C 77 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8295 (mt-10) REVERT: C 84 ARG cc_start: 0.8660 (ptp90) cc_final: 0.8435 (ptp90) REVERT: C 90 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7947 (mm-30) REVERT: C 123 ARG cc_start: 0.8244 (tpp80) cc_final: 0.8029 (tpp80) REVERT: C 207 GLU cc_start: 0.7581 (tt0) cc_final: 0.7326 (mt-10) REVERT: C 218 ASP cc_start: 0.8340 (m-30) cc_final: 0.7830 (t0) REVERT: C 254 GLU cc_start: 0.4642 (tp30) cc_final: 0.2677 (mm-30) REVERT: C 269 LEU cc_start: 0.8666 (mp) cc_final: 0.8438 (mp) REVERT: C 284 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7916 (mm-30) REVERT: C 297 GLU cc_start: 0.7895 (tp30) cc_final: 0.7555 (tp30) REVERT: C 308 ARG cc_start: 0.8393 (mtm180) cc_final: 0.7310 (tmt-80) REVERT: C 337 THR cc_start: 0.8755 (m) cc_final: 0.8340 (p) REVERT: C 377 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8025 (tmm) REVERT: C 386 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7756 (mp0) REVERT: C 392 ASP cc_start: 0.8070 (m-30) cc_final: 0.7758 (m-30) REVERT: C 415 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7862 (tp30) REVERT: C 417 GLU cc_start: 0.7762 (mp0) cc_final: 0.7448 (mp0) REVERT: C 420 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 423 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 19 LYS cc_start: 0.8700 (mmtt) cc_final: 0.8217 (mmmt) REVERT: D 45 GLU cc_start: 0.8382 (tt0) cc_final: 0.8026 (tm-30) REVERT: D 121 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8043 (ptp-110) REVERT: D 157 GLU cc_start: 0.8499 (tt0) cc_final: 0.8137 (tm-30) REVERT: D 181 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7838 (mt-10) REVERT: D 203 ASP cc_start: 0.8139 (t0) cc_final: 0.7861 (t70) REVERT: D 213 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8396 (ttm-80) REVERT: D 257 MET cc_start: 0.8213 (mmm) cc_final: 0.7919 (mtp) REVERT: D 304 ASP cc_start: 0.7423 (t70) cc_final: 0.6435 (t0) REVERT: D 306 ARG cc_start: 0.8182 (mtm180) cc_final: 0.7833 (mtm180) REVERT: D 309 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8147 (mtp85) REVERT: D 323 MET cc_start: 0.8524 (mmm) cc_final: 0.8226 (mmm) REVERT: D 324 LYS cc_start: 0.9128 (tptm) cc_final: 0.8906 (tppt) REVERT: D 325 GLU cc_start: 0.8478 (tp30) cc_final: 0.8172 (tp30) REVERT: D 391 ARG cc_start: 0.8467 (mmm160) cc_final: 0.7143 (mtm110) REVERT: D 404 ASP cc_start: 0.8191 (t0) cc_final: 0.7951 (t0) REVERT: D 410 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7675 (mm-30) REVERT: D 414 ASN cc_start: 0.8069 (m110) cc_final: 0.7677 (m-40) REVERT: D 424 GLN cc_start: 0.8182 (pt0) cc_final: 0.7916 (pp30) REVERT: D 425 TYR cc_start: 0.7657 (m-10) cc_final: 0.7388 (m-10) REVERT: E 3 LEU cc_start: 0.8699 (mt) cc_final: 0.8477 (mp) REVERT: E 53 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6662 (tm-30) REVERT: E 68 GLU cc_start: 0.8055 (tp30) cc_final: 0.7258 (tp30) REVERT: E 72 ARG cc_start: 0.8322 (ptt180) cc_final: 0.8053 (ptt-90) REVERT: E 94 ASN cc_start: 0.8187 (t0) cc_final: 0.7789 (t0) REVERT: E 120 GLU cc_start: 0.7973 (tt0) cc_final: 0.7761 (tt0) REVERT: E 169 ASN cc_start: 0.8058 (m-40) cc_final: 0.7759 (m-40) REVERT: E 206 ASP cc_start: 0.8478 (p0) cc_final: 0.8268 (p0) REVERT: E 213 CYS cc_start: 0.6626 (m) cc_final: 0.6302 (m) REVERT: E 307 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7760 (mmm-85) REVERT: E 314 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7292 (mp10) REVERT: E 327 TYR cc_start: 0.8469 (t80) cc_final: 0.7954 (t80) REVERT: E 451 ASP cc_start: 0.7700 (t0) cc_final: 0.7368 (t0) REVERT: E 483 ASN cc_start: 0.7574 (t0) cc_final: 0.6941 (t0) REVERT: E 556 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7056 (mm-30) REVERT: E 584 SER cc_start: 0.7535 (m) cc_final: 0.7237 (t) outliers start: 54 outliers final: 32 residues processed: 452 average time/residue: 1.6454 time to fit residues: 822.0387 Evaluate side-chains 448 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 414 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 199 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 0.1980 chunk 165 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 35 GLN A 133 GLN B 298 ASN B 335 ASN B 347 ASN B 416 ASN C 356 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.093336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084540 restraints weight = 30102.011| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.98 r_work: 0.3108 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 17849 Z= 0.398 Angle : 0.687 12.256 24276 Z= 0.352 Chirality : 