Starting phenix.real_space_refine on Fri Aug 7 20:48:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.map" model { file = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gao_29902/08_2026/8gao_29902.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.050 sd= 0.387 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 41 5.49 5 Mg 5 5.21 5 S 132 5.16 5 C 15149 2.51 5 N 4000 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23987 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "G" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2781 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 24, 'TRANS': 314} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 117 Unusual residues: {'GTP': 1} Classifications: {'RNAv2': 4, 'undetermined': 1} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3, None: 1} Not linked: pdbres="GTP P 1 " pdbres=" C P 2 " Chain: "T" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 144 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20839 SG CYS G 37 50.110 92.436 69.765 1.00234.26 S ATOM 20859 SG CYS G 40 46.540 91.001 70.356 1.00251.45 S ATOM 21058 SG CYS G 65 49.027 90.884 73.007 1.00220.03 S ATOM 21084 SG CYS G 68 49.610 88.675 69.955 1.00211.90 S Time building chain proxies: 5.60, per 1000 atoms: 0.23 Number of scatterers: 23987 At special positions: 0 Unit cell: (140.973, 137.886, 143.031, 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 132 16.00 P 41 15.00 Mg 5 11.99 O 4659 8.00 N 4000 7.00 C 15149 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: 2.32 Conformation dependent library (CDL) restraints added in 887.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 65 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 37 " pdb="ZN ZN G 401 " - pdb=" SG CYS G 68 " Number of angles added : 6 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 18 sheets defined 54.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.084A pdb=" N PHE A 28 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 removed outlier: 3.718A pdb=" N LEU A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.724A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 242 Processing helix chain 'A' and resid 245 through 252 Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.504A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.642A pdb=" N PHE A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 375 through 381 removed outlier: 3.541A pdb=" N THR A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 4.224A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 48 removed outlier: 3.534A pdb=" N ASN B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 242 removed outlier: 3.613A pdb=" N CYS B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 252 removed outlier: 3.534A pdb=" N ASP B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 269 removed outlier: 3.573A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.529A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.762A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.827A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 removed outlier: 3.558A pdb=" N LEU C 90 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 229 through 242 removed outlier: 3.870A pdb=" N ASN C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 255 through 269 removed outlier: 3.644A pdb=" N LYS C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.731A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 4.085A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.728A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.749A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.504A pdb=" N ASN D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.829A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET D 138 " --> pdb=" O ILE D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 255 through 269 removed outlier: 3.619A pdb=" N LYS D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.675A pdb=" N TRP D 361 " --> pdb=" O LYS D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.764A pdb=" N PHE E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 removed outlier: 3.531A pdb=" N ASN E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 119 removed outlier: 3.513A pdb=" N LEU E 119 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 242 Processing helix chain 'E' and resid 245 through 251 removed outlier: 3.516A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 Processing helix chain 'E' and resid 357 through 361 removed outlier: 3.770A pdb=" N TRP E 361 " --> pdb=" O LYS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.534A pdb=" N PHE F 28 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.722A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 119 removed outlier: 3.593A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 143 removed outlier: 3.616A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 268 Processing helix chain 'F' and resid 286 through 300 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.581A pdb=" N ILE F 371 " --> pdb=" O MET F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'G' and resid 4 through 17 Processing helix chain 'G' and resid 74 through 82 Processing helix chain 'G' and resid 82 through 99 removed outlier: 3.831A pdb=" N ARG G 94 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY G 98 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 130 No H-bonds generated for 'chain 'G' and resid 128 through 130' Processing helix chain 'G' and resid 134 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 3.996A pdb=" N LYS G 151 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 167 Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 235 through 240 Processing helix chain 'G' and resid 274 through 287 removed outlier: 3.677A pdb=" N ILE G 278 " --> pdb=" O HIS G 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 287 " --> pdb=" O LYS G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 Processing helix chain 'G' and resid 303 through 312 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'G' and resid 328 through 341 removed outlier: 4.410A pdb=" N LYS G 341 " --> pdb=" O SER G 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 153 removed outlier: 6.453A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN B 193 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA B 354 " --> pdb=" O ASN B 193 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 195 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.599A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 278 " --> pdb=" O TYR A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.527A pdb=" N VAL C 277 " --> pdb=" O HIS B 152 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.650A pdb=" N ALA B 187 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AA8, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 153 removed outlier: 6.294A pdb=" N VAL E 221 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LYS E 278 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR E 223 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA E 386 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLN E 403 " --> pdb=" O ALA E 386 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ILE E 388 " --> pdb=" O ILE E 401 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE E 401 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB2, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.937A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB4, first strand: chain 'F' and resid 350 through 352 removed outlier: 3.748A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 275 through 279 Processing sheet with id=AB6, first strand: chain 'F' and resid 419 through 422 Processing sheet with id=AB7, first strand: chain 'G' and resid 23 through 27 Processing sheet with id=AB8, first strand: chain 'G' and resid 124 through 126 removed outlier: 5.270A pdb=" N LEU G 180 " --> pdb=" O GLY G 196 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY G 196 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE G 182 " --> pdb=" O PHE G 194 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE G 194 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 184 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 219 through 220 removed outlier: 3.508A pdb=" N ILE G 248 " --> pdb=" O LEU G 233 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG G 264 " --> pdb=" O ARG G 290 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET G 292 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP G 266 " --> pdb=" O MET G 292 " (cutoff:3.500A) 1174 hydrogen bonds defined for protein. 