Starting phenix.real_space_refine on Sun Aug 24 06:06:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v4m_42973/08_2025/8v4m_42973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v4m_42973/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v4m_42973/08_2025/8v4m_42973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v4m_42973/08_2025/8v4m_42973.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v4m_42973/08_2025/8v4m_42973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v4m_42973/08_2025/8v4m_42973.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLU:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'UNK:plan-1': 4, 'GLU:plan': 1} 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: {'ASN:plan1': 2, 'GLU:plan': 14, 'ARG:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 4, 'HIS: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: 4.56, per 1000 atoms: 0.26 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: 1.59 Conformation dependent library (CDL) restraints added in 800.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.53 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: 3.29 Time building geometry restraints manager: 2.04 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 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 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 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: 6.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.760 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.130 ------------------------------------------------------------------------------- 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 17852 Z= 0.322 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 : 2.65 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (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 ARG 0.015 0.001 ARG C 214 TYR 0.048 0.003 TYR A 432 PHE 0.036 0.003 PHE C 255 TRP 0.016 0.003 TRP C 346 HIS 0.010 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00605 (17849) covalent geometry : angle 1.03425 (24276) hydrogen bonds : bond 0.15832 ( 779) hydrogen bonds : angle 7.32642 ( 2259) metal coordination : bond 0.00408 ( 2) Misc. bond : bond 0.04970 ( 1) *********************** 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 : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7249 (p0) cc_final: 0.6787 (p0) REVERT: A 50 ASN cc_start: 0.7862 (t0) cc_final: 0.7222 (t0) REVERT: A 114 ILE cc_start: 0.7936 (pt) cc_final: 0.7718 (pt) REVERT: A 117 LEU cc_start: 0.7393 (tp) cc_final: 0.6587 (tt) 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: 0.7313 (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: 0.8187 (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 22 GLU cc_start: 0.7783 (tt0) cc_final: 0.7578 (tp30) 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: 0.7720 (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: 0.8343 (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: 0.7677 (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: 0.7665 (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: 0.7922 (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: 0.7415 (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: 0.6534 (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: 0.7798 (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: 0.8091 (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: 0.7670 (tm-30) REVERT: D 69 GLU cc_start: 0.7348 (pp20) cc_final: 0.6675 (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: 0.7874 (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: 0.7382 (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: 0.8350 (m) REVERT: D 203 ASP cc_start: 0.7873 (t0) cc_final: 0.7409 (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: 0.7819 (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: 0.7741 (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: 0.7757 (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: 0.7838 (p0) 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: 0.6043 (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: 0.7023 (tt) REVERT: E 294 PRO cc_start: 0.8209 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: E 295 ASP cc_start: 0.7473 (p0) cc_final: 0.5656 (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: 0.7872 (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: 0.7796 time to fit residues: 508.5457 Evaluate side-chains 455 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 256 GLN A 356 ASN B 11 GLN B 190 HIS B 292 GLN B 347 ASN B 416 ASN C 91 GLN C 101 ASN ** 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 535 ASN E 557 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.102693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093779 restraints weight = 30910.029| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.05 r_work: 0.3283 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17852 Z= 0.147 Angle : 0.591 10.523 24276 Z= 0.309 Chirality : 0.045 0.160 2651 Planarity : 0.005 0.062 3170 Dihedral : 10.771 142.734 2517 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.67 % Allowed : 13.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2205 helix: 0.11 (0.16), residues: 912 sheet: 0.11 (0.28), residues: 342 loop : -0.77 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 390 TYR 0.012 0.001 TYR D 340 PHE 0.020 0.002 PHE A 255 TRP 0.013 0.001 TRP D 21 HIS 0.009 0.001 HIS E 339 Details of bonding type rmsd covalent geometry : bond 0.00331 (17849) covalent geometry : angle 0.59097 (24276) hydrogen bonds : bond 0.04306 ( 779) hydrogen bonds : angle 4.89966 ( 2259) metal coordination : bond 0.00341 ( 2) Misc. bond : bond 0.00011 ( 1) *********************** 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 524 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 475 time to evaluate : 0.761 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: A 50 ASN cc_start: 0.8316 (t0) cc_final: 0.7751 (t0) REVERT: A 83 TYR cc_start: 0.8410 (m-80) cc_final: 0.8070 (m-80) REVERT: A 117 LEU cc_start: 0.8155 (tp) cc_final: 0.7813 (tt) REVERT: A 123 ARG cc_start: 0.7898 (tpp-160) cc_final: 0.7532 (tpp80) REVERT: A 124 LYS cc_start: 0.8610 (mttt) cc_final: 0.8230 (ttmm) REVERT: A 254 GLU cc_start: 0.7864 (tt0) cc_final: 0.7272 (mm-30) REVERT: A 280 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8734 (ptmt) REVERT: A 284 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7533 (mm-30) REVERT: A 322 ASP cc_start: 0.8093 (t0) cc_final: 0.7780 (t70) REVERT: A 414 GLU cc_start: 0.8508 (mp0) cc_final: 0.8068 (mp0) REVERT: A 415 GLU cc_start: 0.8206 (tt0) cc_final: 0.7871 (tm-30) REVERT: A 423 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8072 (mm-30) REVERT: A 433 GLU cc_start: 0.8058 (tp30) cc_final: 0.7631 (tp30) REVERT: B 42 LEU cc_start: 0.8681 (mt) cc_final: 0.8117 (mm) REVERT: B 48 ASN cc_start: 0.8752 (p0) cc_final: 0.8282 (p0) REVERT: B 58 LYS cc_start: 0.7738 (tttt) cc_final: 0.7309 (pttt) REVERT: B 88 ASP cc_start: 0.8297 (t0) cc_final: 0.8078 (t0) REVERT: B 103 LYS cc_start: 0.8726 (tttt) cc_final: 0.8292 (mtpp) REVERT: B 121 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7458 (mtt-85) REVERT: B 122 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7997 (ttmm) REVERT: B 147 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8515 (ttt) REVERT: B 158 GLU cc_start: 0.8435 (tp30) cc_final: 0.7959 (tp30) REVERT: B 205 GLU cc_start: 0.8236 (tt0) cc_final: 0.7876 (mt-10) REVERT: B 252 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8618 (ttpt) REVERT: B 257 MET cc_start: 0.8432 (mmm) cc_final: 0.8152 (mmm) REVERT: B 278 SER cc_start: 0.8946 (m) cc_final: 0.8345 (p) REVERT: B 282 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.6826 (ptm-80) REVERT: B 304 ASP cc_start: 0.7043 (t70) cc_final: 0.6696 (t70) REVERT: B 350 LYS cc_start: 0.8888 (tptt) cc_final: 0.8521 (tptm) REVERT: B 362 LYS cc_start: 0.8586 (tptp) cc_final: 0.8256 (tptp) REVERT: B 363 MET cc_start: 0.8405 (mtm) cc_final: 0.7364 (mtm) REVERT: B 364 SER cc_start: 0.8809 (OUTLIER) cc_final: 0.8589 (t) REVERT: B 391 ARG cc_start: 0.7984 (mmm160) cc_final: 0.6444 (mtm180) REVERT: B 404 ASP cc_start: 0.8038 (m-30) cc_final: 0.7611 (m-30) REVERT: B 407 GLU cc_start: 0.7433 (mp0) cc_final: 0.7073 (mp0) REVERT: B 421 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (tt0) REVERT: B 425 TYR cc_start: 0.8732 (m-80) cc_final: 0.8446 (m-80) REVERT: C 36 MET cc_start: 0.8838 (ttp) cc_final: 0.8572 (ttp) REVERT: C 47 ASP cc_start: 0.8492 (p0) cc_final: 0.7859 (t0) REVERT: C 50 ASN cc_start: 0.8659 (t0) cc_final: 0.7896 (t160) REVERT: C 155 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7757 (tp30) REVERT: C 203 MET cc_start: 0.8535 (tpp) cc_final: 0.8243 (mmm) REVERT: C 218 ASP cc_start: 0.8224 (m-30) cc_final: 0.7737 (t0) REVERT: C 284 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7939 (mm-30) REVERT: C 290 GLU cc_start: 0.7963 (mp0) cc_final: 0.7601 (mp0) REVERT: C 308 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7616 (tmm160) REVERT: C 322 ASP cc_start: 0.8312 (t0) cc_final: 0.8095 (t0) REVERT: C 337 THR cc_start: 0.8656 (m) cc_final: 0.8275 (p) REVERT: C 349 THR cc_start: 0.8346 (p) cc_final: 0.8131 (p) REVERT: C 386 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7894 (mp0) REVERT: C 392 ASP cc_start: 0.7917 (m-30) cc_final: 0.7632 (m-30) REVERT: C 423 GLU cc_start: 0.8166 (tp30) cc_final: 0.7713 (mm-30) REVERT: D 19 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8116 (mmmt) REVERT: D 44 LEU cc_start: 0.8566 (tp) cc_final: 0.8320 (tm) REVERT: D 45 GLU cc_start: 0.8169 (tt0) cc_final: 0.7911 (tm-30) REVERT: D 58 LYS cc_start: 0.8682 (tttt) cc_final: 0.8292 (mtpp) REVERT: D 88 ASP cc_start: 0.8172 (t70) cc_final: 0.7823 (t0) REVERT: D 118 ASP cc_start: 0.8033 (m-30) cc_final: 0.7712 (m-30) REVERT: D 121 ARG cc_start: 0.8329 (ttm110) cc_final: 0.7846 (ptp-110) REVERT: D 122 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8353 (ttmm) REVERT: D 203 ASP cc_start: 0.8069 (t0) cc_final: 0.7798 (t0) REVERT: D 233 MET cc_start: 0.8528 (ttm) cc_final: 0.8207 (mtp) REVERT: D 257 MET cc_start: 0.8356 (mmm) cc_final: 0.8021 (mtp) REVERT: D 304 ASP cc_start: 0.7713 (t70) cc_final: 0.6849 (t0) REVERT: D 309 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8123 (mtp85) REVERT: D 324 LYS cc_start: 0.9025 (tptm) cc_final: 0.8780 (tppt) REVERT: D 325 GLU cc_start: 0.8435 (tp30) cc_final: 0.7990 (tp30) REVERT: D 329 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7077 (mm-40) REVERT: D 376 GLU cc_start: 0.7725 (mp0) cc_final: 0.7069 (mp0) REVERT: D 383 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 391 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7292 (mtm180) REVERT: D 407 GLU cc_start: 0.8049 (mp0) cc_final: 0.7683 (mp0) REVERT: D 410 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7866 (mm-30) REVERT: E 11 SER cc_start: 0.8540 (t) cc_final: 0.8301 (p) REVERT: E 15 ASP cc_start: 0.8250 (t0) cc_final: 0.8021 (t0) REVERT: E 94 ASN cc_start: 0.7698 (t0) cc_final: 0.6897 (t0) REVERT: E 120 GLU cc_start: 0.8110 (tt0) cc_final: 0.7896 (tt0) REVERT: E 169 ASN cc_start: 0.7424 (m-40) cc_final: 0.7047 (m-40) REVERT: E 206 ASP cc_start: 0.8515 (p0) cc_final: 0.8304 (p0) REVERT: E 314 GLN cc_start: 0.7261 (mp10) cc_final: 0.6963 (mp10) REVERT: E 327 TYR cc_start: 0.7944 (t80) cc_final: 0.7306 (t80) REVERT: E 444 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7298 (mtp) REVERT: E 456 VAL cc_start: 0.9052 (t) cc_final: 0.8814 (p) REVERT: E 590 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8006 (ttm170) outliers start: 49 outliers final: 12 residues processed: 492 average time/residue: 0.7775 time to fit residues: 419.3535 Evaluate side-chains 436 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 419 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain B residue 147 MET 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 444 MET 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 32 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 181 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 256 GLN B 256 ASN B 292 GLN B 334 GLN B 347 ASN B 416 ASN ** 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.087728 restraints weight = 30642.046| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.04 r_work: 0.3169 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 17852 Z= 0.202 Angle : 0.621 9.417 24276 Z= 0.322 Chirality : 0.047 0.194 2651 Planarity : 0.005 0.054 3170 Dihedral : 10.903 165.231 2517 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.05 % Allowed : 16.22 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2205 helix: 0.86 (0.17), residues: 905 sheet: 0.33 (0.30), residues: 330 loop : -0.73 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 282 TYR 0.033 0.002 TYR E 191 PHE 0.026 0.002 PHE E 262 TRP 0.012 0.002 TRP D 21 HIS 0.008 0.001 HIS B 307 Details of bonding type rmsd covalent geometry : bond 0.00457 (17849) covalent geometry : angle 0.62123 (24276) hydrogen bonds : bond 0.04610 ( 779) hydrogen bonds : angle 4.71814 ( 2259) metal coordination : bond 0.00592 ( 2) Misc. bond : bond 0.00093 ( 1) *********************** 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 511 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 455 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8380 (t0) cc_final: 0.7708 (t0) REVERT: A 76 ASP cc_start: 0.8376 (m-30) cc_final: 0.7677 (m-30) REVERT: A 117 LEU cc_start: 0.8374 (tp) cc_final: 0.8069 (tt) REVERT: A 123 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7649 (tpp80) REVERT: A 124 LYS cc_start: 0.8592 (mttt) cc_final: 0.8230 (ttmm) REVERT: A 203 MET cc_start: 0.8384 (tpp) cc_final: 0.8112 (mmm) REVERT: A 230 LEU cc_start: 0.8768 (mp) cc_final: 0.8563 (mm) REVERT: A 254 GLU cc_start: 0.8124 (tt0) cc_final: 0.7666 (mm-30) REVERT: A 255 PHE cc_start: 0.8550 (p90) cc_final: 0.8304 (p90) REVERT: A 297 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7407 (tp30) REVERT: A 322 ASP cc_start: 0.8246 (t0) cc_final: 0.7816 (t70) REVERT: A 413 MET cc_start: 0.8559 (ttm) cc_final: 0.7552 (ttp) REVERT: A 414 GLU cc_start: 0.8480 (mp0) cc_final: 0.7762 (mp0) REVERT: A 415 GLU cc_start: 0.8223 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 417 GLU cc_start: 0.7409 (tt0) cc_final: 0.7136 (pp20) REVERT: A 420 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7731 (mt-10) REVERT: A 423 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8152 (mm-30) REVERT: A 433 GLU cc_start: 0.8356 (tp30) cc_final: 0.7899 (tp30) REVERT: B 19 LYS cc_start: 0.8589 (tptm) cc_final: 0.8350 (tptt) REVERT: B 42 LEU cc_start: 0.8692 (mt) cc_final: 0.8189 (mm) REVERT: B 48 ASN cc_start: 0.8748 (p0) cc_final: 0.8370 (p0) REVERT: B 58 LYS cc_start: 0.8149 (tttt) cc_final: 0.7825 (pttt) REVERT: B 88 ASP cc_start: 0.8329 (t0) cc_final: 0.8003 (t0) REVERT: B 103 LYS cc_start: 0.8924 (tttt) cc_final: 0.8447 (mtpp) REVERT: B 122 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8268 (ttpt) REVERT: B 157 GLU cc_start: 0.8541 (tp30) cc_final: 0.8073 (tm-30) REVERT: B 161 ASP cc_start: 0.8899 (p0) cc_final: 0.8686 (p0) REVERT: B 205 GLU cc_start: 0.8355 (tt0) cc_final: 0.8019 (mt-10) REVERT: B 209 ASP cc_start: 0.8283 (t0) cc_final: 0.8016 (t0) REVERT: B 213 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.7824 (mtm-85) REVERT: B 267 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8483 (mtm) REVERT: B 278 SER cc_start: 0.8964 (m) cc_final: 0.8408 (p) REVERT: B 334 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: B 350 LYS cc_start: 0.8895 (tptt) cc_final: 0.8608 (tptm) REVERT: B 362 LYS cc_start: 0.8570 (tptp) cc_final: 0.8123 (tptp) REVERT: B 363 MET cc_start: 0.8632 (mtm) cc_final: 0.7836 (mtp) REVERT: B 380 ARG cc_start: 0.8313 (ptp90) cc_final: 0.8111 (ptp-170) REVERT: B 391 ARG cc_start: 0.8206 (mmm160) cc_final: 0.6553 (mtm180) REVERT: B 403 MET cc_start: 0.8338 (mtp) cc_final: 0.8102 (mtm) REVERT: B 421 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: B 425 TYR cc_start: 0.8804 (m-80) cc_final: 0.8564 (m-80) REVERT: C 47 ASP cc_start: 0.8487 (p0) cc_final: 0.7867 (t0) REVERT: C 50 ASN cc_start: 0.8726 (t0) cc_final: 0.7783 (t0) REVERT: C 71 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: C 77 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7820 (mt-10) REVERT: C 203 MET cc_start: 0.8631 (tpp) cc_final: 0.8402 (mmm) REVERT: C 207 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7237 (mt-10) REVERT: C 218 ASP cc_start: 0.8269 (m-30) cc_final: 0.7788 (t0) REVERT: C 221 ARG cc_start: 0.8296 (pmm-80) cc_final: 0.8056 (pmm-80) REVERT: C 284 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 290 GLU cc_start: 0.7996 (mp0) cc_final: 0.7510 (mp0) REVERT: C 308 ARG cc_start: 0.8309 (mtm180) cc_final: 0.7448 (tmt-80) REVERT: C 322 ASP cc_start: 0.8432 (t0) cc_final: 0.8109 (t0) REVERT: C 337 THR cc_start: 0.8814 (m) cc_final: 0.8421 (p) REVERT: C 377 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: C 392 ASP cc_start: 0.8100 (m-30) cc_final: 0.7815 (m-30) REVERT: C 417 GLU cc_start: 0.7690 (mp0) cc_final: 0.7436 (mp0) REVERT: C 420 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7411 (mm-30) REVERT: C 423 GLU cc_start: 0.8307 (tp30) cc_final: 0.7860 (mm-30) REVERT: C 433 GLU cc_start: 0.7812 (tp30) cc_final: 0.7374 (tp30) REVERT: D 19 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8145 (tppt) REVERT: D 45 GLU cc_start: 0.8374 (tt0) cc_final: 0.8069 (tm-30) REVERT: D 57 ASN cc_start: 0.8406 (m-40) cc_final: 0.8172 (m-40) REVERT: D 88 ASP cc_start: 0.8337 (t70) cc_final: 0.7956 (t0) REVERT: D 118 ASP cc_start: 0.8153 (m-30) cc_final: 0.7770 (m-30) REVERT: D 121 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7969 (ptp-110) REVERT: D 122 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8564 (ttmm) REVERT: D 154 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8685 (mptp) REVERT: D 203 ASP cc_start: 0.8215 (t0) cc_final: 0.7907 (t70) REVERT: D 233 MET cc_start: 0.8903 (ttm) cc_final: 0.8683 (mtp) REVERT: D 257 MET cc_start: 0.8321 (mmm) cc_final: 0.8104 (mtp) REVERT: D 304 ASP cc_start: 0.7969 (t70) cc_final: 0.7252 (t0) REVERT: D 306 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7819 (mtm180) REVERT: D 309 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8155 (mtp85) REVERT: D 324 LYS cc_start: 0.9089 (tptm) cc_final: 0.8827 (tppt) REVERT: D 325 GLU cc_start: 0.8459 (tp30) cc_final: 0.8044 (tp30) REVERT: D 377 LEU cc_start: 0.8595 (mt) cc_final: 0.8299 (mp) REVERT: D 391 ARG cc_start: 0.8322 (mmm160) cc_final: 0.7581 (mtm180) REVERT: D 404 ASP cc_start: 0.8116 (t70) cc_final: 0.7796 (t0) REVERT: D 407 GLU cc_start: 0.7914 (mp0) cc_final: 0.7529 (mp0) REVERT: D 410 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7740 (mm-30) REVERT: E 9 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7581 (mt) REVERT: E 15 ASP cc_start: 0.8419 (t0) cc_final: 0.8055 (t0) REVERT: E 67 PHE cc_start: 0.8434 (m-10) cc_final: 0.8187 (m-10) REVERT: E 94 ASN cc_start: 0.8140 (t0) cc_final: 0.7686 (t0) REVERT: E 120 GLU cc_start: 0.8044 (tt0) cc_final: 0.7831 (tt0) REVERT: E 169 ASN cc_start: 0.7877 (m-40) cc_final: 0.7536 (m-40) REVERT: E 206 ASP cc_start: 0.8564 (p0) cc_final: 0.8318 (p0) REVERT: E 221 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6499 (mm-30) REVERT: E 244 ILE cc_start: 0.8266 (mp) cc_final: 0.8065 (tt) REVERT: E 314 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: E 327 TYR cc_start: 0.8326 (t80) cc_final: 0.7802 (t80) REVERT: E 483 ASN cc_start: 0.7529 (t0) cc_final: 0.6906 (t0) REVERT: E 584 SER cc_start: 0.7608 (m) cc_final: 0.7367 (t) outliers start: 56 outliers final: 17 residues processed: 478 average time/residue: 0.7569 time to fit residues: 397.5181 Evaluate side-chains 438 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 412 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 136 