0.049 0.212 2651 Planarity : 0.005 0.058 3170 Dihedral : 11.199 172.320 2517 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.10 % Allowed : 19.76 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2205 helix: 1.10 (0.17), residues: 916 sheet: 0.24 (0.29), residues: 341 loop : -0.57 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 21 HIS 0.006 0.002 HIS A 197 PHE 0.035 0.002 PHE E 262 TYR 0.026 0.002 TYR A 161 ARG 0.011 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 434 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8205 (p0) cc_final: 0.7914 (p0) REVERT: A 113 GLU cc_start: 0.7573 (mp0) cc_final: 0.7166 (mp0) REVERT: A 123 ARG cc_start: 0.7972 (tpp-160) cc_final: 0.7621 (tpp80) REVERT: A 124 LYS cc_start: 0.8655 (mttt) cc_final: 0.8272 (ttmm) REVERT: A 254 GLU cc_start: 0.8353 (tt0) cc_final: 0.7892 (mm-30) REVERT: A 284 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7249 (mm-30) REVERT: A 304 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8280 (mmtm) REVERT: A 322 ASP cc_start: 0.8284 (t0) cc_final: 0.7818 (t70) REVERT: A 326 LYS cc_start: 0.5593 (tppt) cc_final: 0.4326 (mmmm) REVERT: A 358 GLN cc_start: 0.9079 (tp40) cc_final: 0.8852 (mm-40) REVERT: A 414 GLU cc_start: 0.8367 (mp0) cc_final: 0.7954 (mp0) REVERT: A 415 GLU cc_start: 0.8328 (tt0) cc_final: 0.8011 (tm-30) REVERT: A 420 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7679 (mp0) REVERT: A 423 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 433 GLU cc_start: 0.8248 (tp30) cc_final: 0.7853 (tp30) REVERT: B 48 ASN cc_start: 0.8786 (p0) cc_final: 0.8408 (p0) REVERT: B 58 LYS cc_start: 0.8239 (tttt) cc_final: 0.7903 (pttt) REVERT: B 74 ASP cc_start: 0.8315 (t70) cc_final: 0.8086 (t0) REVERT: B 88 ASP cc_start: 0.8506 (t0) cc_final: 0.8159 (t0) REVERT: B 122 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8416 (ttpt) REVERT: B 157 GLU cc_start: 0.8627 (tp30) cc_final: 0.8228 (tm-30) REVERT: B 205 GLU cc_start: 0.8395 (tt0) cc_final: 0.7893 (mt-10) REVERT: B 213 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.7704 (mtm-85) REVERT: B 218 THR cc_start: 0.8728 (p) cc_final: 0.8478 (t) REVERT: B 267 MET cc_start: 0.8697 (mtp) cc_final: 0.8450 (mtm) REVERT: B 295 ASP cc_start: 0.8475 (OUTLIER) cc_final: 0.8270 (t0) REVERT: B 304 ASP cc_start: 0.7860 (t0) cc_final: 0.7645 (t0) REVERT: B 306 ARG cc_start: 0.8604 (mpt-90) cc_final: 0.8307 (mpp80) REVERT: B 327 ASP cc_start: 0.8080 (m-30) cc_final: 0.7871 (m-30) REVERT: B 340 TYR cc_start: 0.8179 (m-80) cc_final: 0.7792 (m-80) REVERT: B 350 LYS cc_start: 0.8859 (tptt) cc_final: 0.8588 (tptm) REVERT: B 362 LYS cc_start: 0.8568 (tptp) cc_final: 0.8343 (tptp) REVERT: B 363 MET cc_start: 0.8847 (mtm) cc_final: 0.8544 (mtp) REVERT: B 377 LEU cc_start: 0.8567 (mt) cc_final: 0.8181 (mt) REVERT: B 391 ARG cc_start: 0.8446 (mmm160) cc_final: 0.6490 (ptp-170) REVERT: B 410 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 2 ARG cc_start: 0.8451 (mtm180) cc_final: 0.8138 (mtm180) REVERT: C 47 ASP cc_start: 0.8357 (p0) cc_final: 0.8058 (p0) REVERT: C 50 ASN cc_start: 0.8657 (t0) cc_final: 0.7897 (t0) REVERT: C 76 ASP cc_start: 0.8511 (m-30) cc_final: 0.8120 (m-30) REVERT: C 77 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8117 (mp0) REVERT: C 90 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7711 (tm-30) REVERT: C 121 ARG cc_start: 0.7609 (tpp80) cc_final: 0.6987 (tpp80) REVERT: C 123 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7940 (tpp80) REVERT: C 158 SER cc_start: 0.8854 (t) cc_final: 0.8575 (t) REVERT: C 207 GLU cc_start: 0.7776 (tt0) cc_final: 0.7465 (mt-10) REVERT: C 218 ASP cc_start: 0.8362 (m-30) cc_final: 0.7871 (t0) REVERT: C 254 GLU cc_start: 0.4503 (tp30) cc_final: 0.2118 (mm-30) REVERT: C 280 LYS cc_start: 0.9080 (mttp) cc_final: 0.8054 (mmtt) REVERT: C 284 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7806 (mm-30) REVERT: C 287 SER cc_start: 0.8777 (t) cc_final: 0.8458 (p) REVERT: C 297 GLU cc_start: 0.7966 (tp30) cc_final: 0.7572 (tp30) REVERT: C 308 ARG cc_start: 0.8432 (mtm180) cc_final: 0.7364 (tmt-80) REVERT: C 349 THR cc_start: 0.8276 (p) cc_final: 0.8059 (p) REVERT: C 377 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7989 (tmm) REVERT: C 386 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7888 (mp0) REVERT: C 392 ASP cc_start: 0.7957 (m-30) cc_final: 0.7623 (m-30) REVERT: C 415 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7820 (tp30) REVERT: C 417 GLU cc_start: 0.7812 (mp0) cc_final: 0.7464 (mp0) REVERT: C 420 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 