3363 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: 4.42 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7692 1.36 - 1.50: 6603 1.50 - 1.65: 9986 1.65 - 1.80: 141 1.80 - 1.95: 88 Bond restraints: 24510 Sorted by residual: bond pdb=" N VAL A 221 " pdb=" CA VAL A 221 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.15e-02 7.56e+03 1.07e+01 bond pdb=" N GLU E 188 " pdb=" CA GLU E 188 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.23e-02 6.61e+03 9.61e+00 bond pdb=" C3' DT M 16 " pdb=" C2' DT M 16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.26e+00 bond pdb=" C3' DT M 11 " pdb=" C2' DT M 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.50e+00 bond pdb=" N ILE A 224 " pdb=" CA ILE A 224 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.08e-02 8.57e+03 8.35e+00 ... (remaining 24505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 32868 2.27 - 4.55: 360 4.55 - 6.82: 21 6.82 - 9.10: 10 9.10 - 11.37: 4 Bond angle restraints: 33263 Sorted by residual: angle pdb=" N LEU A 207 " pdb=" CA LEU A 207 " pdb=" C LEU A 207 " ideal model delta sigma weight residual 111.28 104.72 6.56 1.09e+00 8.42e-01 3.62e+01 angle pdb=" N PRO A 378 " pdb=" CA PRO A 378 " pdb=" C PRO A 378 " ideal model delta sigma weight residual 113.53 106.29 7.24 1.39e+00 5.18e-01 2.72e+01 angle pdb=" N VAL D 201 " pdb=" CA VAL D 201 " pdb=" C VAL D 201 " ideal model delta sigma weight residual 112.29 107.86 4.43 9.40e-01 1.13e+00 2.22e+01 angle pdb=" N3 DT M 15 " pdb=" C4 DT M 15 " pdb=" O4 DT M 15 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT M 10 " pdb=" C4 DT M 10 " pdb=" O4 DT M 10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 33258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14542 35.94 - 71.87: 204 71.87 - 107.81: 6 107.81 - 143.75: 0 143.75 - 179.68: 3 Dihedral angle restraints: 14755 sinusoidal: 6143 harmonic: 8612 Sorted by residual: dihedral pdb=" O5' C P 2 " pdb=" C5' C P 2 " pdb=" C4' C P 2 " pdb=" C3' C P 2 " ideal model delta sinusoidal sigma weight residual 60.00 33.01 26.99 3 6.40e+00 2.44e-02 2.20e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 111.95 -179.68 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -86.76 155.67 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3127 0.055 - 0.109: 473 0.109 - 0.164: 87 0.164 - 0.218: 6 0.218 - 0.273: 4 Chirality restraints: 3697 Sorted by residual: chirality pdb=" P C P 2 " pdb=" OP1 C P 2 " pdb=" OP2 C P 2 " pdb=" O5' C P 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" P C P 3 " pdb=" OP1 C P 3 " pdb=" OP2 C P 3 " pdb=" O5' C P 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" P G P 4 " pdb=" OP1 G P 4 " pdb=" OP2 G P 4 " pdb=" O5' G P 4 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3694 not shown) Planarity restraints: 4105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 187 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C ALA E 187 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA E 187 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 188 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 316 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C CYS F 316 " 0.033 2.00e-02 2.50e+03 pdb=" O CYS F 316 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS F 317 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 377 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C LEU A 377 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU A 377 " -0.012 2.00e-02 2.50e+03 pdb=" N PRO A 378 " -0.011 2.00e-02 2.50e+03 ... (remaining 4102 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 235 2.52 - 3.11: 18826 3.11 - 3.71: 39218 3.71 - 4.30: 55372 4.30 - 4.90: 90320 Nonbonded interactions: 203971 Sorted by model distance: nonbonded pdb=" O2A AGS F 501 " pdb="MG MG F 502 " model vdw 1.924 2.170 nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.932 2.170 nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.934 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 1.938 2.170 nonbonded pdb=" O3G AGS E 501 " pdb="MG MG E 502 " model vdw 1.980 2.170 ... (remaining 203966 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' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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 group one per residue 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 25.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 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 : 0.003 0.052 24515 Z= 0.211 Angle : 0.604 11.371 33269 Z= 0.383 Chirality : 0.043 0.273 3697 Planarity : 0.003 0.044 4105 Dihedral : 12.250 179.685 9193 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.47 % Allowed : 7.64 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.19 (0.16), residues: 2917 helix: 1.46 (0.14), residues: 1419 sheet: -1.24 (0.27), residues: 357 loop : -1.09 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 236 TYR 0.012 0.001 TYR E 15 PHE 0.012 0.001 PHE D 65 TRP 0.015 0.001 TRP B 162 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.21 (24510) covalent geometry : angle 0.60263 / 0.38 (33263) hydrogen bonds : bond 0.15156 / 10.25 ( 1174) hydrogen bonds : angle 6.46390 / 4.55 ( 3363) metal coordination : bond 0.00624 / 0.31 ( 4) metal coordination : angle 3.42775 / 1.75 ( 6) Misc. bond : bond 0.05155 / 2.71 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1290 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 3 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 11 PHE cc_start: 0.8133 (m-80) cc_final: 0.7603 (m-80) REVERT: A 19 VAL cc_start: 0.8366 (m) cc_final: 0.7943 (p) REVERT: A 66 THR cc_start: 0.8833 (p) cc_final: 0.8596 (p) REVERT: A 73 VAL cc_start: 0.8295 (t) cc_final: 0.7454 (p) REVERT: A 79 LYS cc_start: 0.8502 (ttmt) cc_final: 0.7762 (ttmt) REVERT: A 85 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7076 (mm-30) REVERT: A 103 MET cc_start: 0.8244 (mmm) cc_final: 0.7994 (mmm) REVERT: A 104 PHE cc_start: 0.8251 (t80) cc_final: 0.7575 (t80) REVERT: A 113 ILE cc_start: 0.8725 (mt) cc_final: 0.8196 (mt) REVERT: A 123 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7706 (mmmm) REVERT: A 131 VAL cc_start: 0.9071 (t) cc_final: 0.8823 (m) REVERT: A 136 ASP cc_start: 0.7389 (m-30) cc_final: 0.7169 (m-30) REVERT: A 163 LEU cc_start: 0.8984 (tp) cc_final: 0.8781 (tt) REVERT: A 164 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: A 165 TYR cc_start: 0.8497 (m-10) cc_final: 0.8221 (m-10) REVERT: A 174 PHE cc_start: 0.8449 (m-80) cc_final: 0.8138 (m-10) REVERT: A 191 THR cc_start: 0.8949 (p) cc_final: 0.8683 (p) REVERT: A 214 TYR cc_start: 0.9046 (m-10) cc_final: 0.8525 (m-10) REVERT: A 223 TYR cc_start: 0.8071 (t80) cc_final: 0.7777 (t80) REVERT: A 224 ILE cc_start: 0.8288 (mt) cc_final: 0.7834 (mt) REVERT: A 235 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7938 (ttpt) REVERT: A 241 MET cc_start: 0.8216 (mmm) cc_final: 0.7729 (mmm) REVERT: A 255 SER cc_start: 0.8355 (p) cc_final: 0.7368 (p) REVERT: A 265 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8243 (ttpp) REVERT: A 312 TYR cc_start: 0.6557 (t80) cc_final: 0.6022 (t80) REVERT: A 316 CYS cc_start: 0.8081 (m) cc_final: 0.7482 (m) REVERT: A 342 LEU cc_start: 0.8205 (tp) cc_final: 0.7290 (tp) REVERT: A 371 ILE cc_start: 0.6832 (mt) cc_final: 0.6457 (mt) REVERT: A 403 GLN cc_start: 0.7578 (tt0) cc_final: 0.7360 (tt0) REVERT: A 408 TYR cc_start: 0.8731 (m-80) cc_final: 0.8497 (m-80) REVERT: A 416 LYS cc_start: 0.8748 (mptt) cc_final: 0.8484 (mptt) REVERT: A 423 LYS cc_start: 0.8562 (mmmm) cc_final: 0.8310 (mmmm) REVERT: B 3 GLU cc_start: 0.7653 (tt0) cc_final: 