THR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 334 GLN 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 207 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 D residue 154 LYS 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 191 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 197 optimal weight: 0.0870 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** 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 E 104 GLN E 588 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087791 restraints weight = 30500.776| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.03 r_work: 0.3170 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17852 Z= 0.149 Angle : 0.585 9.837 24276 Z= 0.299 Chirality : 0.045 0.161 2651 Planarity : 0.005 0.074 3170 Dihedral : 10.810 171.316 2517 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.72 % Allowed : 17.53 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.18), residues: 2205 helix: 1.16 (0.17), residues: 912 sheet: 0.22 (0.29), residues: 341 loop : -0.68 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 523 TYR 0.019 0.001 TYR E 52 PHE 0.018 0.001 PHE C 49 TRP 0.013 0.001 TRP D 21 HIS 0.009 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00342 (17849) covalent geometry : angle 0.58549 (24276) hydrogen bonds : bond 0.04012 ( 779) hydrogen bonds : angle 4.52799 ( 2259) metal coordination : bond 0.00370 ( 2) Misc. bond : bond 0.00069 ( 1) *********************** 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 482 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 432 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8404 (t0) cc_final: 0.7784 (t0) REVERT: A 83 TYR cc_start: 0.8341 (m-80) cc_final: 0.8087 (m-80) REVERT: A 117 LEU cc_start: 0.8389 (tp) cc_final: 0.8119 (tt) REVERT: A 123 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7612 (tpp80) REVERT: A 124 LYS cc_start: 0.8584 (mttt) cc_final: 0.8236 (ttmm) REVERT: A 203 MET cc_start: 0.8376 (tpp) cc_final: 0.8088 (mmm) REVERT: A 252 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7789 (mt) REVERT: A 254 GLU cc_start: 0.8182 (tt0) cc_final: 0.7726 (mm-30) REVERT: A 255 PHE cc_start: 0.8514 (p90) cc_final: 0.8302 (p90) REVERT: A 284 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 297 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7481 (tp30) REVERT: A 322 ASP cc_start: 0.8222 (t0) cc_final: 0.7818 (t70) REVERT: A 358 GLN cc_start: 0.9140 (tp40) cc_final: 0.8908 (mm-40) REVERT: A 414 GLU cc_start: 0.8470 (mp0) cc_final: 0.8038 (mp0) REVERT: A 415 GLU cc_start: 0.8221 (tt0) cc_final: 0.7967 (tm-30) REVERT: A 423 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8130 (mm-30) REVERT: A 433 GLU cc_start: 0.8351 (tp30) cc_final: 0.7818 (tp30) REVERT: B 19 LYS cc_start: 0.8597 (tptm) cc_final: 0.8333 (tptt) REVERT: B 41 ASP cc_start: 0.8498 (m-30) cc_final: 0.8261 (t70) REVERT: B 45 GLU cc_start: 0.7604 (pm20) cc_final: 0.7284 (pm20) REVERT: B 48 ASN cc_start: 0.8751 (p0) cc_final: 0.8390 (p0) REVERT: B 58 LYS cc_start: 0.8178 (tttt) cc_final: 0.7856 (pttt) REVERT: B 88 ASP cc_start: 0.8319 (t0) cc_final: 0.8058 (t70) REVERT: B 103 LYS cc_start: 0.8938 (tttt) cc_final: 0.8529 (tttt) REVERT: B 122 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8303 (ttpt) REVERT: B 154 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8555 (mttm) REVERT: B 157 GLU cc_start: 0.8571 (tp30) cc_final: 0.8095 (tm-30) REVERT: B 158 GLU cc_start: 0.8554 (tp30) cc_final: 0.8212 (tt0) REVERT: B 205 GLU cc_start: 0.8368 (tt0) cc_final: 0.8000 (mt-10) REVERT: B 209 ASP cc_start: 0.8284 (t0) cc_final: 0.8079 (t0) REVERT: B 278 SER cc_start: 0.8928 (m) cc_final: 0.8697 (m) REVERT: B 282 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7493 (ptm160) REVERT: B 350 LYS cc_start: 0.8878 (tptt) cc_final: 0.8593 (tptm) REVERT: B 362 LYS cc_start: 0.8551 (tptp) cc_final: 0.8133 (tptp) REVERT: B 363 MET cc_start: 0.8637 (mtm) cc_final: 0.8036 (mtp) REVERT: B 379 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8394 (mtpm) REVERT: B 391 ARG cc_start: 0.8242 (mmm160) cc_final: 0.6596 (mtm180) REVERT: B 410 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7518 (mm-30) REVERT: B 421 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: C 47 ASP cc_start: 0.8497 (p0) cc_final: 0.7883 (t0) REVERT: C 50 ASN cc_start: 0.8678 (t0) cc_final: 0.7787 (t0) REVERT: C 76 ASP cc_start: 0.8454 (m-30) cc_final: 0.8083 (m-30) REVERT: C 77 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7681 (mp0) REVERT: C 90 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7986 (mm-30) REVERT: C 203 MET cc_start: 0.8646 (tpp) cc_final: 0.7975 (mmm) REVERT: C 207 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7163 (mt-10) REVERT: C 218 ASP cc_start: 0.8330 (m-30) cc_final: 0.7831 (t0) REVERT: C 221 ARG cc_start: 0.8344 (pmm-80) cc_final: 0.8095 (pmm-80) REVERT: C 284 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7949 (mm-30) REVERT: C 290 GLU cc_start: 0.7986 (mp0) cc_final: 0.7770 (mp0) REVERT: C 297 GLU cc_start: 0.7774 (tp30) cc_final: 0.7546 (tp30) REVERT: C 308 ARG cc_start: 0.8347 (mtm180) cc_final: 0.7337 (tmt-80) REVERT: C 337 THR cc_start: 0.8784 (m) cc_final: 0.8395 (p) REVERT: C 377 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8295 (tpp) REVERT: C 392 ASP cc_start: 0.8118 (m-30) cc_final: 0.7817 (m-30) REVERT: C 415 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7518 (tp30) REVERT: C 417 GLU cc_start: 0.7731 (mp0) cc_final: 0.7476 (mp0) REVERT: C 420 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 433 GLU cc_start: 0.7870 (tp30) cc_final: 0.7505 (tp30) REVERT: D 19 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8181 (tppt) REVERT: D 45 GLU cc_start: 0.8345 (tt0) cc_final: 0.8044 (tm-30) REVERT: D 57 ASN cc_start: 0.8568 (m-40) cc_final: 0.8368 (m-40) REVERT: D 118 ASP cc_start: 0.8118 (m-30) cc_final: 0.7687 (m-30) REVERT: D 121 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8005 (ptp-110) REVERT: D 122 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8569 (ttmm) REVERT: D 128 ASP cc_start: 0.8806 (t0) cc_final: 0.8414 (t0) REVERT: D 203 ASP cc_start: 0.8232 (t0) cc_final: 0.7915 (t70) REVERT: D 213 ARG cc_start: 0.8576 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: D 233 MET cc_start: 0.8941 (ttm) cc_final: 0.8736 (mtp) REVERT: D 257 MET cc_start: 0.8309 (mmm) cc_final: 0.8038 (mtp) REVERT: D 304 ASP cc_start: 0.8080 (t70) cc_final: 0.7096 (t0) REVERT: D 306 ARG cc_start: 0.8214 (mtm180) cc_final: 0.7763 (mtm180) REVERT: D 309 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8200 (mtp85) REVERT: D 324 LYS cc_start: 0.9097 (tptm) cc_final: 0.8838 (tppt) REVERT: D 325 GLU cc_start: 0.8427 (tp30) cc_final: 0.8009 (tp30) REVERT: D 391 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7400 (mtm110) REVERT: D 404 ASP cc_start: 0.8042 (t70) cc_final: 0.7692 (t0) REVERT: D 407 GLU cc_start: 0.7889 (mp0) cc_final: 0.7507 (mp0) REVERT: D 410 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7661 (mm-30) REVERT: D 414 ASN cc_start: 0.8062 (m110) cc_final: 0.7720 (m-40) REVERT: D 425 TYR cc_start: 0.7628 (m-10) cc_final: 0.7409 (m-10) REVERT: E 15 ASP cc_start: 0.8490 (t0) cc_final: 0.8149 (t0) REVERT: E 53 GLU cc_start: 0.7151 (tp30) cc_final: 0.6766 (tm-30) REVERT: E 67 PHE cc_start: 0.8377 (m-10) cc_final: 0.7800 (m-10) REVERT: E 94 ASN cc_start: 0.8217 (t0) cc_final: 0.7818 (t0) REVERT: E 120 GLU cc_start: 0.7936 (tt0) cc_final: 0.7728 (tt0) REVERT: E 156 CYS cc_start: 0.8405 (t) cc_final: 0.8205 (t) REVERT: E 169 ASN cc_start: 0.7971 (m-40) cc_final: 0.7742 (m-40) REVERT: E 206 ASP cc_start: 0.8563 (p0) cc_final: 0.8341 (p0) REVERT: E 307 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7471 (mmm-85) REVERT: E 314 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: E 327 TYR cc_start: 0.8396 (t80) cc_final: 0.7888 (t80) REVERT: E 452 GLU cc_start: 0.8092 (pt0) cc_final: 0.7384 (pt0) REVERT: E 483 ASN cc_start: 0.7469 (t0) cc_final: 0.6970 (t0) REVERT: E 556 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6929 (mm-30) REVERT: E 584 SER cc_start: 0.7561 (m) cc_final: 0.7282 (t) outliers start: 50 outliers final: 22 residues processed: 458 average time/residue: 0.7171 time to fit residues: 361.0773 Evaluate side-chains 441 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 412 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 218 ASP 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 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 207 GLU Chi-restraints excluded: chain C residue 377 MET 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 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 82 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 266 HIS B 298 ASN B 334 GLN B 347 ASN B 348 ASN B 416 ASN C 28 HIS C 356 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 416 ASN E 599 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085149 restraints weight = 30116.721| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.00 r_work: 0.3122 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17852 Z= 0.226 Angle : 0.650 12.286 24276 Z= 0.330 Chirality : 0.047 0.199 2651 Planarity : 0.005 0.065 3170 Dihedral : 11.144 179.039 2517 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.86 % Allowed : 17.75 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.18), residues: 2205 helix: 1.11 (0.17), residues: 915 sheet: 0.23 (0.29), residues: 341 loop : -0.66 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 598 TYR 0.019 0.002 TYR B 340 PHE 0.019 0.002 PHE B 367 TRP 0.012 0.002 TRP B 21 HIS 0.007 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00517 (17849) covalent geometry : angle 0.64976 (24276) hydrogen bonds : bond 0.04549 ( 779) hydrogen bonds : angle 4.57047 ( 2259) metal coordination : bond 0.00548 ( 2) Misc. bond : bond 0.00106 ( 1) *********************** 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 507 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 436 