423 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8050 (mm-30) REVERT: D 19 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8198 (mmmt) REVERT: D 45 GLU cc_start: 0.8472 (tt0) cc_final: 0.8102 (tm-30) REVERT: D 103 LYS cc_start: 0.8963 (mtpm) cc_final: 0.8583 (ttmm) REVERT: D 121 ARG cc_start: 0.8396 (ttm110) cc_final: 0.8118 (ptp-110) REVERT: D 157 GLU cc_start: 0.8635 (tt0) cc_final: 0.8215 (tm-30) REVERT: D 203 ASP cc_start: 0.8132 (t0) cc_final: 0.7838 (t70) REVERT: D 213 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8476 (ttm-80) REVERT: D 257 MET cc_start: 0.8273 (mmm) cc_final: 0.7997 (mtp) REVERT: D 304 ASP cc_start: 0.7524 (t70) cc_final: 0.6428 (t0) REVERT: D 306 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7788 (mtm180) REVERT: D 309 ARG cc_start: 0.8388 (mtp85) cc_final: 0.8152 (mtp85) REVERT: D 323 MET cc_start: 0.8392 (mmm) cc_final: 0.8172 (mmm) REVERT: D 324 LYS cc_start: 0.9126 (tptm) cc_final: 0.8886 (tppt) REVERT: D 325 GLU cc_start: 0.8513 (tp30) cc_final: 0.8160 (tp30) REVERT: D 391 ARG cc_start: 0.8790 (mmm160) cc_final: 0.7487 (mtm180) REVERT: D 401 GLU cc_start: 0.7861 (mp0) cc_final: 0.7585 (mm-30) REVERT: D 404 ASP cc_start: 0.8181 (t0) cc_final: 0.7801 (t0) REVERT: D 407 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 410 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7732 (mm-30) REVERT: D 414 ASN cc_start: 0.8183 (m110) cc_final: 0.7771 (m-40) REVERT: D 424 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8083 (pp30) REVERT: D 425 TYR cc_start: 0.7732 (m-10) cc_final: 0.7477 (m-10) REVERT: E 3 LEU cc_start: 0.8749 (mt) cc_final: 0.8500 (mp) REVERT: E 53 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6766 (tm-30) REVERT: E 94 ASN cc_start: 0.8503 (t0) cc_final: 0.8093 (t0) REVERT: E 120 GLU cc_start: 0.7970 (tt0) cc_final: 0.7715 (tt0) REVERT: E 165 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7812 (mm110) REVERT: E 169 ASN cc_start: 0.8200 (m-40) cc_final: 0.7963 (m-40) REVERT: E 206 ASP cc_start: 0.8522 (p0) cc_final: 0.8321 (p0) REVERT: E 213 CYS cc_start: 0.7159 (m) cc_final: 0.6851 (m) REVERT: E 307 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8018 (tpp80) REVERT: E 327 TYR cc_start: 0.8663 (t80) cc_final: 0.8216 (t80) REVERT: E 483 ASN cc_start: 0.7856 (t0) cc_final: 0.7204 (t0) REVERT: E 556 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7285 (mm-30) REVERT: E 584 SER cc_start: 0.7746 (m) cc_final: 0.7413 (t) outliers start: 57 outliers final: 34 residues processed: 470 average time/residue: 1.6100 time to fit residues: 829.0752 Evaluate side-chains 459 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 421 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 SER Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 100 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 187 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 51 optimal weight: 0.0050 chunk 119 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 133 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.096330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.087363 restraints weight = 29742.677| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.99 r_work: 0.3165 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17849 Z= 0.194 Angle : 0.628 11.382 24276 Z= 0.318 Chirality : 0.044 0.221 2651 Planarity : 0.004 0.059 3170 Dihedral : 10.974 176.005 2517 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.18 % Allowed : 21.99 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2205 helix: 1.30 (0.17), residues: 916 sheet: 0.33 (0.30), residues: 339 loop : -0.58 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 21 HIS 0.005 0.001 HIS B 190 PHE 0.024 0.001 PHE E 262 TYR 0.018 0.001 TYR E 52 ARG 0.012 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 417 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8045 (ptt90) REVERT: A 76 ASP cc_start: 0.8407 (m-30) cc_final: 0.7763 (m-30) REVERT: A 83 TYR cc_start: 0.8293 (m-80) cc_final: 0.8063 (m-80) REVERT: A 98 ASP cc_start: 0.8117 (p0) cc_final: 0.7850 (p0) REVERT: A 113 GLU cc_start: 0.7477 (mp0) cc_final: 0.7099 (mp0) REVERT: A 123 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7643 (tpp80) REVERT: A 124 LYS cc_start: 0.8613 (mttt) cc_final: 0.8227 (ttmm) REVERT: A 254 GLU cc_start: 0.8387 (tt0) cc_final: 0.7889 (mm-30) REVERT: A 284 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7264 (mm-30) REVERT: A 304 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8208 (mmtm) REVERT: A 322 ASP cc_start: 