0.7067 (tt0) REVERT: B 8 HIS cc_start: 0.8299 (m90) cc_final: 0.7749 (m90) REVERT: B 47 TYR cc_start: 0.8572 (m-80) cc_final: 0.7820 (m-10) REVERT: B 70 TYR cc_start: 0.8353 (t80) cc_final: 0.8030 (t80) REVERT: B 79 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8135 (ttmm) REVERT: B 92 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8157 (mmtt) REVERT: B 101 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8277 (tpp-160) REVERT: B 103 MET cc_start: 0.7772 (mmm) cc_final: 0.7558 (mmm) REVERT: B 155 MET cc_start: 0.7613 (tpp) cc_final: 0.7129 (tpp) REVERT: B 159 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 161 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8230 (ttp-110) REVERT: B 175 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.7057 (ttpp) REVERT: B 192 LEU cc_start: 0.8796 (tp) cc_final: 0.8579 (tt) REVERT: B 196 MET cc_start: 0.6887 (mtm) cc_final: 0.6381 (ptp) REVERT: B 213 ASP cc_start: 0.7889 (m-30) cc_final: 0.7631 (m-30) REVERT: B 226 MET cc_start: 0.8432 (mmm) cc_final: 0.7963 (mmp) REVERT: B 231 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7803 (mm-30) REVERT: B 243 ASP cc_start: 0.7077 (t0) cc_final: 0.6723 (t0) REVERT: B 245 SER cc_start: 0.8913 (t) cc_final: 0.8437 (p) REVERT: B 265 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8553 (ttmt) REVERT: B 271 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7550 (t) REVERT: B 300 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7668 (mtpt) REVERT: B 318 SER cc_start: 0.7871 (m) cc_final: 0.7534 (t) REVERT: B 324 TYR cc_start: 0.7557 (t80) cc_final: 0.7320 (t80) REVERT: B 325 SER cc_start: 0.7664 (OUTLIER) cc_final: 0.7230 (p) REVERT: B 345 GLU cc_start: 0.7911 (tt0) cc_final: 0.7675 (tt0) REVERT: B 392 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6842 (tm-30) REVERT: B 403 GLN cc_start: 0.7434 (tt0) cc_final: 0.7103 (tt0) REVERT: B 413 LYS cc_start: 0.8507 (tppt) cc_final: 0.8138 (tppt) REVERT: C 22 TYR cc_start: 0.8779 (m-80) cc_final: 0.8569 (m-10) REVERT: C 26 GLU cc_start: 0.7532 (pt0) cc_final: 0.7279 (pt0) REVERT: C 39 LEU cc_start: 0.8864 (mt) cc_final: 0.8519 (mt) REVERT: C 41 LYS cc_start: 0.8523 (tttt) cc_final: 0.8128 (tttt) REVERT: C 80 LEU cc_start: 0.7835 (mt) cc_final: 0.7583 (mp) REVERT: C 109 LYS cc_start: 0.8730 (tptt) cc_final: 0.8498 (tptt) REVERT: C 114 GLN cc_start: 0.8118 (mt0) cc_final: 0.7684 (mt0) REVERT: C 149 TYR cc_start: 0.7083 (m-10) cc_final: 0.6803 (m-10) REVERT: C 167 ASN cc_start: 0.8304 (p0) cc_final: 0.7855 (p0) REVERT: C 180 ASN cc_start: 0.8597 (m-40) cc_final: 0.8379 (m-40) REVERT: C 181 LYS cc_start: 0.8627 (ttpp) cc_final: 0.8022 (ttpp) REVERT: C 200 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6478 (t160) REVERT: C 226 MET cc_start: 0.7847 (mmt) cc_final: 0.7595 (mmt) REVERT: C 240 ASN cc_start: 0.8067 (t0) cc_final: 0.7607 (t0) REVERT: C 241 MET cc_start: 0.8096 (mmm) cc_final: 0.7642 (mmm) REVERT: C 255 SER cc_start: 0.8313 (m) cc_final: 0.7956 (p) REVERT: C 263 MET cc_start: 0.7325 (mmm) cc_final: 0.6953 (mmm) REVERT: C 272 LEU cc_start: 0.9012 (tp) cc_final: 0.8797 (tt) REVERT: C 280 TYR cc_start: 0.8934 (m-80) cc_final: 0.8618 (m-80) REVERT: C 292 SER cc_start: 0.8802 (m) cc_final: 0.8429 (t) REVERT: C 294 LEU cc_start: 0.9206 (mt) cc_final: 0.8969 (mt) REVERT: C 322 ARG cc_start: 0.7094 (ttp-110) cc_final: 0.6869 (ttp-110) REVERT: C 331 THR cc_start: 0.8178 (m) cc_final: 0.7901 (t) REVERT: C 345 GLU cc_start: 0.7860 (tt0) cc_final: 0.7485 (tt0) REVERT: C 402 LYS cc_start: 0.7986 (pttt) cc_final: 0.7678 (ptmt) REVERT: C 416 LYS cc_start: 0.8189 (mttt) cc_final: 0.7984 (mttt) REVERT: D 11 PHE cc_start: 0.7663 (m-80) cc_final: 0.7089 (m-10) REVERT: D 19 VAL cc_start: 0.8683 (m) cc_final: 0.8066 (p) REVERT: D 40 ILE cc_start: 0.9249 (mt) cc_final: 0.9036 (mm) REVERT: D 41 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8095 (ttmm) REVERT: D 47 TYR cc_start: 0.8899 (m-80) cc_final: 0.8241 (m-80) REVERT: D 54 ASN cc_start: 0.8314 (m-40) cc_final: 0.8090 (m110) REVERT: D 89 TRP cc_start: 0.8046 (t60) cc_final: 0.7466 (t60) REVERT: D 93 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7170 (mm-30) REVERT: D 103 MET cc_start: 0.8158 (mmm) cc_final: 0.7316 (mmm) REVERT: D 109 LYS cc_start: 0.8561 (tttp) cc_final: 0.8212 (ttmm) REVERT: D 111 ILE cc_start: 0.8320 (mt) cc_final: 0.8055 (mt) REVERT: D 118 GLU cc_start: 0.7396 (tp30) cc_final: 0.6831 (tp30) REVERT: D 128 MET cc_start: 0.8694 (tpp) cc_final: 0.8348 (tpp) REVERT: D 143 SER cc_start: 0.8914 (m) cc_final: 0.7972 (t) REVERT: D 153 ASP cc_start: 0.7711 (t0) cc_final: 0.7420 (t0) REVERT: D 154 TRP cc_start: 0.8644 (t60) cc_final: 0.8319 (t60) REVERT: D 159 GLU cc_start: 0.6776 (mm-30) cc_final: 0.6269 (tp30) REVERT: D 189 THR cc_start: 0.8617 (p) cc_final: 0.7373 (p) REVERT: D 192 LEU cc_start: 0.9168 (tp) cc_final: 0.8951 (tp) REVERT: D 226 MET cc_start: 0.7759 (mmm) cc_final: 0.7037 (mmm) REVERT: D 237 ILE cc_start: 0.8894 (mm) cc_final: 0.8417 (mm) REVERT: D 263 MET cc_start: 0.7999 (mmm) cc_final: 0.7529 (mmm) REVERT: D 264 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8126 (mm-30) REVERT: D 267 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7574 (ttm-80) REVERT: D 280 TYR cc_start: 0.8401 (m-80) cc_final: 0.8072 (m-80) REVERT: D 324 TYR cc_start: 0.7427 (m-80) cc_final: 0.7139 (m-80) REVERT: D 326 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7364 (mm-30) REVERT: D 347 GLU cc_start: 0.7136 (tp30) cc_final: 0.6711 (tp30) REVERT: D 392 GLU cc_start: 0.7163 (tp30) cc_final: 0.6819 (tp30) REVERT: D 393 LEU cc_start: 0.8343 (mt) cc_final: 0.8049 (mm) REVERT: D 412 ASN cc_start: 0.8017 (m-40) cc_final: 0.7797 (m-40) REVERT: D 414 TRP cc_start: 0.8324 (m-90) cc_final: 0.8047 (m100) REVERT: D 425 ASN cc_start: 0.8433 (m110) cc_final: 0.8055 (m-40) REVERT: E 4 ILE cc_start: 0.8944 (mt) cc_final: 0.8669 (mt) REVERT: E 35 ASN cc_start: 0.8008 (m-40) cc_final: 0.7414 (m-40) REVERT: E 38 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8459 (mtpt) REVERT: E 39 LEU cc_start: 0.8766 (mt) cc_final: 0.8461 (mt) REVERT: E 104 PHE cc_start: 0.8585 (t80) cc_final: 0.8072 (t80) REVERT: E 127 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8250 (ttmt) REVERT: E 144 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7277 (tt) REVERT: E 158 TYR cc_start: 0.6134 (p90) cc_final: 0.5286 (p90) REVERT: E 216 GLN cc_start: 0.7671 (mt0) cc_final: 0.7394 (mt0) REVERT: E 237 ILE cc_start: 0.8656 (mt) cc_final: 0.8414 (mt) REVERT: E 241 MET cc_start: 0.8022 (mmm) cc_final: 0.7705 (mmm) REVERT: E 242 LEU cc_start: 0.9025 (mp) cc_final: 0.8654 (mp) REVERT: E 245 SER cc_start: 0.8932 (t) cc_final: 0.8466 (p) REVERT: E 259 TYR cc_start: 0.9061 (t80) cc_final: 0.8529 (t80) REVERT: E 260 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8318 (tmmm) REVERT: E 263 MET cc_start: 0.8110 (mmm) cc_final: 0.7573 (tpp) REVERT: E 271 THR cc_start: 0.9139 (p) cc_final: 0.8767 (t) REVERT: E 292 SER cc_start: 0.8575 (m) cc_final: 0.8375 (t) REVERT: E 326 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7574 (mt-10) REVERT: E 329 TYR cc_start: 0.6873 (t80) cc_final: 0.6557 (t80) REVERT: E 365 ASP cc_start: 0.6249 (m-30) cc_final: 0.6002 (m-30) REVERT: F 5 ILE cc_start: 0.9190 (mt) cc_final: 0.8982 (mt) REVERT: F 15 TYR cc_start: 0.7884 (t80) cc_final: 0.7301 (t80) REVERT: F 18 LYS cc_start: 0.8014 (tppp) cc_final: 0.7689 (tppp) REVERT: F 26 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7245 (mm-30) REVERT: F 34 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8462 (ttmm) REVERT: F 43 HIS cc_start: 0.8694 (t-90) cc_final: 0.8224 (t-90) REVERT: F 60 LEU cc_start: 0.8815 (tp) cc_final: 0.8393 (tp) REVERT: F 61 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6508 (mm-30) REVERT: F 95 GLU cc_start: 0.7526 (tt0) cc_final: 0.7066 (tt0) REVERT: F 100 GLN cc_start: 0.8087 (mt0) cc_final: 0.7865 (mt0) REVERT: F 111 ILE cc_start: 0.8521 (mt) cc_final: 0.8304 (mm) REVERT: F 115 THR cc_start: 0.8728 (m) cc_final: 0.8136 (p) REVERT: F 119 LEU cc_start: 0.8492 (mt) cc_final: 0.8246 (mt) REVERT: F 146 PHE cc_start: 0.8275 (m-10) cc_final: 0.7494 (m-10) REVERT: F 157 ASP cc_start: 0.8504 (m-30) cc_final: 0.7880 (m-30) REVERT: F 166 MET cc_start: 0.8072 (ptm) cc_final: 0.7608 (tmm) REVERT: F 183 THR cc_start: 0.8136 (p) cc_final: 0.7709 (t) REVERT: F 200 ASN cc_start: 0.6997 (t0) cc_final: 0.6025 (t0) REVERT: F 237 ILE cc_start: 0.8896 (mm) cc_final: 0.7578 (mt) REVERT: F 256 TYR cc_start: 0.7559 (t80) cc_final: 0.7072 (t80) REVERT: F 263 MET cc_start: 0.7728 (mmm) cc_final: 0.7433 (tpp) REVERT: F 275 LEU cc_start: 0.8864 (tp) cc_final: 0.8478 (tt) REVERT: F 291 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7186 (mtt90) REVERT: F 296 GLU cc_start: 0.7419 (pt0) cc_final: 0.7212 (pt0) REVERT: F 329 TYR cc_start: 0.8045 (t80) cc_final: 0.7680 (t80) REVERT: F 340 ARG cc_start: 0.8858 (ttt-90) cc_final: 0.8634 (ttt-90) REVERT: F 345 GLU cc_start: 0.7935 (tt0) cc_final: 0.7334 (tt0) REVERT: F 419 MET cc_start: 0.3589 (mmp) cc_final: 0.3191 (tpt) REVERT: F 421 VAL cc_start: 0.7885 (t) cc_final: 0.7653 (p) REVERT: G 4 ILE cc_start: 0.9098 (mm) cc_final: 0.8820 (mm) REVERT: G 11 PHE cc_start: 0.8687 (m-80) cc_final: 0.8321 (m-80) REVERT: G 19 LEU cc_start: 0.8717 (mt) cc_final: 0.8387 (tt) REVERT: G 21 LYS cc_start: 0.8286 (mmtt) cc_final: 0.7613 (mmtp) REVERT: G 35 PHE cc_start: 0.8475 (p90) cc_final: 0.8218 (p90) REVERT: G 46 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: G 47 GLN cc_start: 0.7793 (mt0) cc_final: 0.6225 (pt0) REVERT: G 77 TYR cc_start: 0.9066 (t80) cc_final: 0.8466 (t80) REVERT: G 80 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8420 (mm-30) REVERT: G 81 PHE cc_start: 0.8774 (m-80) cc_final: 0.8552 (m-80) REVERT: G 84 ASP cc_start: 0.9403 (p0) cc_final: 0.9199 (p0) REVERT: G 85 LEU cc_start: 0.9518 (mt) cc_final: 0.8847 (mm) REVERT: G 91 PHE cc_start: 0.9182 (t80) cc_final: 0.8528 (t80) REVERT: G 93 ILE cc_start: 0.9315 (tt) cc_final: 0.8939 (tt) REVERT: G 94 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7958 (tpp80) REVERT: G 95 LYS cc_start: 0.9328 (tttt) cc_final: 0.8626 (mtpp) REVERT: G 97 LYS cc_start: 0.8504 (tptm) cc_final: 0.8263 (mptm) REVERT: G 100 SER cc_start: 0.8468 (p) cc_final: 0.7849 (p) REVERT: G 194 PHE cc_start: 0.7795 (p90) cc_final: 0.7506 (p90) REVERT: G 210 ILE cc_start: 0.8876 (mm) cc_final: 0.8658 (mp) REVERT: G 231 TYR cc_start: 0.8867 (m-80) cc_final: 0.8409 (m-80) REVERT: G 238 ASP cc_start: 0.9241 (m-30) cc_final: 0.8544 (m-30) REVERT: G 243 GLU cc_start: 0.9412 (mp0) cc_final: 0.9179 (mp0) REVERT: G 263 ARG cc_start: 0.7843 (ptt180) cc_final: 0.7429 (ptt180) REVERT: G 265 VAL cc_start: 0.9017 (t) cc_final: 0.8128 (t) REVERT: G 266 TRP cc_start: 0.8438 (m100) cc_final: 0.7664 (m100) REVERT: G 295 ASP cc_start: 0.7469 (p0) cc_final: 0.5549 (p0) REVERT: G 304 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9013 (p) REVERT: G 305 ASN cc_start: 0.9068 (t0) cc_final: 0.8681 (t0) REVERT: G 307 MET cc_start: 0.9407 (mmt) cc_final: 0.8893 (mmm) REVERT: G 309 ARG cc_start: 0.8732 (mtp180) cc_final: 0.8503 (mtp180) REVERT: G 310 LYS cc_start: 0.9309 (mttt) cc_final: 0.8912 (mmtm) REVERT: G 317 GLN cc_start: 0.9428 (mt0) cc_final: 0.9193 (mt0) REVERT: G 334 MET cc_start: 0.8126 (tpp) cc_final: 0.7566 (tpp) outliers start: 88 outliers final: 28 residues processed: 1336 average time/residue: 0.1767 time to fit residues: 357.0810 Evaluate side-chains 1159 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 1123 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 116 ASN A 193 ASN A 219 HIS A 240 ASN A 295 ASN B 114 GLN C 45 ASN C 114 GLN C 227 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 253 HIS D 422 GLN F 48 HIS F 62 ASN ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101621 restraints weight = 48905.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105201 restraints weight = 25520.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107643 restraints weight = 15623.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109246 restraints weight = 10737.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110396 restraints weight = 8148.398| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24515 Z= 0.203 Angle : 0.681 10.029 33269 Z= 0.356 Chirality : 0.046 0.311 3697 Planarity : 0.005 0.156 4105 Dihedral : 10.453 178.854 3441 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.12 % Allowed : 3.39 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.01 (0.16), residues: 2917 helix: 1.24 (0.14), residues: 1446 sheet: -1.27 (0.26), residues: 387 loop : -1.19 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 36 TYR 0.036 0.002 TYR G 54 PHE 0.040 0.002 PHE G 293 TRP 0.022 0.002 TRP F 89 HIS 0.009 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (24510) covalent geometry : angle 0.67617 / 0.36 (33263) hydrogen bonds : bond 0.04333 / 2.87 ( 1174) hydrogen bonds : angle 5.26334 / 3.75 ( 3363) metal coordination : bond 0.01055 / 0.53 ( 4) metal coordination : angle 6.20221 / 3.04 ( 6) Misc. bond : bond 0.00324 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1212 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8397 (tpp) cc_final: 0.7713 (tpp) REVERT: A 3 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 11 PHE cc_start: 0.7797 (m-80) cc_final: 0.7442 (m-10) REVERT: A 19 VAL cc_start: 0.8178 (m) cc_final: 0.7867 (p) REVERT: A 26 GLU cc_start: 0.7924 (pm20) cc_final: 0.7460 (pm20) REVERT: A 29 GLU cc_start: 0.7662 (tt0) cc_final: 0.7328 (tt0) REVERT: A 35 ASN cc_start: 0.8560 (m-40) cc_final: 0.8180 (m110) REVERT: A 42 SER cc_start: 0.8578 (m) cc_final: 0.8144 (p) REVERT: A 47 TYR cc_start: 0.6376 (m-80) cc_final: 0.6094 (m-80) REVERT: A 53 ILE cc_start: 0.8831 (mm) cc_final: 0.8630 (mm) REVERT: A 60 LEU cc_start: 0.9155 (tp) cc_final: 0.8863 (tp) REVERT: A 66 THR cc_start: 0.8678 (p) cc_final: 0.8281 (p) REVERT: A 73 VAL cc_start: 0.8888 (t) cc_final: 0.8125 (p) REVERT: A 79 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8061 (ttmt) REVERT: A 93 GLU cc_start: 0.8092 (tp30) cc_final: 0.7611 (tp30) REVERT: A 103 MET cc_start: 0.7732 (mmm) cc_final: 0.7398 (mmp) REVERT: A 113 ILE cc_start: 0.9037 (mt) cc_final: 0.8616 (mt) REVERT: A 123 LYS cc_start: 0.8230 (mmmm) cc_final: 0.7960 (mmmm) REVERT: A 131 VAL cc_start: 0.9033 (t) cc_final: 0.8664 (m) REVERT: A 146 PHE cc_start: 0.8382 (m-10) cc_final: 0.7888 (m-10) REVERT: A 163 LEU cc_start: 0.8816 (tp) cc_final: 0.8564 (tt) REVERT: A 171 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7501 (mmtm) REVERT: A 174 PHE cc_start: 0.8649 (m-80) cc_final: 0.8198 (m-10) REVERT: A 189 THR cc_start: 0.8389 (p) cc_final: 0.8189 (m) REVERT: A 214 TYR cc_start: 0.8523 (m-80) cc_final: 0.7568 (m-10) REVERT: A 215 LEU cc_start: 0.8597 (tp) cc_final: 0.8351 (tp) REVERT: A 235 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8125 (ttpt) REVERT: A 241 MET cc_start: 0.8137 (mmm) cc_final: 0.7654 (mmm) REVERT: A 260 LYS cc_start: 0.8775 (tppt) cc_final: 0.8567 (mmmm) REVERT: A 265 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8629 (ttpp) REVERT: A 267 ARG cc_start: 0.6953 (ttm-80) cc_final: 0.5480 (ttm-80) REVERT: A 278 LYS cc_start: 0.8422 (tptm) cc_final: 0.8090 (tptm) REVERT: A 291 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.8260 (ttm110) REVERT: A 313 LEU cc_start: 0.7020 (tt) cc_final: 0.6781 (tt) REVERT: A 316 CYS cc_start: 0.8136 (m) cc_final: 0.7688 (m) REVERT: A 384 MET cc_start: 0.8365 (ttt) cc_final: 0.7971 (ttm) REVERT: A 401 ILE cc_start: 0.7894 (mm) cc_final: 0.7660 (pt) REVERT: A 403 GLN cc_start: 0.8211 (tt0) cc_final: 0.7934 (tt0) REVERT: A 408 TYR cc_start: 0.8639 (m-80) cc_final: 0.8414 (m-80) REVERT: A 416 LYS cc_start: 0.8946 (mptt) cc_final: 0.8719 (mptt) REVERT: A 426 GLN cc_start: 0.8084 (mt0) cc_final: 0.7715 (mt0) REVERT: B 3 GLU cc_start: 0.7532 (tt0) cc_final: 0.7020 (tt0) REVERT: B 8 HIS cc_start: 0.8172 (m90) cc_final: 0.7232 (m90) REVERT: B 15 TYR cc_start: 0.8239 (t80) cc_final: 0.7782 (t80) REVERT: B 43 HIS cc_start: 0.8753 (t-90) cc_final: 0.8356 (t-170) REVERT: B 47 TYR cc_start: 0.8577 (m-80) cc_final: 0.7490 (m-10) REVERT: B 64 SER cc_start: 0.8766 (t) cc_final: 0.8422 (p) REVERT: B 