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7838 (t70) cc_final: 0.7310 (t0) REVERT: A 50 ASN cc_start: 0.8467 (t0) cc_final: 0.7773 (t0) REVERT: A 83 TYR cc_start: 0.8372 (m-80) cc_final: 0.8072 (m-80) REVERT: A 113 GLU cc_start: 0.7462 (mp0) cc_final: 0.7073 (mp0) REVERT: A 117 LEU cc_start: 0.8448 (tp) cc_final: 0.8157 (tt) REVERT: A 123 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7653 (tpp80) REVERT: A 124 LYS cc_start: 0.8641 (mttt) cc_final: 0.8272 (ttmm) REVERT: A 254 GLU cc_start: 0.8356 (tt0) cc_final: 0.7892 (mm-30) REVERT: A 284 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7099 (mm-30) REVERT: A 322 ASP cc_start: 0.8283 (t0) cc_final: 0.7834 (t70) REVERT: A 326 LYS cc_start: 0.5561 (tppt) cc_final: 0.4272 (mmmm) REVERT: A 414 GLU cc_start: 0.8438 (mp0) cc_final: 0.7723 (mp0) REVERT: A 415 GLU cc_start: 0.8204 (tt0) cc_final: 0.7952 (tm-30) REVERT: A 423 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 433 GLU cc_start: 0.8230 (tp30) cc_final: 0.7767 (tp30) REVERT: B 19 LYS cc_start: 0.8583 (tptm) cc_final: 0.8377 (tptt) REVERT: B 22 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 48 ASN cc_start: 0.8806 (p0) cc_final: 0.8450 (p0) REVERT: B 58 LYS cc_start: 0.8255 (tttt) cc_final: 0.8014 (pttt) REVERT: B 88 ASP cc_start: 0.8322 (t0) cc_final: 0.7991 (t0) REVERT: B 103 LYS cc_start: 0.8862 (tttt) cc_final: 0.7895 (mtpm) REVERT: B 122 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8379 (ttpt) REVERT: B 154 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8571 (mttm) REVERT: B 157 GLU cc_start: 0.8609 (tp30) cc_final: 0.8219 (tm-30) REVERT: B 158 GLU cc_start: 0.8628 (tp30) cc_final: 0.8389 (tp30) REVERT: B 205 GLU cc_start: 0.8506 (tt0) cc_final: 0.8092 (mt-10) REVERT: B 213 ARG cc_start: 0.8497 (ttp80) cc_final: 0.8171 (ttp-110) REVERT: B 218 THR cc_start: 0.8719 (p) cc_final: 0.8472 (t) REVERT: B 267 MET cc_start: 0.8657 (mtp) cc_final: 0.8448 (mtm) REVERT: B 327 ASP cc_start: 0.7860 (m-30) cc_final: 0.7658 (m-30) REVERT: B 340 TYR cc_start: 0.8134 (m-80) cc_final: 0.7687 (m-80) REVERT: B 350 LYS cc_start: 0.8879 (tptt) cc_final: 0.8550 (tptm) REVERT: B 363 MET cc_start: 0.8721 (mtm) cc_final: 0.8497 (mtp) REVERT: B 380 ARG cc_start: 0.8382 (ptp90) cc_final: 0.8135 (ptp90) REVERT: B 391 ARG cc_start: 0.8375 (mmm160) cc_final: 0.6445 (ptp-170) REVERT: B 410 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 421 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: C 47 ASP cc_start: 0.8440 (p0) cc_final: 0.7728 (t0) REVERT: C 50 ASN cc_start: 0.8682 (t0) cc_final: 0.7831 (t0) REVERT: C 76 ASP cc_start: 0.8457 (m-30) cc_final: 0.8077 (m-30) REVERT: C 77 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 84 ARG cc_start: 0.8661 (ptp90) cc_final: 0.8461 (ptp90) REVERT: C 90 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 123 ARG cc_start: 0.8251 (tpp80) cc_final: 0.8032 (tpp80) REVERT: C 158 SER cc_start: 0.8859 (t) cc_final: 0.8595 (t) REVERT: C 203 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8058 (mmm) REVERT: C 207 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7313 (mt-10) REVERT: C 218 ASP cc_start: 0.8335 (m-30) cc_final: 0.7851 (t0) REVERT: C 284 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7971 (mm-30) REVERT: C 290 GLU cc_start: 0.7992 (mp0) cc_final: 0.7724 (mp0) REVERT: C 308 ARG cc_start: 0.8458 (mtm180) cc_final: 0.7356 (tmt-80) REVERT: C 377 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8035 (tmm) REVERT: C 392 ASP cc_start: 0.8090 (m-30) cc_final: 0.7797 (m-30) REVERT: C 415 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7762 (tp30) REVERT: C 417 GLU cc_start: 0.7860 (mp0) cc_final: 0.7500 (mp0) REVERT: C 420 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7744 (mm-30) REVERT: C 433 GLU cc_start: 0.8032 (tp30) cc_final: 0.7731 (tp30) REVERT: D 19 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8157 (tppt) REVERT: D 45 GLU cc_start: 0.8474 (tt0) cc_final: 0.8123 (tm-30) REVERT: D 121 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8071 (ptp-110) REVERT: D 122 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8685 (ttmm) REVERT: D 128 ASP cc_start: 0.8667 (t0) cc_final: 0.8332 (t0) REVERT: D 203 ASP cc_start: 0.8203 (t0) cc_final: 0.7912 (t70) REVERT: D 209 ASP cc_start: 0.8474 (t0) cc_final: 0.8230 (t0) REVERT: D 257 MET cc_start: 0.8337 (mmm) cc_final: 0.8070 (mtp) REVERT: D 304 ASP cc_start: 0.7532 (t70) cc_final: 0.6585 (t0) REVERT: D 306 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7780 (mtm180) REVERT: D 309 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8269 (mtp85) REVERT: D 324 LYS cc_start: 0.9133 (tptm) cc_final: 0.8855 (tppt) REVERT: D 325 GLU cc_start: 0.8544 (tp30) cc_final: 0.8192 (tp30) REVERT: D 391 ARG cc_start: 0.8660 (mmm160) cc_final: 0.7428 (mtm110) REVERT: D 404 ASP cc_start: 0.7984 (t70) cc_final: 0.7626 (t0) REVERT: D 407 GLU cc_start: 0.7889 (mp0) cc_final: 0.7466 (mp0) REVERT: D 410 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7691 (mm-30) REVERT: D 414 ASN cc_start: 0.8141 (m110) cc_final: 0.7758 (m-40) REVERT: D 425 TYR cc_start: 0.7698 (m-10) cc_final: 0.7469 (m-10) REVERT: E 15 ASP cc_start: 0.8526 (t0) cc_final: 0.8209 (t0) REVERT: E 67 PHE cc_start: 0.8442 (m-10) cc_final: 0.7507 (m-10) REVERT: E 94 ASN cc_start: 0.8378 (t0) cc_final: 0.7967 (t0) REVERT: E 120 GLU cc_start: 0.7908 (tt0) cc_final: 0.7688 (tt0) REVERT: E 134 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7616 (mp-120) REVERT: E 165 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7542 (mm110) REVERT: E 169 ASN cc_start: 0.8082 (m-40) cc_final: 0.7759 (m-40) REVERT: E 206 ASP cc_start: 0.8534 (p0) cc_final: 0.8272 (p0) REVERT: E 213 CYS cc_start: 0.7346 (m) cc_final: 0.7078 (m) REVERT: E 305 ASP cc_start: 0.8166 (t0) cc_final: 0.7843 (t0) REVERT: E 307 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7480 (mmm160) REVERT: E 314 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: E 327 TYR cc_start: 0.8528 (t80) cc_final: 0.8037 (t80) REVERT: E 483 ASN cc_start: 0.7651 (t0) cc_final: 0.7163 (t0) REVERT: E 556 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7208 (mm-30) REVERT: E 584 SER cc_start: 0.7709 (m) cc_final: 0.7427 (t) outliers start: 71 outliers final: 30 residues processed: 478 average time/residue: 0.7278 time to fit residues: 381.5538 Evaluate side-chains 453 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 418 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS 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 364 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 421 GLU Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 203 MET 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 395 LEU 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 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 503 ILE 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 42 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 329 GLN B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 599 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.095149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.086194 restraints weight = 29816.742| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.00 r_work: 0.3140 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17852 Z= 0.157 Angle : 0.625 11.943 24276 Z= 0.316 Chirality : 0.046 0.210 2651 Planarity : 0.005 0.062 3170 Dihedral : 11.075 177.419 2517 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.27 % Allowed : 19.22 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.18), residues: 2205 helix: 1.18 (0.17), residues: 923 sheet: 0.24 (0.29), residues: 339 loop : -0.67 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 598 TYR 0.025 0.001 TYR A 161 PHE 0.017 0.001 PHE A 418 TRP 0.013 0.001 TRP B 21 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00364 (17849) covalent geometry : angle 0.62502 (24276) hydrogen bonds : bond 0.04008 ( 779) hydrogen bonds : angle 4.49054 ( 2259) metal coordination : bond 0.00363 ( 2) Misc. bond : bond 0.00071 ( 1) *********************** 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 490 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7842 (t70) cc_final: 0.7283 (t0) REVERT: A 50 ASN cc_start: 0.8486 (t0) cc_final: 0.7855 (t0) REVERT: A 76 ASP cc_start: 0.8445 (m-30) cc_final: 0.7764 (m-30) REVERT: A 83 TYR cc_start: 0.8360 (m-80) cc_final: 0.8067 (m-80) REVERT: A 113 GLU cc_start: 0.7480 (mp0) cc_final: 0.7102 (mp0) REVERT: A 117 LEU cc_start: 0.8419 (tp) cc_final: 0.8140 (tt) REVERT: A 123 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.7653 (tpp80) REVERT: A 124 LYS cc_start: 0.8664 (mttt) cc_final: 0.8284 (ttmm) REVERT: A 254 GLU cc_start: 0.8349 (tt0) cc_final: 0.7879 (mm-30) REVERT: A 284 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7099 (mm-30) REVERT: A 322 ASP cc_start: 0.8296 (t0) cc_final: 0.7853 (t70) REVERT: A 358 GLN cc_start: 0.9115 (tp40) cc_final: 0.8899 (mm-40) REVERT: A 399 TYR cc_start: 0.8783 (t80) cc_final: 0.8359 (t80) REVERT: A 414 GLU cc_start: 0.8073 (mp0) cc_final: 0.7610 (mp0) REVERT: A 415 GLU cc_start: 0.8101 (tt0) cc_final: 0.7889 (tm-30) REVERT: A 423 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 433 GLU cc_start: 0.8258 (tp30) cc_final: 0.7795 (tp30) REVERT: B 19 LYS cc_start: 0.8554 (tptm) cc_final: 0.8350 (tptt) REVERT: B 42 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 48 ASN cc_start: 0.8751 (p0) cc_final: 0.8397 (p0) REVERT: B 53 GLU cc_start: 0.7964 (tt0) cc_final: 0.7704 (mm-30) REVERT: B 58 LYS cc_start: 0.8226 (tttt) cc_final: 0.7978 (pttt) REVERT: B 88 ASP cc_start: 0.8329 (t0) cc_final: 0.8118 (t70) REVERT: B 122 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8262 (ttmm) REVERT: B 154 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8510 (mttm) REVERT: B 157 GLU cc_start: 0.8559 (tp30) cc_final: 0.8148 (tm-30) REVERT: B 158 GLU cc_start: 0.8540 (tp30) cc_final: 0.8299 (tp30) REVERT: B 205 GLU cc_start: 0.8460 (tt0) cc_final: 0.8057 (mt-10) REVERT: B 213 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8115 (ttp80) REVERT: B 218 THR cc_start: 0.8762 (p) cc_final: 0.8506 (t) REVERT: B 267 MET cc_start: 0.8658 (mtp) cc_final: 0.8447 (mtm) REVERT: B 295 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8194 (t0) REVERT: B 306 ARG cc_start: 0.8532 (mpt-90) cc_final: 0.8139 (mpp80) REVERT: B 324 LYS cc_start: 0.8863 (tptp) cc_final: 0.8634 (tppt) REVERT: B 340 TYR cc_start: 0.8131 (m-80) cc_final: 0.7630 (m-80) REVERT: B 363 MET cc_start: 0.8697 (mtm) cc_final: 0.8431 (mtp) REVERT: B 380 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7983 (ptp90) REVERT: B 391 ARG cc_start: 0.8378 (mmm160) cc_final: 0.6441 (ptp-170) REVERT: B 410 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7538 (mm-30) REVERT: B 421 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (tt0) REVERT: C 47 ASP cc_start: 0.8391 (p0) cc_final: 0.7730 (t0) REVERT: C 50 ASN cc_start: 0.8661 (t0) cc_final: 0.7815 (t0) REVERT: C 76 ASP cc_start: 0.8465 (m-30) cc_final: 0.8062 (m-30) REVERT: C 77 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7700 (mt-10) REVERT: C 90 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7689 (tm-30) REVERT: C 120 ASP cc_start: 0.8177 (m-30) cc_final: 0.7958 (m-30) REVERT: C 121 ARG cc_start: 0.7626 (tpp80) cc_final: 0.7249 (tpp-160) REVERT: C 203 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: C 207 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: C 218 ASP cc_start: 0.8363 (m-30) cc_final: 0.7818 (t0) REVERT: C 269 LEU cc_start: 0.8742 (mp) cc_final: 0.8455 (mp) REVERT: C 280 LYS cc_start: 0.9023 (mttp) cc_final: 0.7959 (mmtt) REVERT: C 284 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8037 (mm-30) REVERT: C 290 GLU cc_start: 0.8014 (mp0) cc_final: 0.7736 (mp0) REVERT: C 297 GLU cc_start: 0.7829 (tp30) cc_final: 0.7299 (tp30) REVERT: C 308 ARG cc_start: 0.8436 (mtm180) cc_final: 0.7343 (tmt-80) REVERT: C 377 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8018 (tmm) REVERT: C 392 ASP cc_start: 0.8116 (m-30) cc_final: 0.7806 (m-30) REVERT: C 415 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7732 (tp30) REVERT: C 417 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 420 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7712 (mm-30) REVERT: C 433 GLU cc_start: 0.7992 (tp30) cc_final: 0.7379 (tm-30) REVERT: D 1 MET cc_start: 0.7783 (tpp) cc_final: 0.7552 (mmm) REVERT: D 19 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8251 (mmmt) REVERT: D 45 GLU cc_start: 0.8427 (tt0) cc_final: 0.8086 (tm-30) REVERT: D 121 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8061 (ptp-110) REVERT: D 128 ASP cc_start: 0.8661 (t0) cc_final: 0.8424 (t0) REVERT: D 203 ASP cc_start: 0.8223 (t0) cc_final: 0.7934 (t70) REVERT: D 209 ASP cc_start: 0.8498 (t0) cc_final: 0.8268 (t0) REVERT: D 257 MET cc_start: 0.8267 (mmm) cc_final: 0.7987 (mtp) REVERT: D 304 ASP cc_start: 0.7699 (t70) cc_final: 0.6645 (t0) REVERT: D 306 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7712 (mtm180) REVERT: D 309 ARG cc_start: 0.8495 (mtp85) cc_final: 0.8150 (mtp85) REVERT: D 324 LYS cc_start: 0.9156 (tptm) cc_final: 0.8903 (tppt) REVERT: D 325 GLU cc_start: 0.8538 (tp30) cc_final: 0.8179 (tp30) REVERT: D 391 ARG cc_start: 0.8697 (mmm160) cc_final: 0.7302 (mtm110) REVERT: D 401 GLU cc_start: 0.7491 (mp0) cc_final: 0.7250 (mm-30) REVERT: D 404 ASP cc_start: 0.7981 (t70) cc_final: 0.7589 (t0) REVERT: D 407 GLU cc_start: 0.7891 (mp0) cc_final: 0.7463 (mp0) REVERT: D 410 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7687 (mm-30) REVERT: D 414 ASN cc_start: 0.8125 (m110) cc_final: 0.7713 (m-40) REVERT: D 424 GLN cc_start: 0.8275 (pt0) cc_final: 0.8065 (pp30) REVERT: D 425 TYR cc_start: 0.7688 (m-10) cc_final: 0.7442 (m-10) REVERT: E 15 ASP cc_start: 0.8534 (t0) cc_final: 0.8220 (t0) REVERT: E 67 PHE cc_start: 0.8440 (m-10) cc_final: 0.7904 (m-10) REVERT: E 68 GLU cc_start: 0.8107 (tp30) cc_final: 0.7235 (tp30) REVERT: E 94 ASN cc_start: 0.8376 (t0) cc_final: 0.7986 (t0) REVERT: E 120 GLU cc_start: 0.7902 (tt0) cc_final: 0.7696 (tt0) REVERT: E 134 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7603 (mp-120) REVERT: E 165 GLN cc_start: 0.7980 (mm-40) cc_final: 0.7543 (mm110) REVERT: E 169 ASN cc_start: 0.8111 (m-40) cc_final: 0.7790 (m-40) REVERT: E 206 ASP cc_start: 0.8490 (p0) cc_final: 0.8231 (p0) REVERT: E 213 CYS cc_start: 0.7235 (m) cc_final: 0.6926 (m) REVERT: E 307 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7223 (tpp80) REVERT: E 314 GLN cc_start: 0.7777 (mp10) cc_final: 0.7401 (mp10) REVERT: E 327 TYR cc_start: 0.8581 (t80) cc_final: 0.8158 (t80) REVERT: E 483 ASN cc_start: 0.7690 (t0) cc_final: 0.7104 (t0) REVERT: E 556 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7149 (mm-30) REVERT: E 584 SER cc_start: 0.7661 (m) cc_final: 0.7383 (t) outliers start: 60 outliers final: 36 residues processed: 463 average time/residue: 0.7500 time to fit residues: 380.8052 Evaluate side-chains 457 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 413 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 218 ASP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 154 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 364 SER 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 203 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE 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 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 151 THR Chi-restraints excluded: chain E residue 163 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085963 restraints weight = 30025.705| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.99 r_work: 0.3136 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17852 Z= 0.169 Angle : 0.629 12.083 24276 Z= 0.319 Chirality : 0.046 0.216 2651 Planarity : 0.005 0.061 3170 Dihedral : 11.058 174.302 2517 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.38 % Allowed : 20.36 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.18), residues: 2205 helix: 1.23 (0.17), residues: 915 sheet: 0.23 (0.29), residues: 339 loop : -0.68 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 221 TYR 0.022 0.001 TYR A 161 PHE 0.018 0.001 PHE A 255 TRP 0.012 0.001 TRP C 21 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00392 (17849) covalent geometry : angle 0.62935 (24276) hydrogen bonds : bond 0.04036 ( 779) hydrogen bonds : angle 4.45384 ( 2259) metal coordination : bond 0.00422 ( 2) Misc. bond : bond 0.00062 ( 1) *********************** 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: 62 poor density : 429 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7911 (t70) cc_final: 0.7340 (t0) REVERT: A 50 ASN cc_start: 0.8412 (t0) cc_final: 0.7760 (t0) REVERT: A 76 ASP cc_start: 0.8450 (m-30) cc_final: 0.7746 (m-30) REVERT: A 83 TYR cc_start: 0.8369 (m-80) cc_final: 0.8081 (m-80) REVERT: A 113 GLU cc_start: 0.7503 (mp0) cc_final: 0.7125 (mp0) REVERT: A 117 LEU cc_start: 0.8344 (tp) cc_final: 0.8082 (tt) REVERT: A 123 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7648 (tpp80) REVERT: A 124 LYS cc_start: 0.8674 (mttt) cc_final: 0.8269 (ttmm) REVERT: A 254 GLU cc_start: 0.8311 (tt0) cc_final: 0.7803 (mm-30) REVERT: A 255 PHE cc_start: 0.8609 (p90) cc_final: 0.8380 (p90) REVERT: A 284 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 322 ASP cc_start: 0.8272 (t0) cc_final: 0.7816 (t70) REVERT: A 358 GLN cc_start: 0.9104 (tp40) cc_final: 0.8868 (mm-40) REVERT: A 399 TYR cc_start: 0.8842 (t80) cc_final: 0.8422 (t80) REVERT: A 414 GLU cc_start: 0.7928 (mp0) cc_final: 0.7418 (mp0) REVERT: A 415 GLU cc_start: 0.8237 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 420 GLU cc_start: 0.7702 (pp20) cc_final: 0.7393 (pp20) REVERT: A 423 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 433 GLU cc_start: 0.8270 (tp30) cc_final: 0.7859 (tp30) REVERT: B 19 LYS cc_start: 0.8533 (tptm) cc_final: 0.8326 (tptt) REVERT: B 48 ASN cc_start: 0.8742 (p0) cc_final: 0.8379 (p0) REVERT: B 57 ASN cc_start: 0.8315 (m-40) cc_final: 0.8057 (m-40) REVERT: B 58 LYS cc_start: 0.8228 (tttt) cc_final: 0.7949 (pttt) REVERT: B 88 ASP cc_start: 0.8462 (t0) cc_final: 0.8134 (t0) REVERT: B 122 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8371 (ttpt) REVERT: B 157 GLU cc_start: 0.8613 (tp30) cc_final: 0.8178 (tm-30) REVERT: B 158 GLU cc_start: 0.8627 (tp30) cc_final: 0.8294 (tt0) REVERT: B 205 GLU cc_start: 0.8420 (tt0) cc_final: 0.7996 (mt-10) REVERT: B 213 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8123 (ttp80) REVERT: B 218 THR cc_start: 0.8754 (p) cc_final: 0.8504 (t) REVERT: B 267 MET cc_start: 0.8687 (mtp) cc_final: 0.8481 (mtm) REVERT: B 282 ARG cc_start: 0.7932 (ptm160) cc_final: 0.7333 (tmm-80) REVERT: B 306 ARG cc_start: 0.8570 (mpt-90) cc_final: 0.8259 (mpp80) REVERT: B 340 TYR cc_start: 0.8175 (m-80) cc_final: 0.7866 (m-80) REVERT: B 350 LYS cc_start: 0.8890 (tptt) cc_final: 0.8584 (tptm) REVERT: B 363 MET cc_start: 0.8801 (mtm) cc_final: 0.8537 (mtp) REVERT: B 380 ARG cc_start: 0.8344 (ptp90) cc_final: 0.8075 (ptp90) REVERT: B 391 ARG cc_start: 0.8440 (mmm160) cc_final: 0.6443 (ptp-170) REVERT: B 410 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 421 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: C 47 ASP cc_start: 0.8333 (p0) cc_final: 0.7682 (t0) REVERT: C 50 ASN cc_start: 0.8660 (t0) cc_final: 0.7807 (t0) REVERT: C 76 ASP cc_start: 0.8442 (m-30) cc_final: 0.8122 (m-30) REVERT: C 77 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 90 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7626 (tm-30) REVERT: C 121 ARG cc_start: 0.7571 (tpp80) cc_final: 0.7182 (tpp-160) REVERT: C 207 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: C 218 ASP cc_start: 0.8345 (m-30) cc_final: 0.7800 (t0) REVERT: C 269 LEU cc_start: 0.8723 (mp) cc_final: 0.8487 (mp) REVERT: C 280 LYS cc_start: 0.9066 (mttp) cc_final: 0.8014 (mmtt) REVERT: C 284 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7966 (mm-30) REVERT: C 290 GLU cc_start: 0.8031 (mp0) cc_final: 0.7735 (mp0) REVERT: C 297 GLU cc_start: 0.7834 (tp30) cc_final: 0.7550 (tp30) REVERT: C 308 ARG cc_start: 0.8425 (mtm180) cc_final: 0.7349 (tmt-80) REVERT: C 377 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7924 (tmm) REVERT: C 392 ASP cc_start: 0.8014 (m-30) cc_final: 0.7669 (m-30) REVERT: C 415 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7868 (tp30) REVERT: C 417 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7505 (mp0) REVERT: C 420 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7737 (mm-30) REVERT: C 433 GLU cc_start: 0.8093 (tp30) cc_final: 0.7470 (tm-30) REVERT: D 19 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8227 (mmmt) REVERT: D 45 GLU cc_start: 0.8470 (tt0) cc_final: 0.8104 (tm-30) REVERT: D 121 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8104 (ptp-110) REVERT: D 128 ASP cc_start: 0.8651 (t0) cc_final: 0.8260 (t0) REVERT: D 157 GLU cc_start: 0.8660 (tt0) cc_final: 0.8274 (tm-30) REVERT: D 203 ASP cc_start: 0.8211 (t0) cc_final: 0.7888 (t70) REVERT: D 209 ASP cc_start: 0.8461 (t0) cc_final: 0.8248 (t0) REVERT: D 257 MET cc_start: 0.8254 (mmm) cc_final: 0.7985 (mtp) REVERT: D 304 ASP cc_start: 0.7688 (t70) cc_final: 0.6546 (t0) REVERT: D 306 ARG cc_start: 0.8188 (mtm180) cc_final: 0.7745 (mtm180) REVERT: D 309 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8146 (mtp85) REVERT: D 323 MET cc_start: 0.8481 (mmm) cc_final: 0.8189 (mmm) REVERT: D 324 LYS cc_start: 0.9164 (tptm) cc_final: 0.8942 (tppt) REVERT: D 325 GLU cc_start: 0.8512 (tp30) cc_final: 0.8201 (tp30) REVERT: D 391 ARG cc_start: 0.8754 (mmm160) cc_final: 0.7290 (mtm110) REVERT: D 407 GLU cc_start: 0.7879 (mp0) cc_final: 0.7325 (mp0) REVERT: D 410 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7673 (mm-30) REVERT: D 414 ASN cc_start: 0.8121 (m110) cc_final: 0.7702 (m-40) REVERT: D 424 GLN cc_start: 0.8343 (pt0) cc_final: 0.8088 (pp30) REVERT: D 425 TYR cc_start: 0.7698 (m-10) cc_final: 0.7446 (m-10) REVERT: E 15 ASP cc_start: 0.8486 (t0) cc_final: 0.8190 (t0) REVERT: E 72 ARG cc_start: 0.8369 (ptt180) cc_final: 0.8050 (ptt-90) REVERT: E 94 ASN cc_start: 0.8421 (t0) cc_final: 0.8070 (t0) REVERT: E 120 GLU cc_start: 0.7826 (tt0) cc_final: 0.7618 (tt0) REVERT: E 165 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7570 (mm110) REVERT: E 169 ASN cc_start: 0.8116 (m-40) cc_final: 0.7781 (m-40) REVERT: E 213 CYS cc_start: 0.7184 (m) cc_final: 0.6843 (m) REVERT: E 314 GLN cc_start: 0.7760 (mp10) cc_final: 0.7316 (mp10) REVERT: E 327 TYR cc_start: 0.8632 (t80) cc_final: 0.8078 (t80) REVERT: E 483 ASN cc_start: 0.7742 (t0) cc_final: 0.7182 (t0) REVERT: E 556 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7153 (mm-30) REVERT: E 584 SER cc_start: 0.7699 (m) cc_final: 0.7358 (t) outliers start: 62 outliers final: 41 residues processed: 457 average time/residue: 0.8099 time to fit residues: 405.2980 Evaluate side-chains 455 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 410 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 336 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 42 LEU 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 177 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 289 LEU 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 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 207 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 64 ILE 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 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 163 ASP 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 283 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 91 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 A 216 ASN B 83 GLN B 416 ASN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS E 535 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.086072 restraints weight = 30004.863| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.99 r_work: 0.3136 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17852 Z= 0.164 Angle : 0.646 13.269 24276 Z= 0.325 Chirality : 0.046 0.233 2651 Planarity : 0.005 0.060 3170 Dihedral : 11.038 173.820 2517 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.16 % Allowed : 21.45 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.18), residues: 2205 helix: 1.26 (0.17), residues: 909 sheet: 0.21 (0.29), residues: 339 loop : -0.67 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 213 TYR 0.023 0.001 TYR C 161 PHE 0.018 0.001 PHE A 255 TRP 0.012 0.001 TRP D 21 HIS 0.005 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00383 (17849) covalent geometry : angle 0.64579 (24276) hydrogen bonds : bond 0.03975 ( 779) hydrogen bonds : angle 4.46218 ( 2259) metal coordination : bond 0.00386 ( 2) Misc. bond : bond 0.00053 ( 1) *********************** 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 472 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 414 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7953 (t70) cc_final: 0.7349 (t0) REVERT: A 50 ASN cc_start: 0.8443 (t0) cc_final: 0.7772 (t0) REVERT: A 76 ASP cc_start: 0.8395 (m-30) cc_final: 0.7714 (m-30) REVERT: A 83 TYR cc_start: 0.8387 (m-80) cc_final: 0.8078 (m-80) REVERT: A 98 ASP cc_start: 0.8165 (p0) cc_final: 0.7899 (p0) REVERT: A 113 GLU cc_start: 0.7555 (mp0) cc_final: 0.7152 (mp0) REVERT: A 117 LEU cc_start: 0.8354 (tp) cc_final: 0.8086 (tt) REVERT: A 123 ARG cc_start: 0.7993 (tpp-160) cc_final: 0.7634 (tpp80) REVERT: A 124 LYS cc_start: 0.8677 (mttt) cc_final: 0.8273 (ttmm) REVERT: A 176 GLN cc_start: 0.8262 (mm110) cc_final: 0.8013 (mp10) REVERT: A 254 GLU cc_start: 0.8307 (tt0) cc_final: 0.7820 (mm-30) REVERT: A 255 PHE cc_start: 0.8635 (OUTLIER) cc_final: 0.8430 (p90) REVERT: A 284 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7014 (mm-30) REVERT: A 322 ASP cc_start: 0.8290 (t0) cc_final: 0.7827 (t70) REVERT: A 399 TYR cc_start: 0.8852 (t80) cc_final: 0.8424 (t80) REVERT: A 415 GLU cc_start: 0.8328 (tt0) cc_final: 0.7992 (tm-30) REVERT: A 420 GLU cc_start: 0.7766 (pp20) cc_final: 0.7428 (pp20) REVERT: A 423 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 433 GLU cc_start: 0.8242 (tp30) cc_final: 0.7843 (tp30) REVERT: B 19 LYS cc_start: 0.8525 (tptm) cc_final: 0.8314 (tptt) REVERT: B 48 ASN cc_start: 0.8792 (p0) cc_final: 0.8420 (p0) REVERT: B 57 ASN cc_start: 0.8363 (m-40) cc_final: 0.8100 (m-40) REVERT: B 58 LYS cc_start: 0.8237 (tttt) cc_final: 0.7942 (pttt) REVERT: B 88 ASP cc_start: 0.8474 (t0) cc_final: 0.8249 (t70) REVERT: B 122 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8412 (ttpt) REVERT: B 157 GLU cc_start: 0.8635 (tp30) cc_final: 0.8199 (tm-30) REVERT: B 158 GLU cc_start: 0.8644 (tp30) cc_final: 0.8308 (tt0) REVERT: B 205 GLU cc_start: 0.8433 (tt0) cc_final: 0.7987 (mt-10) REVERT: B 213 ARG cc_start: 0.8443 (ttp80) cc_final: 0.8098 (ttp-110) REVERT: B 218 THR cc_start: 0.8778 (p) cc_final: 0.8527 (t) REVERT: B 295 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8286 (t0) REVERT: B 306 ARG cc_start: 0.8595 (mpt-90) cc_final: 0.8263 (mpp80) REVERT: B 340 TYR cc_start: 0.8186 (m-80) cc_final: 0.7876 (m-80) REVERT: B 350 LYS cc_start: 0.8887 (tptt) cc_final: 0.8597 (tptm) REVERT: B 363 MET cc_start: 0.8759 (mtm) cc_final: 0.8509 (mtp) REVERT: B 380 ARG cc_start: 0.8307 (ptp90) cc_final: 0.8059 (ptp90) REVERT: B 391 ARG cc_start: 0.8455 (mmm160) cc_final: 0.6456 (ptp-170) REVERT: B 410 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 421 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 47 ASP cc_start: 0.8336 (p0) cc_final: 0.7702 (t0) REVERT: C 50 ASN cc_start: 0.8662 (t0) cc_final: 0.7821 (t0) REVERT: C 77 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7641 (mt-10) REVERT: C 90 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7715 (tm-30) REVERT: C 121 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7050 (tpp-160) REVERT: C 203 MET cc_start: 0.8654 (tpp) cc_final: 0.7952 (mmm) REVERT: C 207 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: C 218 ASP cc_start: 0.8337 (m-30) cc_final: 0.7756 (t0) REVERT: C 269 LEU cc_start: 0.8718 (mp) cc_final: 0.8459 (mp) REVERT: C 280 LYS cc_start: 0.9092 (mttp) cc_final: 0.8021 (mmtt) REVERT: C 284 GLU cc_start: 0.8210 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 290 GLU cc_start: 0.8065 (mp0) cc_final: 0.7749 (mp0) REVERT: C 308 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7305 (tmt-80) REVERT: C 377 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7892 (tmm) REVERT: C 392 ASP cc_start: 0.7908 (m-30) cc_final: 0.7591 (m-30) REVERT: C 415 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7723 (tp30) REVERT: C 420 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 433 GLU cc_start: 0.8090 (tp30) cc_final: 0.7541 (tm-30) REVERT: D 1 MET cc_start: 0.7724 (tpp) cc_final: 0.7505 (mmm) REVERT: D 19 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8225 (mmmt) REVERT: D 45 GLU cc_start: 0.8429 (tt0) cc_final: 0.8085 (tm-30) REVERT: D 103 LYS cc_start: 0.8944 (mtpm) cc_final: 0.8634 (mtpp) REVERT: D 121 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8122 (ptp-110) REVERT: D 128 ASP cc_start: 0.8605 (t0) cc_final: 0.8371 (t0) REVERT: D 157 GLU cc_start: 0.8623 (tt0) cc_final: 0.8296 (tm-30) REVERT: D 203 ASP cc_start: 0.8204 (t0) cc_final: 0.7881 (t70) REVERT: D 257 MET cc_start: 0.8250 (mmm) cc_final: 0.7984 (mtp) REVERT: D 289 LEU cc_start: 0.8645 (mt) cc_final: 0.8406 (mp) REVERT: D 304 ASP cc_start: 0.7742 (t70) cc_final: 0.6572 (t0) REVERT: D 306 ARG cc_start: 0.8188 (mtm180) cc_final: 0.7746 (mtm180) REVERT: D 309 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8157 (mtp85) REVERT: D 323 MET cc_start: 0.8443 (mmm) cc_final: 0.8122 (mmm) REVERT: D 325 GLU cc_start: 0.8501 (tp30) cc_final: 0.8141 (tp30) REVERT: D 391 ARG cc_start: 0.8790 (mmm160) cc_final: 0.7410 (mtm180) REVERT: D 401 GLU cc_start: 0.7495 (mp0) cc_final: 0.7198 (mm-30) REVERT: D 410 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7681 (mm-30) REVERT: D 414 ASN cc_start: 0.8102 (m110) cc_final: 0.7712 (m-40) REVERT: D 424 GLN cc_start: 0.8319 (pt0) cc_final: 0.8107 (pp30) REVERT: D 425 TYR cc_start: 0.7739 (m-80) cc_final: 0.7465 (m-80) REVERT: E 15 ASP cc_start: 0.8504 (t0) cc_final: 0.8206 (t0) REVERT: E 94 ASN cc_start: 0.8466 (t0) cc_final: 0.8024 (t0) REVERT: E 120 GLU cc_start: 0.7844 (tt0) cc_final: 0.7637 (tt0) REVERT: E 165 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7539 (mm110) REVERT: E 169 ASN cc_start: 0.8173 (m-40) cc_final: 0.7843 (m-40) REVERT: E 213 CYS cc_start: 0.7106 (m) cc_final: 0.6822 (m) REVERT: E 314 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: E 327 TYR cc_start: 0.8657 (t80) cc_final: 0.8130 (t80) REVERT: E 483 ASN cc_start: 0.7810 (t0) cc_final: 0.7249 (t0) REVERT: E 556 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7146 (mm-30) REVERT: E 584 SER cc_start: 0.7693 (m) cc_final: 0.7359 (t) outliers start: 58 outliers final: 36 residues processed: 448 average time/residue: 0.7732 time to fit residues: 380.6027 Evaluate side-chains 461 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 419 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain B residue 42 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 179 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 LEU 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 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 207 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain 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 176 SER 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 163 ASP Chi-restraints excluded: chain E residue 231 THR 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 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 206 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 0 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 416 ASN D 105 HIS ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.096265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087290 restraints weight = 29850.771| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.00 r_work: 0.3159 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17852 Z= 0.133 Angle : 0.637 12.441 24276 Z= 0.323 Chirality : 0.045 0.211 2651 Planarity : 0.005 0.062 3170 Dihedral : 10.927 177.970 2517 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.56 % Allowed : 22.32 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.18), residues: 2205 helix: 1.28 (0.17), residues: 918 sheet: 0.22 (0.29), residues: 339 loop : -0.62 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 213 TYR 0.025 0.001 TYR C 161 PHE 0.017 0.001 PHE A 255 TRP 0.014 0.001 TRP D 21 HIS 0.006 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00312 (17849) covalent geometry : angle 0.63744 (24276) hydrogen bonds : bond 0.03654 ( 779) hydrogen bonds : angle 4.40845 ( 2259) metal coordination : bond 0.00224 ( 2) Misc. bond : bond 0.00021 ( 1) *********************** 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 479 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 432 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7975 (t70) cc_final: 0.7334 (t0) REVERT: A 50 ASN cc_start: 0.8396 (t0) cc_final: 0.7750 (t0) REVERT: A 76 ASP cc_start: 0.8358 (m-30) cc_final: 0.7670 (m-30) REVERT: A 83 TYR cc_start: 0.8385 (m-80) cc_final: 0.8074 (m-80) REVERT: A 98 ASP cc_start: 0.8142 (p0) cc_final: 0.7875 (p0) REVERT: A 113 GLU cc_start: 0.7448 (mp0) cc_final: 0.7057 (mp0) REVERT: A 117 LEU cc_start: 0.8250 (tp) cc_final: 0.7997 (tt) REVERT: A 123 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7638 (tpp80) REVERT: A 124 LYS cc_start: 0.8657 (mttt) cc_final: 0.8260 (ttmm) REVERT: A 176 GLN cc_start: 0.8266 (mm110) cc_final: 0.8028 (mp10) REVERT: A 254 GLU cc_start: 0.8302 (tt0) cc_final: 0.7833 (mm-30) REVERT: A 255 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8385 (p90) REVERT: A 284 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7042 (mm-30) REVERT: A 302 MET cc_start: 0.8429 (mtp) cc_final: 0.8210 (mtm) REVERT: A 322 ASP cc_start: 0.8250 (t0) cc_final: 0.7798 (t70) REVERT: A 399 TYR cc_start: 0.8813 (t80) cc_final: 0.8362 (t80) REVERT: A 415 GLU cc_start: 0.8341 (tt0) cc_final: 0.8023 (tm-30) REVERT: A 420 GLU cc_start: 0.7875 (pp20) cc_final: 0.7483 (pp20) REVERT: A 423 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 433 GLU cc_start: 0.8211 (tp30) cc_final: 0.7816 (tp30) REVERT: B 48 ASN cc_start: 0.8750 (p0) cc_final: 0.8388 (p0) REVERT: B 57 ASN cc_start: 0.8354 (m-40) cc_final: 0.8093 (m-40) REVERT: B 58 LYS cc_start: 0.8175 (tttt) cc_final: 0.7866 (pttt) REVERT: B 88 ASP cc_start: 0.8485 (t0) cc_final: 0.8173 (t0) REVERT: B 122 LYS cc_start: 0.8609 (ttpt) cc_final: 0.8389 (ttpt) REVERT: B 157 GLU cc_start: 0.8632 (tp30) cc_final: 0.8194 (tm-30) REVERT: B 158 GLU cc_start: 0.8610 (tp30) cc_final: 0.8269 (tt0) REVERT: B 161 ASP cc_start: 0.8923 (p0) cc_final: 0.8611 (p0) REVERT: B 179 VAL cc_start: 0.8739 (m) cc_final: 0.8357 (t) REVERT: B 205 GLU cc_start: 0.8412 (tt0) cc_final: 0.7971 (mt-10) REVERT: B 213 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8221 (ttp-110) REVERT: B 267 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8372 (mtm) REVERT: B 285 THR cc_start: 0.8341 (t) cc_final: 0.7840 (p) REVERT: B 295 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8286 (t70) REVERT: B 306 ARG cc_start: 0.8599 (mpt-90) cc_final: 0.7971 (mpp80) REVERT: B 340 TYR cc_start: 0.8202 (m-80) cc_final: 0.7592 (m-80) REVERT: B 350 LYS cc_start: 0.8935 (tptt) cc_final: 0.8602 (tptm) REVERT: B 380 ARG cc_start: 0.8317 (ptp90) cc_final: 0.8064 (ptp90) REVERT: B 391 ARG cc_start: 0.8435 (mmm160) cc_final: 0.6437 (ptp-170) REVERT: B 410 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 421 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 47 ASP cc_start: 0.8349 (p0) cc_final: 0.7718 (t0) REVERT: C 50 ASN cc_start: 0.8689 (t0) cc_final: 0.7840 (t0) REVERT: C 76 ASP cc_start: 0.8435 (m-30) cc_final: 0.8106 (m-30) REVERT: C 77 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 90 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7641 (tm-30) REVERT: C 121 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7230 (tpp80) REVERT: C 207 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: C 218 ASP cc_start: 0.8330 (m-30) cc_final: 0.7832 (t0) REVERT: C 269 LEU cc_start: 0.8849 (mp) cc_final: 0.8616 (mp) REVERT: C 280 LYS cc_start: 0.9091 (mttp) cc_final: 0.8036 (mmtt) REVERT: C 284 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 290 GLU cc_start: 0.8051 (mp0) cc_final: 0.7729 (mp0) REVERT: C 297 GLU cc_start: 0.7842 (tp30) cc_final: 0.7304 (tp30) REVERT: C 308 ARG cc_start: 0.8461 (mtm180) cc_final: 0.7435 (tmt-80) REVERT: C 377 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7870 (tmm) REVERT: C 392 ASP cc_start: 0.7902 (m-30) cc_final: 0.7570 (m-30) REVERT: C 420 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 433 GLU cc_start: 0.8047 (tp30) cc_final: 0.7399 (tm-30) REVERT: D 1 MET cc_start: 0.7712 (tpp) cc_final: 0.7436 (mmm) REVERT: D 19 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8230 (mmmt) REVERT: D 45 GLU cc_start: 0.8418 (tt0) cc_final: 0.8072 (tm-30) REVERT: D 53 GLU cc_start: 0.7861 (tp30) cc_final: 0.7542 (tm-30) REVERT: D 121 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8095 (ptp-110) REVERT: D 128 ASP cc_start: 0.8567 (t0) cc_final: 0.8333 (t0) REVERT: D 157 GLU cc_start: 0.8585 (tt0) cc_final: 0.8185 (tm-30) REVERT: D 203 ASP cc_start: 0.8200 (t0) cc_final: 0.7873 (t70) REVERT: D 216 LYS cc_start: 0.9258 (mmmm) cc_final: 0.8961 (mmmt) REVERT: D 257 MET cc_start: 0.8225 (mmm) cc_final: 0.7969 (mtp) REVERT: D 289 LEU cc_start: 0.8643 (mt) cc_final: 0.8385 (mp) REVERT: D 300 MET cc_start: 0.8807 (mtm) cc_final: 0.8528 (mtm) REVERT: D 304 ASP cc_start: 0.7963 (t70) cc_final: 0.6889 (t0) REVERT: D 306 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7758 (mtm180) REVERT: D 309 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8077 (mtp85) REVERT: D 323 MET cc_start: 0.8400 (mmm) cc_final: 0.8025 (mmm) REVERT: D 325 GLU cc_start: 0.8420 (tp30) cc_final: 0.8150 (tp30) REVERT: D 391 ARG cc_start: 0.8767 (mmm160) cc_final: 0.7372 (mtm180) REVERT: D 404 ASP cc_start: 0.8287 (t0) cc_final: 0.7946 (t0) REVERT: D 407 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7658 (mm-30) REVERT: D 410 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7675 (mm-30) REVERT: D 414 ASN cc_start: 0.8074 (m110) cc_final: 0.7707 (m-40) REVERT: D 425 TYR cc_start: 0.7715 (m-80) cc_final: 0.7447 (m-80) REVERT: E 15 ASP cc_start: 0.8503 (t0) cc_final: 0.8211 (t0) REVERT: E 72 ARG cc_start: 0.8147 (ptt180) cc_final: 0.7360 (mtm-85) REVERT: E 94 ASN cc_start: 0.8259 (t0) cc_final: 0.7723 (t0) REVERT: E 120 GLU cc_start: 0.7786 (tt0) cc_final: 0.7580 (tt0) REVERT: E 165 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7500 (mm110) REVERT: E 169 ASN cc_start: 0.8120 (m-40) cc_final: 0.7786 (m-40) REVERT: E 213 CYS cc_start: 0.6998 (m) cc_final: 0.6648 (m) REVERT: E 305 ASP cc_start: 0.8108 (t70) cc_final: 0.7784 (t0) REVERT: E 313 ARG cc_start: 0.7454 (mmt-90) cc_final: 0.7234 (mmt-90) REVERT: E 314 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: E 327 TYR cc_start: 0.8668 (t80) cc_final: 0.8164 (t80) REVERT: E 483 ASN cc_start: 0.7792 (t0) cc_final: 0.7279 (t0) REVERT: E 556 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7076 (mm-30) REVERT: E 584 SER cc_start: 0.7633 (m) cc_final: 0.7326 (t) outliers start: 47 outliers final: 27 residues processed: 456 average time/residue: 0.7803 time to fit residues: 390.7160 Evaluate side-chains 441 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 407 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 42 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 267 MET 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 B residue 421 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER 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 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 163 ASP Chi-restraints excluded: chain E residue 231 THR 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 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 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 205 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 B 423 GLN ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.086926 restraints weight = 29919.441| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.01 r_work: 0.3152 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17852 Z= 0.150 Angle : 0.657 12.500 24276 Z= 0.332 Chirality : 0.045 0.216 2651 Planarity : 0.005 0.062 3170 Dihedral : 10.847 178.727 2517 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 22.65 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.18), residues: 2205 helix: 1.30 (0.17), residues: 918 sheet: 0.23 (0.29), residues: 339 loop : -0.62 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 4 TYR 0.028 0.001 TYR C 161 PHE 0.019 0.001 PHE A 49 TRP 0.012 0.001 TRP D 21 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00354 (17849) covalent geometry : angle 0.65715 (24276) hydrogen bonds : bond 0.03807 ( 779) hydrogen bonds : angle 4.40509 ( 2259) metal coordination : bond 0.00339 ( 2) Misc. bond : bond 0.00029 ( 1) ********************** 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 463 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 416 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7980 (t70) cc_final: 0.7327 (t0) REVERT: A 50 ASN cc_start: 0.8380 (t0) cc_final: 0.7741 (t0) REVERT: A 76 ASP cc_start: 0.8361 (m-30) cc_final: 0.7677 (m-30) REVERT: A 83 TYR cc_start: 0.8397 (m-80) cc_final: 0.8083 (m-80) REVERT: A 98 ASP cc_start: 0.8155 (p0) cc_final: 0.7854 (p0) REVERT: A 113 GLU cc_start: 0.7467 (mp0) cc_final: 0.7067 (mp0) REVERT: A 117 LEU cc_start: 0.8288 (tp) cc_final: 0.8027 (tt) REVERT: A 123 ARG cc_start: 0.7897 (tpp-160) cc_final: 0.7629 (tpp80) REVERT: A 124 LYS cc_start: 0.8671 (mttt) cc_final: 0.8275 (ttmm) REVERT: A 176 GLN cc_start: 0.8295 (mm110) cc_final: 0.8056 (mp10) REVERT: A 188 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 207 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7378 (mt-10) REVERT: A 254 GLU cc_start: 0.8284 (tt0) cc_final: 0.7788 (mm-30) REVERT: A 255 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8430 (p90) REVERT: A 284 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7022 (mm-30) REVERT: A 302 MET cc_start: 0.8430 (mtp) cc_final: 0.8229 (mtm) REVERT: A 322 ASP cc_start: 0.8289 (t0) cc_final: 0.7833 (t70) REVERT: A 399 TYR cc_start: 0.8820 (t80) cc_final: 0.8354 (t80) REVERT: A 415 GLU cc_start: 0.8337 (tt0) cc_final: 0.8037 (tm-30) REVERT: A 420 GLU cc_start: 0.7823 (pp20) cc_final: 0.7422 (pp20) REVERT: A 423 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 433 GLU cc_start: 0.8226 (tp30) cc_final: 0.7812 (tp30) REVERT: B 48 ASN cc_start: 0.8760 (p0) cc_final: 0.8416 (p0) REVERT: B 58 LYS cc_start: 0.8157 (tttt) cc_final: 0.7885 (pttt) REVERT: B 73 MET cc_start: 0.7770 (ptp) cc_final: 0.7482 (mtm) REVERT: B 88 ASP cc_start: 0.8482 (t0) cc_final: 0.8209 (t70) REVERT: B 122 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8395 (ttpt) REVERT: B 157 GLU cc_start: 0.8657 (tp30) cc_final: 0.8212 (tm-30) REVERT: B 158 GLU cc_start: 0.8618 (tp30) cc_final: 0.8284 (tt0) REVERT: B 205 GLU cc_start: 0.8459 (tt0) cc_final: 0.8036 (mt-10) REVERT: B 252 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8290 (tttt) REVERT: B 267 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8361 (mtm) REVERT: B 282 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7700 (ptm-80) REVERT: B 306 ARG cc_start: 0.8616 (mpt-90) cc_final: 0.8189 (mpp80) REVERT: B 325 GLU cc_start: 0.8054 (tp30) cc_final: 0.7452 (tp30) REVERT: B 340 TYR cc_start: 0.8228 (m-80) cc_final: 0.7910 (m-80) REVERT: B 350 LYS cc_start: 0.8919 (tptt) cc_final: 0.8645 (tptm) REVERT: B 380 ARG cc_start: 0.8308 (ptp90) cc_final: 0.7991 (ptp90) REVERT: B 391 ARG cc_start: 0.8460 (mmm160) cc_final: 0.6509 (ptp-170) REVERT: B 410 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 421 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: C 47 ASP cc_start: 0.8347 (p0) cc_final: 0.7715 (t0) REVERT: C 50 ASN cc_start: 0.8686 (t0) cc_final: 0.7841 (t0) REVERT: C 77 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7701 (mt-10) REVERT: C 90 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7640 (tm-30) REVERT: C 121 ARG cc_start: 0.7569 (tpp80) cc_final: 0.7240 (tpp80) REVERT: C 207 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: C 218 ASP cc_start: 0.8334 (m-30) cc_final: 0.7829 (t0) REVERT: C 269 LEU cc_start: 0.8844 (mp) cc_final: 0.8617 (mp) REVERT: C 280 LYS cc_start: 0.9126 (mttp) cc_final: 0.8136 (mmtt) REVERT: C 284 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 290 GLU cc_start: 0.8027 (mp0) cc_final: 0.7694 (mp0) REVERT: C 297 GLU cc_start: 0.7854 (tp30) cc_final: 0.7304 (tp30) REVERT: C 308 ARG cc_start: 0.8432 (mtm180) cc_final: 0.7397 (tmt-80) REVERT: C 377 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7889 (tmm) REVERT: C 392 ASP cc_start: 0.7920 (m-30) cc_final: 0.7614 (m-30) REVERT: C 420 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 433 GLU cc_start: 0.8124 (tp30) cc_final: 0.7484 (tm-30) REVERT: D 19 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8232 (mmmt) REVERT: D 22 GLU cc_start: 0.8373 (tp30) cc_final: 0.7900 (mm-30) REVERT: D 45 GLU cc_start: 0.8421 (tt0) cc_final: 0.8068 (tm-30) REVERT: D 53 GLU cc_start: 0.7864 (tp30) cc_final: 0.7539 (tm-30) REVERT: D 103 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8638 (mtpm) REVERT: D 121 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8130 (ptp-110) REVERT: D 128 ASP cc_start: 0.8570 (t0) cc_final: 0.8219 (t0) REVERT: D 157 GLU cc_start: 0.8609 (tt0) cc_final: 0.8366 (tm-30) REVERT: D 203 ASP cc_start: 0.8235 (t0) cc_final: 0.7927 (t70) REVERT: D 257 MET cc_start: 0.8235 (mmm) cc_final: 0.7983 (mtp) REVERT: D 289 LEU cc_start: 0.8643 (mt) cc_final: 0.8415 (mp) REVERT: D 300 MET cc_start: 0.8846 (mtm) cc_final: 0.8594 (mtm) REVERT: D 304 ASP cc_start: 0.7987 (t70) cc_final: 0.6932 (t0) REVERT: D 306 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7759 (mtm180) REVERT: D 309 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8194 (mtp85) REVERT: D 323 MET cc_start: 0.8385 (mmm) cc_final: 0.7936 (mmm) REVERT: D 325 GLU cc_start: 0.8435 (tp30) cc_final: 0.8190 (tp30) REVERT: D 401 GLU cc_start: 0.7501 (mp0) cc_final: 0.7106 (mm-30) REVERT: D 404 ASP cc_start: 0.8216 (t0) cc_final: 0.7863 (t0) REVERT: D 407 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7664 (mm-30) REVERT: D 410 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7692 (mm-30) REVERT: D 414 ASN cc_start: 0.8091 (m110) cc_final: 0.7724 (m-40) REVERT: E 15 ASP cc_start: 0.8506 (t0) cc_final: 0.8205 (t0) REVERT: E 72 ARG cc_start: 0.8125 (ptt180) cc_final: 0.7325 (mtm-85) REVERT: E 94 ASN cc_start: 0.8141 (t0) cc_final: 0.7624 (t0) REVERT: E 98 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7203 (mt0) REVERT: E 120 GLU cc_start: 0.7828 (tt0) cc_final: 0.7620 (tt0) REVERT: E 165 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7713 (mm110) REVERT: E 169 ASN cc_start: 0.8121 (m-40) cc_final: 0.7791 (m-40) REVERT: E 213 CYS cc_start: 0.6992 (m) cc_final: 0.6688 (m) REVERT: E 219 ASP cc_start: 0.7282 (p0) cc_final: 0.7035 (p0) REVERT: E 314 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: E 327 TYR cc_start: 0.8690 (t80) cc_final: 0.8201 (t80) REVERT: E 483 ASN cc_start: 0.7812 (t0) cc_final: 0.7344 (t0) REVERT: E 496 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7530 (tm-30) REVERT: E 556 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7151 (mm-30) REVERT: E 584 SER cc_start: 0.7679 (m) cc_final: 0.7365 (t) outliers start: 47 outliers final: 28 residues processed: 441 average time/residue: 0.7706 time to fit residues: 372.9149 Evaluate side-chains 443 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 406 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain B residue 42 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 252 LYS Chi-restraints excluded: chain B residue 267 MET 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 B residue 421 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain D residue 40 SER 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 E residue 9 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 163 ASP Chi-restraints excluded: chain E residue 231 THR 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 431 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 581 SER 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 135 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 98 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.086190 restraints weight = 30091.763| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.01 r_work: 0.3140 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17852 Z= 0.175 Angle : 0.672 12.466 24276 Z= 0.341 Chirality : 0.046 0.220 2651 Planarity : 0.005 0.063 3170 Dihedral : 10.825 179.294 2517 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.56 % Allowed : 22.81 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.18), residues: 2205 helix: 1.28 (0.17), residues: 913 sheet: 0.19 (0.29), residues: 339 loop : -0.62 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 4 TYR 0.031 0.001 TYR C 161 PHE 0.022 0.001 PHE A 49 TRP 0.012 0.001 TRP D 21 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00409 (17849) covalent geometry : angle 0.67243 (24276) hydrogen bonds : bond 0.03978 ( 779) hydrogen bonds : angle 4.41602 ( 2259) metal coordination : bond 0.00436 ( 2) Misc. bond : bond 0.00038 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8086.72 seconds wall clock time: 138 minutes 39.76 seconds (8319.76 seconds total)