0.8251 (t0) cc_final: 0.7802 (t70) REVERT: A 399 TYR cc_start: 0.8721 (t80) cc_final: 0.8295 (t80) REVERT: A 414 GLU cc_start: 0.8393 (mp0) cc_final: 0.7977 (mp0) REVERT: A 415 GLU cc_start: 0.8164 (tt0) cc_final: 0.7945 (tm-30) REVERT: A 417 GLU cc_start: 0.7407 (tt0) cc_final: 0.6564 (tt0) REVERT: A 423 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 433 GLU cc_start: 0.8194 (tp30) cc_final: 0.7810 (tp30) REVERT: B 42 LEU cc_start: 0.8685 (mm) cc_final: 0.8464 (mt) REVERT: B 48 ASN cc_start: 0.8744 (p0) cc_final: 0.8389 (p0) REVERT: B 58 LYS cc_start: 0.8116 (tttt) cc_final: 0.7843 (pttt) REVERT: B 74 ASP cc_start: 0.8278 (t70) cc_final: 0.8046 (OUTLIER) REVERT: B 88 ASP cc_start: 0.8321 (t0) cc_final: 0.7990 (t0) REVERT: B 122 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8336 (ttpt) REVERT: B 157 GLU cc_start: 0.8577 (tp30) cc_final: 0.8168 (tm-30) REVERT: B 179 VAL cc_start: 0.8718 (m) cc_final: 0.8326 (t) REVERT: B 205 GLU cc_start: 0.8387 (tt0) cc_final: 0.7950 (mt-10) REVERT: B 213 ARG cc_start: 0.8466 (ttp-110) cc_final: 0.7658 (mtm-85) REVERT: B 218 THR cc_start: 0.8775 (p) cc_final: 0.8523 (t) REVERT: B 267 MET cc_start: 0.8633 (mtp) cc_final: 0.8415 (mtm) REVERT: B 288 GLU cc_start: 0.7947 (pp20) cc_final: 0.7343 (pp20) REVERT: B 295 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 304 ASP cc_start: 0.7766 (t0) cc_final: 0.7551 (t0) REVERT: B 306 ARG cc_start: 0.8505 (mpt-90) cc_final: 0.7975 (mpp80) REVERT: B 332 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 340 TYR cc_start: 0.8182 (m-80) cc_final: 0.7579 (m-80) REVERT: B 350 LYS cc_start: 0.8904 (tptt) cc_final: 0.8649 (tptm) REVERT: B 362 LYS cc_start: 0.8529 (tptp) cc_final: 0.8276 (tptp) REVERT: B 363 MET cc_start: 0.8690 (mtm) cc_final: 0.8477 (mtp) REVERT: B 391 ARG cc_start: 0.8336 (mmm160) cc_final: 0.6420 (ptp-170) REVERT: B 410 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 421 GLU cc_start: 0.8282 (tt0) cc_final: 0.8012 (tm-30) REVERT: C 2 ARG cc_start: 0.8386 (mtm180) cc_final: 0.8089 (mtm180) REVERT: C 3 GLU cc_start: 0.8299 (mp0) cc_final: 0.7633 (mp0) REVERT: C 47 ASP cc_start: 0.8383 (p0) cc_final: 0.7692 (t0) REVERT: C 50 ASN cc_start: 0.8655 (t0) cc_final: 0.7843 (t0) REVERT: C 71 GLU cc_start: 0.7875 (tt0) cc_final: 0.7549 (pt0) REVERT: C 77 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8283 (mt-10) REVERT: C 90 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7742 (tm-30) REVERT: C 121 ARG cc_start: 0.7616 (tpp80) cc_final: 0.7171 (tpp80) REVERT: C 123 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7809 (tmm-80) REVERT: C 207 GLU cc_start: 0.7647 (tt0) cc_final: 0.7287 (mt-10) REVERT: C 218 ASP cc_start: 0.8364 (m-30) cc_final: 0.7861 (t0) REVERT: C 254 GLU cc_start: 0.4387 (tp30) cc_final: 0.2524 (mm-30) REVERT: C 269 LEU cc_start: 0.8684 (mp) cc_final: 0.8453 (mp) REVERT: C 280 LYS cc_start: 0.9029 (mttp) cc_final: 0.7958 (mmtt) REVERT: C 284 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7885 (mm-30) REVERT: C 297 GLU cc_start: 0.8002 (tp30) cc_final: 0.7604 (tp30) REVERT: C 308 ARG cc_start: 0.8433 (mtm180) cc_final: 0.7354 (tmt-80) REVERT: C 377 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8045 (tmm) REVERT: C 392 ASP cc_start: 0.7949 (m-30) cc_final: 0.7638 (m-30) REVERT: C 415 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7812 (tp30) REVERT: C 417 GLU cc_start: 0.7856 (mp0) cc_final: 0.7522 (mp0) REVERT: C 420 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7529 (mm-30) REVERT: C 423 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7886 (mm-30) REVERT: D 19 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8215 (mmmt) REVERT: D 45 GLU cc_start: 0.8387 (tt0) cc_final: 0.8060 (tm-30) REVERT: D 121 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8139 (ptp-110) REVERT: D 154 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8629 (mptp) REVERT: D 157 GLU cc_start: 0.8491 (tt0) cc_final: 0.8130 (tm-30) REVERT: D 203 ASP cc_start: 0.8129 (t0) cc_final: 0.7869 (t70) REVERT: D 213 ARG cc_start: 0.8733 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: D 216 LYS cc_start: 0.9291 (mmmm) cc_final: 0.8989 (mmmt) REVERT: D 257 MET cc_start: 0.8191 (mmm) cc_final: 0.7923 (mtp) REVERT: D 289 LEU cc_start: 0.8644 (mt) cc_final: 0.8385 (mp) REVERT: D 304 ASP cc_start: 0.7654 (t70) cc_final: 0.6537 (t0) REVERT: D 306 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7786 (mtm180) REVERT: D 309 ARG cc_start: 0.8513 (mtp85) cc_final: 0.8155 (mtp85) REVERT: D 323 MET cc_start: 0.8409 (mmm) cc_final: 0.8040 (mmm) REVERT: D 325 GLU cc_start: 0.8388 (tp30) cc_final: 0.8160 (tp30) REVERT: D 391 ARG cc_start: 0.8663 (mmm160) cc_final: 0.7297 (mtm180) REVERT: D 404 ASP cc_start: 0.8136 (t0) cc_final: 0.7936 (t0) REVERT: D 410 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7674 (mm-30) REVERT: D 414 ASN cc_start: 0.8070 (m110) cc_final: 0.7695 (m-40) REVERT: D 424 GLN cc_start: 0.8304 (pt0) cc_final: 0.8045 (pp30) REVERT: D 425 TYR cc_start: 0.7692 (m-80) cc_final: 0.7451 (m-10) REVERT: E 53 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6798 (tm-30) REVERT: E 72 ARG cc_start: 0.8317 (ptt180) cc_final: 0.7997 (ptt-90) REVERT: E 94 ASN cc_start: 0.8330 (t0) cc_final: 0.8027 (t0) REVERT: E 120 GLU cc_start: 0.7926 (tt0) cc_final: 0.7708 (tt0) REVERT: E 165 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7440 (mm110) REVERT: E 169 ASN cc_start: 0.8163 (m-40) cc_final: 0.7821 (m-40) REVERT: E 213 CYS cc_start: 0.6986 (m) cc_final: 0.6657 (m) REVERT: E 307 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8004 (tpp80) REVERT: E 314 GLN cc_start: 0.7493 (mp10) cc_final: 0.7239 (mp10) REVERT: E 327 TYR cc_start: 0.8636 (t80) cc_final: 0.8104 (t80) REVERT: E 483 ASN cc_start: 0.7736 (t0) cc_final: 0.7122 (t0) REVERT: E 556 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7107 (mm-30) REVERT: E 584 SER cc_start: 0.7630 (m) cc_final: 0.7282 (t) outliers start: 40 outliers final: 27 residues processed: 441 average time/residue: 1.5602 time to fit residues: 754.3199 Evaluate side-chains 447 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 416 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 364 SER 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 377 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 133 GLN A 216 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 335 ASN B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.094783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085908 restraints weight = 30195.835| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.99 r_work: 0.3135 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17849 Z= 0.295 Angle : 0.667 10.453 24276 Z= 0.340 Chirality : 0.046 0.191 2651 Planarity : 0.005 0.101 3170 Dihedral : 11.038 174.327 2517 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.40 % Allowed : 22.05 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2205 helix: 1.21 (0.17), residues: 922 sheet: 0.29 (0.29), residues: 341 loop : -0.58 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.006 0.001 HIS B 190 PHE 0.025 0.002 PHE E 262 TYR 0.022 0.001 TYR C 161 ARG 0.012 0.001 ARG E 4 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 418 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7986 (ptt90) REVERT: A 50 ASN cc_start: 0.8533 (t0) cc_final: 0.7903 (t0) REVERT: A 76 ASP cc_start: 0.8429 (m-30) cc_final: 0.7791 (m-30) REVERT: A 83 TYR cc_start: 0.8296 (m-80) cc_final: 0.8078 (m-80) REVERT: A 98 ASP cc_start: 0.8173 (p0) cc_final: 0.7894 (p0) REVERT: A 113 GLU cc_start: 0.7533 (mp0) cc_final: 0.7089 (mp0) REVERT: A 123 ARG cc_start: 0.7891 (tpp-160) cc_final: 0.7619 (tpp80) REVERT: A 124 LYS cc_start: 0.8669 (mttt) cc_final: 0.8270 (ttmm) REVERT: A 254 GLU cc_start: 0.8344 (tt0) cc_final: 0.7856 (mm-30) REVERT: A 284 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 304 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8254 (mmtm) REVERT: A 322 ASP cc_start: 0.8279 (t0) cc_final: 0.7821 (t70) REVERT: A 399 TYR cc_start: 0.8862 (t80) cc_final: 0.8393 (t80) REVERT: A 414 GLU cc_start: 0.8342 (mp0) cc_final: 0.7910 (mp0) REVERT: A 415 GLU cc_start: 0.8331 (tt0) cc_final: 0.8030 (tm-30) REVERT: A 423 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 433 GLU cc_start: 0.8169 (tp30) cc_final: 0.7826 (tp30) REVERT: B 22 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8190 (mt-10) REVERT: B 42 LEU cc_start: 0.8666 (mm) cc_final: 0.8443 (mt) REVERT: B 48 ASN cc_start: 0.8774 (p0) cc_final: 0.8429 (p0) REVERT: B 58 LYS cc_start: 0.8169 (tttt) cc_final: 0.7873 (pttt) REVERT: B 88 ASP cc_start: 0.8483 (t0) cc_final: 0.8190 (t0) REVERT: B 122 LYS cc_start: 0.8631 (ttpt) cc_final: 0.8413 (ttpt) REVERT: B 157 GLU cc_start: 0.8649 (tp30) cc_final: 0.8210 (tm-30) REVERT: B 205 GLU cc_start: 0.8357 (tt0) cc_final: 0.7929 (mt-10) REVERT: B 213 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.7541 (mtm-85) REVERT: B 218 THR cc_start: 0.8769 (p) cc_final: 0.8516 (t) REVERT: B 267 MET cc_start: 0.8670 (mtp) cc_final: 0.8439 (mtm) REVERT: B 295 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8270 (t70) REVERT: B 306 ARG cc_start: 0.8601 (mpt-90) cc_final: 0.8335 (mpp80) REVERT: B 340 TYR cc_start: 0.8203 (m-80) cc_final: 0.7876 (m-80) REVERT: B 362 LYS cc_start: 0.8583 (tptp) cc_final: 0.8299 (tptp) REVERT: B 363 MET cc_start: 0.8802 (mtm) cc_final: 0.8561 (mtp) REVERT: B 391 ARG cc_start: 0.8454 (mmm160) cc_final: 0.6482 (ptp-170) REVERT: B 410 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7530 (mm-30) REVERT: B 421 GLU cc_start: 0.8253 (tt0) cc_final: 0.7906 (tm-30) REVERT: C 2 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8112 (mtm180) REVERT: C 47 ASP cc_start: 0.8363 (p0) cc_final: 0.7677 (t0) REVERT: C 50 ASN cc_start: 0.8668 (t0) cc_final: 0.7836 (t0) REVERT: C 77 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8277 (mt-10) REVERT: C 90 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7742 (tm-30) REVERT: C 121 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7156 (tpp80) REVERT: C 123 ARG cc_start: 0.8338 (tpp80) cc_final: 0.8123 (tpp80) REVERT: C 207 GLU cc_start: 0.7764 (tt0) cc_final: 0.7391 (mt-10) REVERT: C 218 ASP cc_start: 0.8329 (m-30) cc_final: 0.7830 (t0) REVERT: C 254 GLU cc_start: 0.4619 (tp30) cc_final: 0.2489 (mm-30) REVERT: C 269 LEU cc_start: 0.8701 (mp) cc_final: 0.8465 (mp) REVERT: C 280 LYS cc_start: 0.9099 (mttp) cc_final: 0.8014 (mmtt) REVERT: C 284 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7883 (mm-30) REVERT: C 290 GLU cc_start: 0.7921 (mp0) cc_final: 0.7693 (mp0) REVERT: C 297 GLU cc_start: 0.8008 (tp30) cc_final: 0.7597 (tp30) REVERT: C 308 ARG cc_start: 0.8460 (mtm180) cc_final: 0.7460 (tmt170) REVERT: C 349 THR cc_start: 0.8237 (p) cc_final: 0.8019 (p) REVERT: C 377 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: C 392 ASP cc_start: 0.7889 (m-30) cc_final: 0.7571 (m-30) REVERT: C 415 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7830 (tp30) REVERT: C 417 GLU cc_start: 0.7816 (mp0) cc_final: 0.7441 (mp0) REVERT: C 420 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 423 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7997 (mm-30) REVERT: D 19 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8217 (mmmt) REVERT: D 45 GLU cc_start: 0.8465 (tt0) cc_final: 0.8102 (tm-30) REVERT: D 121 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8120 (ptp-110) REVERT: D 154 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8665 (mptp) REVERT: D 157 GLU cc_start: 0.8572 (tt0) cc_final: 0.8319 (tm-30) REVERT: D 181 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7967 (mt-10) REVERT: D 203 ASP cc_start: 0.8162 (t0) cc_final: 0.7838 (t70) REVERT: D 213 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8458 (ttm-80) REVERT: D 257 MET cc_start: 0.8238 (mmm) cc_final: 0.7985 (mtp) REVERT: D 289 LEU cc_start: 0.8655 (mt) cc_final: 0.8401 (mp) REVERT: D 304 ASP cc_start: 0.7645 (t70) cc_final: 0.6603 (t0) REVERT: D 306 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7776 (mtm180) REVERT: D 309 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8182 (mtp85) REVERT: D 323 MET cc_start: 0.8401 (mmm) cc_final: 0.8041 (mmm) REVERT: D 325 GLU cc_start: 0.8462 (tp30) cc_final: 0.8145 (tp30) REVERT: D 404 ASP cc_start: 0.8145 (t0) cc_final: 0.7913 (t0) REVERT: D 410 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7692 (mm-30) REVERT: D 414 ASN cc_start: 0.8104 (m110) cc_final: 0.7727 (m-40) REVERT: D 424 GLN cc_start: 0.8337 (pt0) cc_final: 0.8080 (pp30) REVERT: D 425 TYR cc_start: 0.7746 (m-80) cc_final: 0.7515 (m-10) REVERT: E 72 ARG cc_start: 0.8322 (ptt180) cc_final: 0.7963 (ptt-90) REVERT: E 94 ASN cc_start: 0.8334 (t0) cc_final: 0.8012 (t0) REVERT: E 120 GLU cc_start: 0.7968 (tt0) cc_final: 0.7729 (tt0) REVERT: E 165 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7801 (mm110) REVERT: E 169 ASN cc_start: 0.8237 (m-40) cc_final: 0.7988 (m-40) REVERT: E 213 CYS cc_start: 0.7086 (m) cc_final: 0.6778 (m) REVERT: E 220 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6784 (mmt90) REVERT: E 237 PHE cc_start: 0.8007 (m-10) cc_final: 0.7718 (m-10) REVERT: E 307 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8034 (tpp80) REVERT: E 314 GLN cc_start: 0.7697 (mp10) cc_final: 0.7325 (mp10) REVERT: E 483 ASN cc_start: 0.7864 (t0) cc_final: 0.7223 (t0) REVERT: E 556 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7165 (mm-30) REVERT: E 584 SER cc_start: 0.7699 (m) cc_final: 0.7363 (t) outliers start: 44 outliers final: 26 residues processed: 444 average time/residue: 1.5880 time to fit residues: 772.3597 Evaluate side-chains 434 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 404 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 89 optimal weight: 5.9990 chunk 121 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 335 ASN B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.096304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087443 restraints weight = 29984.691| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.99 r_work: 0.3161 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17849 Z= 0.215 Angle : 0.672 12.591 24276 Z= 0.338 Chirality : 0.045 0.220 2651 Planarity : 0.005 0.060 3170 Dihedral : 10.920 179.053 2517 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.80 % Allowed : 23.24 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2205 helix: 1.29 (0.17), residues: 924 sheet: 0.34 (0.29), residues: 339 loop : -0.59 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.014 0.001 HIS B 307 PHE 0.023 0.001 PHE E 262 TYR 0.026 0.001 TYR C 161 ARG 0.013 0.001 ARG E 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4410 Ramachandran restraints generated. 2205 Oldfield, 0 Emsley, 2205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 410 time to evaluate : 1.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8069 (ptt90) REVERT: A 50 ASN cc_start: 0.8513 (t0) cc_final: 0.7882 (t0) REVERT: A 76 ASP cc_start: 0.8402 (m-30) cc_final: 0.7745 (m-30) REVERT: A 98 ASP cc_start: 0.8145 (p0) cc_final: 0.7873 (p0) REVERT: A 113 GLU cc_start: 0.7416 (mp0) cc_final: 0.7191 (mp0) REVERT: A 123 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7609 (tpp80) REVERT: A 124 LYS cc_start: 0.8640 (mttt) cc_final: 0.8263 (ttmm) REVERT: A 254 GLU cc_start: 0.8300 (tt0) cc_final: 0.7816 (mm-30) REVERT: A 284 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7268 (mm-30) REVERT: A 304 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8245 (mmtm) REVERT: A 322 ASP cc_start: 0.8312 (t0) cc_final: 0.7854 (t70) REVERT: A 399 TYR cc_start: 0.8807 (t80) cc_final: 0.8305 (t80) REVERT: A 414 GLU cc_start: 0.8324 (mp0) cc_final: 0.7838 (mp0) REVERT: A 415 GLU cc_start: 0.8312 (tt0) cc_final: 0.8003 (tm-30) REVERT: A 417 GLU cc_start: 0.7195 (tt0) cc_final: 0.6536 (tp30) REVERT: A 423 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8141 (mm-30) REVERT: A 433 GLU cc_start: 0.8154 (tp30) cc_final: 0.7787 (tp30) REVERT: B 22 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8215 (mt-10) REVERT: B 42 LEU cc_start: 0.8670 (mm) cc_final: 0.8445 (mt) REVERT: B 48 ASN cc_start: 0.8769 (p0) cc_final: 0.8422 (p0) REVERT: B 58 LYS cc_start: 0.8286 (tttt) cc_final: 0.7934 (pttt) REVERT: B 73 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7480 (mtm) REVERT: B 88 ASP cc_start: 0.8465 (t0) cc_final: 0.8227 (t70) REVERT: B 103 LYS cc_start: 0.8664 (tttt) cc_final: 0.8276 (ttmm) REVERT: B 157 GLU cc_start: 0.8640 (tp30) cc_final: 0.8178 (tm-30) REVERT: B 179 VAL cc_start: 0.8745 (m) cc_final: 0.8355 (t) REVERT: B 205 GLU cc_start: 0.8351 (tt0) cc_final: 0.7932 (mt-10) REVERT: B 213 ARG cc_start: 0.8457 (ttp-110) cc_final: 0.8157 (ttp80) REVERT: B 267 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: B 306 ARG cc_start: 0.8611 (mpt-90) cc_final: 0.8193 (mpp80) REVERT: B 340 TYR cc_start: 0.8164 (m-80) cc_final: 0.7804 (m-80) REVERT: B 350 LYS cc_start: 0.8849 (tptt) cc_final: 0.8549 (tptm) REVERT: B 362 LYS cc_start: 0.8568 (tptp) cc_final: 0.8228 (tptp) REVERT: B 363 MET cc_start: 0.8757 (mtm) cc_final: 0.8514 (mtp) REVERT: B 391 ARG cc_start: 0.8422 (mmm160) cc_final: 0.6451 (ptp-170) REVERT: B 410 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7551 (mm-30) REVERT: B 421 GLU cc_start: 0.8267 (tt0) cc_final: 0.7760 (tm-30) REVERT: B 424 GLN cc_start: 0.8635 (tt0) cc_final: 0.8192 (pt0) REVERT: C 2 ARG cc_start: 0.8384 (mtm180) cc_final: 0.8077 (mtm180) REVERT: C 47 ASP cc_start: 0.8350 (p0) cc_final: 0.7678 (t0) REVERT: C 50 ASN cc_start: 0.8686 (t0) cc_final: 0.7859 (t0) REVERT: C 71 GLU cc_start: 0.7912 (tt0) cc_final: 0.7623 (pt0) REVERT: C 90 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7706 (tm-30) REVERT: C 121 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7206 (tpp80) REVERT: C 123 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8015 (tpp80) REVERT: C 207 GLU cc_start: 0.7750 (tt0) cc_final: 0.7367 (mt-10) REVERT: C 218 ASP cc_start: 0.8298 (m-30) cc_final: 0.7802 (t0) REVERT: C 254 GLU cc_start: 0.4385 (tp30) cc_final: 0.2386 (mm-30) REVERT: C 280 LYS cc_start: 0.9091 (mttp) cc_final: 0.8019 (mmtt) REVERT: C 284 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7865 (mm-30) REVERT: C 290 GLU cc_start: 0.7947 (mp0) cc_final: 0.7733 (mp0) REVERT: C 297 GLU cc_start: 0.8025 (tp30) cc_final: 0.7620 (tp30) REVERT: C 308 ARG cc_start: 0.8425 (mtm180) cc_final: 0.7333 (tmt-80) REVERT: C 377 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: C 392 ASP cc_start: 0.7865 (m-30) cc_final: 0.7543 (m-30) REVERT: C 415 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7815 (tp30) REVERT: C 417 GLU cc_start: 0.7796 (mp0) cc_final: 0.7430 (mp0) REVERT: C 420 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7489 (mm-30) REVERT: C 423 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7996 (mm-30) REVERT: D 19 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8244 (mmmt) REVERT: D 45 GLU cc_start: 0.8410 (tt0) cc_final: 0.8059 (tm-30) REVERT: D 121 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8127 (ptp-110) REVERT: D 154 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8592 (mptp) REVERT: D 157 GLU cc_start: 0.8544 (tt0) cc_final: 0.8324 (tm-30) REVERT: D 181 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7972 (mt-10) REVERT: D 203 ASP cc_start: 0.8172 (t0) cc_final: 0.7851 (t70) REVERT: D 213 ARG cc_start: 0.8791 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: D 216 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8886 (mmmt) REVERT: D 257 MET cc_start: 0.8207 (mmm) cc_final: 0.7951 (mtp) REVERT: D 289 LEU cc_start: 0.8622 (mt) cc_final: 0.8345 (mp) REVERT: D 304 ASP cc_start: 0.7599 (t70) cc_final: 0.6387 (t0) REVERT: D 306 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7783 (mtm180) REVERT: D 309 ARG cc_start: 0.8448 (mtp85) cc_final: 0.8087 (mtp85) REVERT: D 323 MET cc_start: 0.8333 (mmm) cc_final: 0.7854 (mmm) REVERT: D 325 GLU cc_start: 0.8452 (tp30) cc_final: 0.8154 (tp30) REVERT: D 404 ASP cc_start: 0.8152 (t0) cc_final: 0.7767 (t0) REVERT: D 407 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7692 (mm-30) REVERT: D 410 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7681 (mm-30) REVERT: D 414 ASN cc_start: 0.8047 (m110) cc_final: 0.7684 (m-40) REVERT: D 424 GLN cc_start: 0.8323 (pt0) cc_final: 0.8068 (pp30) REVERT: D 425 TYR cc_start: 0.7708 (m-80) cc_final: 0.7432 (m-80) REVERT: E 72 ARG cc_start: 0.8326 (ptt180) cc_final: 0.7969 (ptt-90) REVERT: E 94 ASN cc_start: 0.8232 (t0) cc_final: 0.7944 (t0) REVERT: E 98 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7165 (mt0) REVERT: E 120 GLU cc_start: 0.7927 (tt0) cc_final: 0.7716 (tt0) REVERT: E 165 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7498 (mm110) REVERT: E 169 ASN cc_start: 0.8178 (m-40) cc_final: 0.7829 (m-40) REVERT: E 213 CYS cc_start: 0.7000 (m) cc_final: 0.6674 (m) REVERT: E 307 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8032 (tpp80) REVERT: E 314 GLN cc_start: 0.7565 (mp10) cc_final: 0.7220 (mp10) REVERT: E 483 ASN cc_start: 0.7842 (t0) cc_final: 0.7203 (t0) REVERT: E 556 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7147 (mm-30) REVERT: E 584 SER cc_start: 0.7638 (m) cc_final: 0.7302 (t) REVERT: E 593 MET cc_start: 0.8378 (tpp) cc_final: 0.8068 (tpp) outliers start: 33 outliers final: 23 residues processed: 428 average time/residue: 1.6061 time to fit residues: 752.5100 Evaluate side-chains 435 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 406 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 151 THR Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 583 HIS Chi-restraints excluded: chain E residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 131 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 339 HIS ** 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 = 0.3417 r_free = 0.3417 target = 0.095455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086591 restraints weight = 29955.178| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.98 r_work: 0.3147 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17849 Z= 0.277 Angle : 0.675 12.337 24276 Z= 0.341 Chirality : 0.046 0.236 2651 Planarity : 0.005 0.126 3170 Dihedral : 10.922 177.525 2517 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.01 % Allowed : 23.14 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2205 helix: 1.24 (0.17), residues: 922 sheet: 0.31 (0.29), residues: 339 loop : -0.62 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.006 0.001 HIS B 190 PHE 0.026 0.002 PHE A 49 TYR 0.032 0.001 TYR E 327 ARG 0.014 0.001 ARG E 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15886.87 seconds wall clock time: 280 minutes 20.27 seconds (16820.27 seconds total)