79 LYS cc_start: 0.8992 (ttmm) cc_final: 0.8412 (ttmm) REVERT: B 103 MET cc_start: 0.7895 (mmm) cc_final: 0.7539 (mmm) REVERT: B 139 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7658 (ttp-170) REVERT: B 144 ILE cc_start: 0.8916 (tt) cc_final: 0.8680 (tt) REVERT: B 145 SER cc_start: 0.8407 (p) cc_final: 0.7908 (p) REVERT: B 147 ASP cc_start: 0.7197 (m-30) cc_final: 0.6908 (m-30) REVERT: B 194 VAL cc_start: 0.8629 (t) cc_final: 0.8038 (t) REVERT: B 213 ASP cc_start: 0.7851 (m-30) cc_final: 0.7513 (m-30) REVERT: B 226 MET cc_start: 0.8206 (mmm) cc_final: 0.7543 (mmp) REVERT: B 231 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7496 (mm-30) REVERT: B 243 ASP cc_start: 0.7336 (t0) cc_final: 0.6955 (t0) REVERT: B 245 SER cc_start: 0.8414 (t) cc_final: 0.7716 (p) REVERT: B 258 GLU cc_start: 0.8363 (pt0) cc_final: 0.8136 (pt0) REVERT: B 260 LYS cc_start: 0.8819 (tttp) cc_final: 0.8512 (tttp) REVERT: B 263 MET cc_start: 0.8016 (mmm) cc_final: 0.7734 (mmt) REVERT: B 265 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8613 (ttmt) REVERT: B 278 LYS cc_start: 0.8454 (tptp) cc_final: 0.8236 (tptp) REVERT: B 279 GLN cc_start: 0.8466 (tt0) cc_final: 0.8028 (tt0) REVERT: B 318 SER cc_start: 0.8167 (m) cc_final: 0.7401 (t) REVERT: B 324 TYR cc_start: 0.7501 (t80) cc_final: 0.7270 (t80) REVERT: B 368 MET cc_start: 0.8345 (tpp) cc_final: 0.7906 (ttt) REVERT: B 391 GLU cc_start: 0.7398 (tp30) cc_final: 0.7150 (tp30) REVERT: B 392 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 413 LYS cc_start: 0.8734 (tppt) cc_final: 0.8183 (tppt) REVERT: C 3 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 13 GLN cc_start: 0.7640 (tp40) cc_final: 0.7432 (tp40) REVERT: C 26 GLU cc_start: 0.8075 (pt0) cc_final: 0.7760 (pt0) REVERT: C 39 LEU cc_start: 0.8760 (mt) cc_final: 0.8417 (mt) REVERT: C 41 LYS cc_start: 0.8826 (tttt) cc_final: 0.8562 (tttt) REVERT: C 85 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7766 (mm-30) REVERT: C 140 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7723 (tm-30) REVERT: C 155 MET cc_start: 0.7498 (tpt) cc_final: 0.7264 (tpt) REVERT: C 181 LYS cc_start: 0.8438 (ttpp) cc_final: 0.8079 (ttpp) REVERT: C 203 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7711 (mtmm) REVERT: C 224 ILE cc_start: 0.7845 (mt) cc_final: 0.7635 (tp) REVERT: C 241 MET cc_start: 0.8181 (mmm) cc_final: 0.7454 (mmm) REVERT: C 263 MET cc_start: 0.7500 (mmm) cc_final: 0.7101 (mmm) REVERT: C 269 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7418 (mttm) REVERT: C 279 GLN cc_start: 0.8201 (tt0) cc_final: 0.7788 (tt0) REVERT: C 292 SER cc_start: 0.9095 (m) cc_final: 0.8746 (t) REVERT: C 312 TYR cc_start: 0.6572 (t80) cc_final: 0.6112 (t80) REVERT: C 318 SER cc_start: 0.7986 (t) cc_final: 0.7724 (t) REVERT: C 333 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7586 (ttmt) REVERT: C 342 LEU cc_start: 0.9013 (tp) cc_final: 0.8723 (tp) REVERT: C 345 GLU cc_start: 0.8182 (tt0) cc_final: 0.7825 (tt0) REVERT: C 393 LEU cc_start: 0.8861 (mt) cc_final: 0.8595 (mt) REVERT: C 411 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8580 (mtmm) REVERT: D 1 MET cc_start: 0.8043 (ppp) cc_final: 0.7351 (ppp) REVERT: D 35 ASN cc_start: 0.8682 (m110) cc_final: 0.8344 (m110) REVERT: D 41 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8133 (ttmm) REVERT: D 47 TYR cc_start: 0.9010 (m-80) cc_final: 0.8096 (m-80) REVERT: D 66 THR cc_start: 0.8090 (p) cc_final: 0.7589 (p) REVERT: D 67 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7696 (tm-30) REVERT: D 89 TRP cc_start: 0.8101 (t60) cc_final: 0.7389 (t60) REVERT: D 93 GLU cc_start: 0.7874 (mm-30) cc_final: 0.6857 (mm-30) REVERT: D 96 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7978 (ttpp) REVERT: D 103 MET cc_start: 0.8000 (mmm) cc_final: 0.7444 (mmm) REVERT: D 109 LYS cc_start: 0.8241 (tttp) cc_final: 0.7916 (ttmm) REVERT: D 118 GLU cc_start: 0.7476 (tp30) cc_final: 0.6883 (tp30) REVERT: D 128 MET cc_start: 0.8703 (tpp) cc_final: 0.8404 (tpp) REVERT: D 139 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7706 (ttp-170) REVERT: D 143 SER cc_start: 0.8944 (m) cc_final: 0.8118 (t) REVERT: D 147 ASP cc_start: 0.7494 (p0) cc_final: 0.7238 (p0) REVERT: D 154 TRP cc_start: 0.8813 (t60) cc_final: 0.8407 (t60) REVERT: D 155 MET cc_start: 0.8066 (tpt) cc_final: 0.7021 (tpt) REVERT: D 189 THR cc_start: 0.8622 (p) cc_final: 0.6875 (p) REVERT: D 196 MET cc_start: 0.7541 (mtp) cc_final: 0.7257 (mtp) REVERT: D 226 MET cc_start: 0.7263 (mmm) cc_final: 0.6670 (mmm) REVERT: D 263 MET cc_start: 0.7955 (mmm) cc_final: 0.7680 (mmm) REVERT: D 264 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8342 (mm-30) REVERT: D 280 TYR cc_start: 0.8441 (m-80) cc_final: 0.7938 (m-80) REVERT: D 293 LEU cc_start: 0.8704 (tp) cc_final: 0.8454 (tp) REVERT: D 324 TYR cc_start: 0.7755 (m-80) cc_final: 0.7342 (m-80) REVERT: D 326 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 329 TYR cc_start: 0.6163 (t80) cc_final: 0.5519 (t80) REVERT: D 333 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7688 (ttmt) REVERT: D 338 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6918 (mt-10) REVERT: D 347 GLU cc_start: 0.7707 (tp30) cc_final: 0.6939 (tp30) REVERT: D 349 VAL cc_start: 0.9162 (t) cc_final: 0.8936 (p) REVERT: D 392 GLU cc_start: 0.7701 (tp30) cc_final: 0.7206 (tp30) REVERT: D 393 LEU cc_start: 0.8218 (mt) cc_final: 0.7987 (mm) REVERT: D 397 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7837 (mt-10) REVERT: D 416 LYS cc_start: 0.8219 (mppt) cc_final: 0.7351 (mppt) REVERT: E 1 MET cc_start: 0.7947 (ptm) cc_final: 0.6644 (ptm) REVERT: E 4 ILE cc_start: 0.8941 (mt) cc_final: 0.8727 (mt) REVERT: E 23 MET cc_start: 0.8190 (mmt) cc_final: 0.7986 (tpp) REVERT: E 34 LYS cc_start: 0.8844 (tttp) cc_final: 0.8291 (tttp) REVERT: E 38 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8398 (mtpt) REVERT: E 39 LEU cc_start: 0.8869 (mt) cc_final: 0.8628 (mt) REVERT: E 47 TYR cc_start: 0.6376 (t80) cc_final: 0.6047 (t80) REVERT: E 85 GLU cc_start: 0.7245 (mp0) cc_final: 0.6672 (mp0) REVERT: E 86 ASP cc_start: 0.8473 (t0) cc_final: 0.8052 (t70) REVERT: E 93 GLU cc_start: 0.7989 (tp30) cc_final: 0.7065 (tp30) REVERT: E 104 PHE cc_start: 0.8638 (t80) cc_final: 0.8174 (t80) REVERT: E 113 ILE cc_start: 0.9329 (mm) cc_final: 0.8079 (mm) REVERT: E 118 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 158 TYR cc_start: 0.5962 (p90) cc_final: 0.5590 (p90) REVERT: E 216 GLN cc_start: 0.8031 (mt0) cc_final: 0.7667 (mt0) REVERT: E 226 MET cc_start: 0.5898 (mmm) cc_final: 0.5478 (mmm) REVERT: E 238 ASP cc_start: 0.8640 (m-30) cc_final: 0.8412 (m-30) REVERT: E 241 MET cc_start: 0.7912 (mmm) cc_final: 0.7496 (mmm) REVERT: E 247 ASP cc_start: 0.8109 (p0) cc_final: 0.7847 (p0) REVERT: E 265 LYS cc_start: 0.8940 (mtpt) cc_final: 0.8694 (mtpt) REVERT: E 269 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8598 (ttmm) REVERT: E 271 THR cc_start: 0.9175 (p) cc_final: 0.8856 (t) REVERT: E 326 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7700 (mt-10) REVERT: E 333 LYS cc_start: 0.7899 (tttp) cc_final: 0.7508 (tttp) REVERT: E 402 LYS cc_start: 0.7718 (ttmm) cc_final: 0.7347 (ttpp) REVERT: E 423 LYS cc_start: 0.9018 (mttm) cc_final: 0.8718 (mtpp) REVERT: F 5 ILE cc_start: 0.9005 (mt) cc_final: 0.8577 (mt) REVERT: F 15 TYR cc_start: 0.8624 (t80) cc_final: 0.7308 (t80) REVERT: F 22 TYR cc_start: 0.8196 (m-80) cc_final: 0.7968 (m-80) REVERT: F 24 ASP cc_start: 0.8512 (t70) cc_final: 0.8232 (t70) REVERT: F 29 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7549 (mm-30) REVERT: F 34 LYS cc_start: 0.8999 (ttmt) cc_final: 0.8591 (ttmm) REVERT: F 38 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8857 (mmtp) REVERT: F 43 HIS cc_start: 0.8477 (t-90) cc_final: 0.7837 (t-90) REVERT: F 60 LEU cc_start: 0.8642 (tp) cc_final: 0.8371 (tp) REVERT: F 61 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7388 (mm-30) REVERT: F 62 ASN cc_start: 0.8448 (m-40) cc_final: 0.8200 (t0) REVERT: F 74 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8784 (ttmm) REVERT: F 93 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7940 (mt-10) REVERT: F 95 GLU cc_start: 0.8126 (tt0) cc_final: 0.7882 (tt0) REVERT: F 96 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8277 (ttpp) REVERT: F 116 ASN cc_start: 0.8700 (t0) cc_final: 0.8237 (t0) REVERT: F 119 LEU cc_start: 0.8631 (mt) cc_final: 0.8236 (mt) REVERT: F 123 LYS cc_start: 0.8771 (tptt) cc_final: 0.8465 (tptt) REVERT: F 155 MET cc_start: 0.7011 (tpp) cc_final: 0.5368 (tpp) REVERT: F 158 TYR cc_start: 0.7409 (p90) cc_final: 0.6864 (p90) REVERT: F 183 THR cc_start: 0.7972 (p) cc_final: 0.7405 (t) REVERT: F 189 THR cc_start: 0.8301 (p) cc_final: 0.7783 (t) REVERT: F 235 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8218 (tttm) REVERT: F 236 ARG cc_start: 0.8498 (ttm170) cc_final: 0.7903 (tpp80) REVERT: F 237 ILE cc_start: 0.8939 (mm) cc_final: 0.7128 (mt) REVERT: F 256 TYR cc_start: 0.7616 (t80) cc_final: 0.6985 (t80) REVERT: F 260 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7950 (ttmm) REVERT: F 280 TYR cc_start: 0.8047 (m-80) cc_final: 0.7706 (m-80) REVERT: F 291 ARG cc_start: 0.8083 (mtt90) cc_final: 0.7305 (mtt90) REVERT: F 326 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7626 (mm-30) REVERT: F 329 TYR cc_start: 0.8011 (t80) cc_final: 0.7647 (t80) REVERT: F 333 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8314 (ttpp) REVERT: F 338 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7032 (mm-30) REVERT: F 345 GLU cc_start: 0.7477 (tt0) cc_final: 0.6933 (tt0) REVERT: F 370 ASP cc_start: 0.7308 (m-30) cc_final: 0.6980 (m-30) REVERT: F 422 GLN cc_start: 0.7376 (mt0) cc_final: 0.7153 (mt0) REVERT: G 4 ILE cc_start: 0.8954 (mm) cc_final: 0.8359 (mm) REVERT: G 8 ASP cc_start: 0.8879 (m-30) cc_final: 0.8043 (m-30) REVERT: G 19 LEU cc_start: 0.8211 (mt) cc_final: 0.7915 (tt) REVERT: G 77 TYR cc_start: 0.8436 (t80) cc_final: 0.7877 (t80) REVERT: G 78 LEU cc_start: 0.9497 (mt) cc_final: 0.9209 (mt) REVERT: G 89 TYR cc_start: 0.8145 (t80) cc_final: 0.7777 (t80) REVERT: G 100 SER cc_start: 0.8609 (p) cc_final: 0.8180 (p) REVERT: G 147 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8638 (mmmt) REVERT: G 151 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8528 (pttp) REVERT: G 157 THR cc_start: 0.8474 (p) cc_final: 0.7976 (m) REVERT: G 238 ASP cc_start: 0.8706 (m-30) cc_final: 0.8233 (m-30) REVERT: G 240 LEU cc_start: 0.9006 (mt) cc_final: 0.8803 (mt) REVERT: G 278 ILE cc_start: 0.9180 (mp) cc_final: 0.8955 (mp) REVERT: G 307 MET cc_start: 0.8960 (mmt) cc_final: 0.8571 (mmt) REVERT: G 323 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8917 (pttm) REVERT: G 328 GLN cc_start: 0.6663 (tp40) cc_final: 0.6350 (tp40) REVERT: G 333 LYS cc_start: 0.9178 (tttp) cc_final: 0.8913 (tttp) REVERT: G 334 MET cc_start: 0.7894 (tpp) cc_final: 0.7413 (tpp) outliers start: 3 outliers final: 1 residues processed: 1213 average time/residue: 0.1775 time to fit residues: 325.3983 Evaluate side-chains 1077 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1076 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 33 optimal weight: 7.9990 chunk 284 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 chunk 226 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.0370 chunk 127 optimal weight: 7.9990 chunk 231 optimal weight: 0.3980 chunk 198 optimal weight: 2.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 GLN A 193 ASN A 220 ASN A 240 ASN A 403 GLN B 193 ASN B 403 GLN D 100 GLN D 114 GLN D 422 GLN E 105 ASN F 48 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.129156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.106820 restraints weight = 48481.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110825 restraints weight = 24140.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113529 restraints weight = 14445.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115338 restraints weight = 9754.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116592 restraints weight = 7261.246| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24515 Z= 0.148 Angle : 0.650 10.177 33269 Z= 0.340 Chirality : 0.045 0.286 3697 Planarity : 0.005 0.083 4105 Dihedral : 10.392 173.199 3441 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.12 % Allowed : 2.76 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.13 (0.16), residues: 2917 helix: 1.19 (0.14), residues: 1441 sheet: -1.35 (0.26), residues: 398 loop : -1.29 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 264 TYR 0.032 0.002 TYR A 165 PHE 0.029 0.002 PHE A 417 TRP 0.020 0.002 TRP G 294 HIS 0.006 0.001 HIS G 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (24510) covalent geometry : angle 0.64514 / 0.34 (33263) hydrogen bonds : bond 0.03824 / 2.55 ( 1174) hydrogen bonds : angle 5.05561 / 3.61 ( 3363) metal coordination : bond 0.00997 / 0.50 ( 4) metal coordination : angle 5.63949 / 2.92 ( 6) Misc. bond : bond 0.00116 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1164 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8095 (tpp) cc_final: 0.7769 (tpp) REVERT: A 3 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7286 (mm-30) REVERT: A 11 PHE cc_start: 0.7921 (m-80) cc_final: 0.7377 (m-10) REVERT: A 19 VAL cc_start: 0.8167 (m) cc_final: 0.7913 (p) REVERT: A 26 GLU cc_start: 0.7914 (pm20) cc_final: 0.7391 (pm20) REVERT: A 29 GLU cc_start: 0.7699 (tt0) cc_final: 0.7407 (tt0) REVERT: A 35 ASN cc_start: 0.8603 (m-40) cc_final: 0.8108 (m110) REVERT: A 42 SER cc_start: 0.8488 (m) cc_final: 0.8211 (p) REVERT: A 47 TYR cc_start: 0.6304 (m-80) cc_final: 0.6046 (m-80) REVERT: A 53 ILE cc_start: 0.8835 (mm) cc_final: 0.8607 (mm) REVERT: A 60 LEU cc_start: 0.9117 (tp) cc_final: 0.8844 (tp) REVERT: A 66 THR cc_start: 0.8625 (p) cc_final: 0.8244 (p) REVERT: A 73 VAL cc_start: 0.8867 (t) cc_final: 0.8137 (p) REVERT: A 79 LYS cc_start: 0.8675 (ttmt) cc_final: 0.7963 (ttmt) REVERT: A 93 GLU cc_start: 0.8091 (tp30) cc_final: 0.7581 (tp30) REVERT: A 95 GLU cc_start: 0.8820 (tt0) cc_final: 0.8069 (tt0) REVERT: A 103 MET cc_start: 0.7828 (mmm) cc_final: 0.7555 (mmp) REVERT: A 104 PHE cc_start: 0.7924 (t80) cc_final: 0.7467 (t80) REVERT: A 113 ILE cc_start: 0.9058 (mt) cc_final: 0.8768 (mt) REVERT: A 123 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7903 (mmmm) REVERT: A 146 PHE cc_start: 0.8243 (m-10) cc_final: 0.7833 (m-10) REVERT: A 149 TYR cc_start: 0.6268 (t80) cc_final: 0.6060 (t80) REVERT: A 174 PHE cc_start: 0.8648 (m-80) cc_final: 0.8287 (m-10) REVERT: A 188 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7236 (mt-10) REVERT: A 214 TYR cc_start: 0.8444 (m-80) cc_final: 0.7565 (m-80) REVERT: A 215 LEU cc_start: 0.8571 (tp) cc_final: 0.8354 (tp) REVERT: A 235 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8102 (ttpt) REVERT: A 241 MET cc_start: 0.8084 (mmm) cc_final: 0.7504 (mmm) REVERT: A 255 SER cc_start: 0.8879 (p) cc_final: 0.8258 (p) REVERT: A 260 LYS cc_start: 0.8783 (tppp) cc_final: 0.8387 (mmmm) REVERT: A 265 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8527 (ttpp) REVERT: A 267 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6173 (ttm-80) REVERT: A 268 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 278 LYS cc_start: 0.8301 (tptm) cc_final: 0.7782 (tptm) REVERT: A 279 GLN cc_start: 0.8585 (tt0) cc_final: 0.8372 (tt0) REVERT: A 316 CYS cc_start: 0.8088 (m) cc_final: 0.7591 (m) REVERT: A 345 GLU cc_start: 0.7106 (pp20) cc_final: 0.6902 (pp20) REVERT: A 384 MET cc_start: 0.8374 (ttt) cc_final: 0.7987 (ttm) REVERT: A 408 TYR cc_start: 0.8535 (m-80) cc_final: 0.8317 (m-80) REVERT: B 3 GLU cc_start: 0.7490 (tt0) cc_final: 0.6860 (tt0) REVERT: B 4 ILE cc_start: 0.8513 (tp) cc_final: 0.8103 (tp) REVERT: B 15 TYR cc_start: 0.8236 (t80) cc_final: 0.7309 (t80) REVERT: B 36 THR cc_start: 0.8552 (m) cc_final: 0.8299 (p) REVERT: B 41 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8384 (ttmt) REVERT: B 43 HIS cc_start: 0.8724 (t-90) cc_final: 0.8299 (t-170) REVERT: B 47 TYR cc_start: 0.8542 (m-80) cc_final: 0.7478 (m-10) REVERT: B 79 LYS cc_start: 0.8927 (ttmm) cc_final: 0.7978 (ttmm) REVERT: B 86 ASP cc_start: 0.7611 (t70) cc_final: 0.7411 (t0) REVERT: B 103 MET cc_start: 0.7867 (mmm) cc_final: 0.7498 (mmm) REVERT: B 139 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.7614 (ttp-170) REVERT: B 145 SER cc_start: 0.8429 (p) cc_final: 0.7754 (p) REVERT: B 147 ASP cc_start: 0.7181 (m-30) cc_final: 0.6822 (m-30) REVERT: B 166 MET cc_start: 0.7339 (ppp) cc_final: 0.7068 (ppp) REVERT: B 167 ASN cc_start: 0.8522 (m-40) cc_final: 0.8262 (m-40) REVERT: B 192 LEU cc_start: 0.8426 (tp) cc_final: 0.8212 (tt) REVERT: B 194 VAL cc_start: 0.8301 (t) cc_final: 0.8038 (t) REVERT: B 213 ASP cc_start: 0.7823 (m-30) cc_final: 0.7525 (m-30) REVERT: B 226 MET cc_start: 0.8206 (mmm) cc_final: 0.7598 (mmp) REVERT: B 231 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7508 (mm-30) REVERT: B 238 ASP cc_start: 0.8755 (m-30) cc_final: 0.8521 (m-30) REVERT: B 243 ASP cc_start: 0.7238 (t0) cc_final: 0.6922 (t0) REVERT: B 245 SER cc_start: 0.8316 (t) cc_final: 0.7103 (p) REVERT: B 248 ASP cc_start: 0.7390 (m-30) cc_final: 0.7126 (m-30) REVERT: B 258 GLU cc_start: 0.8362 (pt0) cc_final: 0.8057 (pt0) REVERT: B 260 LYS cc_start: 0.8788 (tttp) cc_final: 0.8471 (tttp) REVERT: B 274 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7380 (mtm-85) REVERT: B 276 ILE cc_start: 0.8425 (mt) cc_final: 0.8146 (tt) REVERT: B 278 LYS cc_start: 0.8445 (tptp) cc_final: 0.8245 (tptp) REVERT: B 279 GLN cc_start: 0.8517 (tt0) cc_final: 0.7966 (tt0) REVERT: B 280 TYR cc_start: 0.8535 (m-80) cc_final: 0.8303 (m-80) REVERT: B 298 LYS cc_start: 0.8644 (pttp) cc_final: 0.8429 (pttp) REVERT: B 318 SER cc_start: 0.8168 (m) cc_final: 0.7382 (t) REVERT: B 324 TYR cc_start: 0.7469 (t80) cc_final: 0.7250 (t80) REVERT: B 368 MET cc_start: 0.8293 (tpp) cc_final: 0.8086 (ttt) REVERT: B 392 GLU cc_start: 0.7360 (tm-30) cc_final: 0.6958 (tm-30) REVERT: B 413 LYS cc_start: 0.8574 (tppt) cc_final: 0.7946 (tppt) REVERT: C 13 GLN cc_start: 0.7646 (tp40) cc_final: 0.7203 (tp40) REVERT: C 26 GLU cc_start: 0.8085 (pt0) cc_final: 0.7772 (pt0) REVERT: C 39 LEU cc_start: 0.8632 (mt) cc_final: 0.8323 (mt) REVERT: C 85 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7687 (mm-30) REVERT: C 103 MET cc_start: 0.8201 (mmt) cc_final: 0.7962 (mmt) REVERT: C 109 LYS cc_start: 0.8802 (tppt) cc_final: 0.8420 (mmmm) REVERT: C 113 ILE cc_start: 0.8909 (mt) cc_final: 0.8238 (mm) REVERT: C 128 MET cc_start: 0.7952 (mmm) cc_final: 0.7664 (mmm) REVERT: C 166 MET cc_start: 0.7322 (tpt) cc_final: 0.6646 (tpt) REVERT: C 178 ILE cc_start: 0.8103 (tp) cc_final: 0.7610 (mm) REVERT: C 224 ILE cc_start: 0.7990 (mt) cc_final: 0.7765 (tp) REVERT: C 226 MET cc_start: 0.8573 (mmm) cc_final: 0.8278 (mmm) REVERT: C 241 MET cc_start: 0.8154 (mmm) cc_final: 0.7458 (mmm) REVERT: C 247 ASP cc_start: 0.7996 (m-30) cc_final: 0.7714 (m-30) REVERT: C 263 MET cc_start: 0.7483 (mmm) cc_final: 0.7205 (mmm) REVERT: C 279 GLN cc_start: 0.8164 (tt0) cc_final: 0.7812 (tt0) REVERT: C 280 TYR cc_start: 0.8568 (m-80) cc_final: 0.7567 (m-80) REVERT: C 291 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8260 (mtt90) REVERT: C 292 SER cc_start: 0.9093 (m) cc_final: 0.8710 (t) REVERT: C 293 LEU cc_start: 0.8600 (tp) cc_final: 0.8165 (tp) REVERT: C 295 ASN cc_start: 0.8173 (t0) cc_final: 0.7923 (t0) REVERT: C 318 SER cc_start: 0.7880 (t) cc_final: 0.7638 (p) REVERT: C 345 GLU cc_start: 0.8282 (tt0) cc_final: 0.7724 (tt0) REVERT: C 367 ASN cc_start: 0.7913 (m-40) cc_final: 0.7682 (m-40) REVERT: C 393 LEU cc_start: 0.8860 (mt) cc_final: 0.8609 (mt) REVERT: C 411 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8540 (mtmm) REVERT: C 423 LYS cc_start: 0.8706 (mtpp) cc_final: 0.8395 (mmmm) REVERT: D 19 VAL cc_start: 0.8503 (m) cc_final: 0.8163 (p) REVERT: D 41 LYS cc_start: 0.8678 (ttpp) cc_final: 0.7999 (ttmm) REVERT: D 47 TYR cc_start: 0.9005 (m-80) cc_final: 0.8188 (m-80) REVERT: D 67 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 79 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8591 (mtmt) REVERT: D 103 MET cc_start: 0.7991 (mmm) cc_final: 0.7389 (mmm) REVERT: D 109 LYS cc_start: 0.8231 (tttp) cc_final: 0.7853 (ttmm) REVERT: D 118 GLU cc_start: 0.7293 (tp30) cc_final: 0.6858 (tp30) REVERT: D 128 MET cc_start: 0.8661 (tpp) cc_final: 0.8373 (tpp) REVERT: D 143 SER cc_start: 0.8921 (m) cc_final: 0.8206 (t) REVERT: D 147 ASP cc_start: 0.7396 (p0) cc_final: 0.7096 (p0) REVERT: D 154 TRP cc_start: 0.8800 (t60) cc_final: 0.8499 (t60) REVERT: D 155 MET cc_start: 0.7797 (tpt) cc_final: 0.6996 (tpt) REVERT: D 159 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7582 (tp30) REVERT: D 189 THR cc_start: 0.8650 (p) cc_final: 0.6865 (p) REVERT: D 196 MET cc_start: 0.7501 (mtp) cc_final: 0.7141 (mtp) REVERT: D 213 ASP cc_start: 0.7824 (m-30) cc_final: 0.7584 (m-30) REVERT: D 226 MET cc_start: 0.7183 (mmm) cc_final: 0.6660 (mmm) REVERT: D 228 MET cc_start: 0.7387 (mtm) cc_final: 0.7155 (ptp) REVERT: D 235 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8491 (ttpp) REVERT: D 241 MET cc_start: 0.8307 (mmm) cc_final: 0.7707 (mmm) REVERT: D 263 MET cc_start: 0.7967 (mmm) cc_final: 0.7735 (mmm) REVERT: D 280 TYR cc_start: 0.8461 (m-80) cc_final: 0.7955 (m-80) REVERT: D 286 ASP cc_start: 0.7139 (p0) cc_final: 0.6824 (p0) REVERT: D 293 LEU cc_start: 0.8703 (tp) cc_final: 0.8415 (tp) REVERT: D 296 GLU cc_start: 0.7619 (pt0) cc_final: 0.7280 (pt0) REVERT: D 300 LYS cc_start: 0.8431 (mttm) cc_final: 0.7996 (mttm) REVERT: D 307 ILE cc_start: 0.8292 (mm) cc_final: 0.8060 (mm) REVERT: D 324 TYR cc_start: 0.7681 (m-80) cc_final: 0.7365 (m-80) REVERT: D 326 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7153 (mm-30) REVERT: D 329 TYR cc_start: 0.5988 (t80) cc_final: 0.5370 (t80) REVERT: D 333 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7579 (ttmt) REVERT: D 347 GLU cc_start: 0.7782 (tp30) cc_final: 0.6965 (tp30) REVERT: D 349 VAL cc_start: 0.9125 (t) cc_final: 0.8925 (p) REVERT: D 392 GLU cc_start: 0.7734 (tp30) cc_final: 0.7125 (tp30) REVERT: D 397 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 416 LYS cc_start: 0.8094 (mppt) cc_final: 0.7362 (mppt) REVERT: E 18 LYS cc_start: 0.9164 (tppt) cc_final: 0.8920 (tppt) REVERT: E 34 LYS cc_start: 0.8823 (tttp) cc_final: 0.8326 (tttp) REVERT: E 38 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8445 (mtpt) REVERT: E 39 LEU cc_start: 0.8849 (mt) cc_final: 0.8497 (mt) REVERT: E 41 LYS cc_start: 0.8942 (ttpt) cc_final: 0.8587 (ttpt) REVERT: E 47 TYR cc_start: 0.6294 (t80) cc_final: 0.6005 (t80) REVERT: E 53 ILE cc_start: 0.8982 (mm) cc_final: 0.8733 (tp) REVERT: E 79 LYS cc_start: 0.8284 (mtmt) cc_final: 0.8013 (tttt) REVERT: E 85 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.5787 (mp0) REVERT: E 86 ASP cc_start: 0.8414 (t0) cc_final: 0.8048 (t70) REVERT: E 95 GLU cc_start: 0.8473 (tt0) cc_final: 0.7848 (tt0) REVERT: E 104 PHE cc_start: 0.8603 (t80) cc_final: 0.8246 (t80) REVERT: E 118 GLU cc_start: 0.8232 (mt-10) cc_final: 0.8026 (mt-10) REVERT: E 139 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7650 (ttp80) REVERT: E 146 PHE cc_start: 0.7519 (m-10) cc_final: 0.7158 (m-10) REVERT: E 193 ASN cc_start: 0.8387 (m-40) cc_final: 0.8152 (m-40) REVERT: E 215 LEU cc_start: 0.9041 (tp) cc_final: 0.8833 (tp) REVERT: E 228 MET cc_start: 0.7206 (ptm) cc_final: 0.6868 (ptm) REVERT: E 241 MET cc_start: 0.7904 (mmm) cc_final: 0.7531 (mmm) REVERT: E 242 LEU cc_start: 0.8716 (mp) cc_final: 0.8141 (mp) REVERT: E 258 GLU cc_start: 0.8245 (mp0) cc_final: 0.7717 (mp0) REVERT: E 259 TYR cc_start: 0.9248 (t80) cc_final: 0.8827 (t80) REVERT: E 263 MET cc_start: 0.8789 (mmp) cc_final: 0.8363 (tpp) REVERT: E 265 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8700 (mtpt) REVERT: E 269 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8490 (ttmm) REVERT: E 271 THR cc_start: 0.9211 (p) cc_final: 0.8823 (t) REVERT: E 301 LYS cc_start: 0.8104 (ptpt) cc_final: 0.7601 (ptpt) REVERT: E 326 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7464 (mt-10) REVERT: E 329 TYR cc_start: 0.6842 (t80) cc_final: 0.6635 (t80) REVERT: E 333 LYS cc_start: 0.7847 (tttp) cc_final: 0.7365 (tttp) REVERT: E 411 LYS cc_start: 0.8288 (mtpp) cc_final: 0.8064 (ttmm) REVERT: E 416 LYS cc_start: 0.8197 (mttp) cc_final: 0.7611 (mttp) REVERT: F 29 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7582 (mm-30) REVERT: F 34 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8181 (ttmm) REVERT: F 43 HIS cc_start: 0.8410 (t-90) cc_final: 0.7866 (t-90) REVERT: F 60 LEU cc_start: 0.8747 (tp) cc_final: 0.8523 (tp) REVERT: F 61 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7269 (mm-30) REVERT: F 62 ASN cc_start: 0.8491 (m-40) cc_final: 0.8150 (t0) REVERT: F 82 ASP cc_start: 0.7582 (t0) cc_final: 0.7286 (t0) REVERT: F 93 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7986 (mt-10) REVERT: F 95 GLU cc_start: 0.8160 (tt0) cc_final: 0.7801 (tt0) REVERT: F 96 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8171 (ttpp) REVERT: F 116 ASN cc_start: 0.8649 (t0) cc_final: 0.8133 (t0) REVERT: F 119 LEU cc_start: 0.8599 (mt) cc_final: 0.8229 (mt) REVERT: F 156 ASP cc_start: 0.8250 (t0) cc_final: 0.7869 (t0) REVERT: F 157 ASP cc_start: 0.7836 (m-30) cc_final: 0.6675 (m-30) REVERT: F 158 TYR cc_start: 0.7492 (p90) cc_final: 0.6837 (p90) REVERT: F 183 THR cc_start: 0.7942 (p) cc_final: 0.7400 (t) REVERT: F 184 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7729 (mmmt) REVERT: F 189 THR cc_start: 0.8137 (p) cc_final: 0.7612 (t) REVERT: F 237 ILE cc_start: 0.9116 (mm) cc_final: 0.8484 (mt) REVERT: F 246 LEU cc_start: 0.8016 (mt) cc_final: 0.7656 (mt) REVERT: F 256 TYR cc_start: 0.7571 (t80) cc_final: 0.6579 (t80) REVERT: F 258 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7797 (mt-10) REVERT: F 275 LEU cc_start: 0.8473 (tp) cc_final: 0.8158 (tt) REVERT: F 291 ARG cc_start: 0.8138 (mtt90) cc_final: 0.6978 (mtt90) REVERT: F 295 ASN cc_start: 0.8199 (m-40) cc_final: 0.7934 (m-40) REVERT: F 296 GLU cc_start: 0.7500 (pt0) cc_final: 0.7201 (pt0) REVERT: F 326 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 333 LYS cc_start: 0.8553 (ttpp) cc_final: 0.8285 (ttpp) REVERT: F 338 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6967 (mm-30) REVERT: F 370 ASP cc_start: 0.7246 (m-30) cc_final: 0.6962 (m-30) REVERT: F 404 ILE cc_start: 0.8587 (mt) cc_final: 0.8109 (mt) REVERT: F 405 LYS cc_start: 0.7292 (tptp) cc_final: 0.5855 (mmmt) REVERT: F 407 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7682 (tmm-80) REVERT: F 426 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7129 (mm-40) REVERT: G 8 ASP cc_start: 0.8655 (m-30) cc_final: 0.8190 (m-30) REVERT: G 19 LEU cc_start: 0.8205 (mt) cc_final: 0.7885 (tt) REVERT: G 77 TYR cc_start: 0.8556 (t80) cc_final: 0.7945 (t80) REVERT: G 78 LEU cc_start: 0.9499 (mt) cc_final: 0.9245 (mt) REVERT: G 82 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8204 (tp30) REVERT: G 84 ASP cc_start: 0.8827 (p0) cc_final: 0.8568 (p0) REVERT: G 85 LEU cc_start: 0.9295 (mt) cc_final: 0.9093 (mm) REVERT: G 89 TYR cc_start: 0.8107 (t80) cc_final: 0.7677 (t80) REVERT: G 91 PHE cc_start: 0.8612 (t80) cc_final: 0.8359 (t80) REVERT: G 97 LYS cc_start: 0.8183 (tppp) cc_final: 0.7315 (tppp) REVERT: G 186 ASN cc_start: 0.8059 (p0) cc_final: 0.5394 (p0) REVERT: G 230 VAL cc_start: 0.8189 (m) cc_final: 0.7888 (m) REVERT: G 238 ASP cc_start: 0.8456 (m-30) cc_final: 0.8050 (m-30) REVERT: G 240 LEU cc_start: 0.9073 (mt) cc_final: 0.8869 (mt) REVERT: G 276 ASP cc_start: 0.8545 (p0) cc_final: 0.8017 (p0) REVERT: G 283 LYS cc_start: 0.9211 (pttm) cc_final: 0.8912 (pttp) REVERT: G 285 VAL cc_start: 0.9167 (p) cc_final: 0.7720 (p) REVERT: G 296 LYS cc_start: 0.8889 (mppt) cc_final: 0.8631 (mmmt) REVERT: G 307 MET cc_start: 0.8910 (mmt) cc_final: 0.8462 (mmm) REVERT: G 328 GLN cc_start: 0.6920 (tp40) cc_final: 0.6626 (tp40) REVERT: G 338 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8785 (mmtt) outliers start: 3 outliers final: 0 residues processed: 1166 average time/residue: 0.1782 time to fit residues: 311.9829 Evaluate side-chains 1071 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1070 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 52 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 285 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 184 optimal weight: 9.9990 chunk 219 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 193 ASN A 219 HIS A 240 ASN B 99 GLN B 295 ASN B 403 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 114 GLN D 403 GLN D 422 GLN E 219 HIS F 13 GLN F 48 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 HIS ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104009 restraints weight = 48885.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107631 restraints weight = 25395.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.110066 restraints weight = 15538.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111680 restraints weight = 10691.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112647 restraints weight = 8096.330| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24515 Z= 0.155 Angle : 0.644 9.236 33269 Z= 0.338 Chirality : 0.044 0.280 3697 Planarity : 0.004 0.076 4105 Dihedral : 10.329 168.502 3441 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.04 % Allowed : 2.24 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.17 (0.16), residues: 2917 helix: 1.16 (0.14), residues: 1446 sheet: -1.33 (0.27), residues: 389 loop : -1.35 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 143 TYR 0.036 0.002 TYR B 165 PHE 0.024 0.002 PHE G 91 TRP 0.036 0.002 TRP F 154 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (24510) covalent geometry : angle 0.63979 / 0.34 (33263) hydrogen bonds : bond 0.03586 / 2.43 ( 1174) hydrogen bonds : angle 4.95868 / 3.56 ( 3363) metal coordination : bond 0.01019 / 0.51 ( 4) metal coordination : angle 5.37955 / 2.79 ( 6) Misc. bond : bond 0.00107 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1159 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8055 (tpp) cc_final: 0.7758 (tpp) REVERT: A 3 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7447 (mm-30) REVERT: A 11 PHE cc_start: 0.7962 (m-80) cc_final: 0.7421 (m-10) REVERT: A 19 VAL cc_start: 0.8215 (m) cc_final: 0.7929 (p) REVERT: A 26 GLU cc_start: 0.7837 (pm20) cc_final: 0.7183 (pm20) REVERT: A 35 ASN cc_start: 0.8524 (m-40) cc_final: 0.8156 (m110) REVERT: A 39 LEU cc_start: 0.9109 (mt) cc_final: 0.8883 (mt) REVERT: A 42 SER cc_start: 0.8542 (m) cc_final: 0.8310 (p) REVERT: A 47 TYR cc_start: 0.6351 (m-10) cc_final: 0.6140 (m-80) REVERT: A 60 LEU cc_start: 0.9135 (tp) cc_final: 0.8923 (tp) REVERT: A 73 VAL cc_start: 0.8929 (t) cc_final: 0.8213 (p) REVERT: A 85 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7089 (mm-30) REVERT: A 93 GLU cc_start: 0.8107 (tp30) cc_final: 0.7592 (tp30) REVERT: A 113 ILE cc_start: 0.9035 (mt) cc_final: 0.8813 (mt) REVERT: A 123 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7907 (mmmm) REVERT: A 136 ASP cc_start: 0.7469 (m-30) cc_final: 0.7260 (m-30) REVERT: A 146 PHE cc_start: 0.8299 (m-10) cc_final: 0.7852 (m-10) REVERT: A 171 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7783 (mmtm) REVERT: A 174 PHE cc_start: 0.8644 (m-80) cc_final: 0.8410 (m-80) REVERT: A 184 LYS cc_start: 0.8575 (mmtp) cc_final: 0.8304 (mmtp) REVERT: A 214 TYR cc_start: 0.8504 (m-80) cc_final: 0.7760 (m-80) REVERT: A 215 LEU cc_start: 0.8418 (tp) cc_final: 0.8167 (tp) REVERT: A 235 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8145 (ttpt) REVERT: A 238 ASP cc_start: 0.8603 (m-30) cc_final: 0.8398 (m-30) REVERT: A 241 MET cc_start: 0.8160 (mmm) cc_final: 0.7557 (mmm) REVERT: A 248 ASP cc_start: 0.7716 (m-30) cc_final: 0.7341 (m-30) REVERT: A 265 LYS cc_start: 0.8915 (ttpp) cc_final: 0.8609 (ttpp) REVERT: A 268 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 278 LYS cc_start: 0.8283 (tptm) cc_final: 0.7838 (mtpp) REVERT: A 316 CYS cc_start: 0.8019 (m) cc_final: 0.7481 (m) REVERT: A 345 GLU cc_start: 0.7176 (pp20) cc_final: 0.6933 (pp20) REVERT: A 347 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 384 MET cc_start: 0.8335 (ttt) cc_final: 0.7997 (ttm) REVERT: A 404 ILE cc_start: 0.8520 (mt) cc_final: 0.8028 (mt) REVERT: A 408 TYR cc_start: 0.8476 (m-80) cc_final: 0.8209 (m-80) REVERT: A 426 GLN cc_start: 0.8256 (mt0) cc_final: 0.7933 (mt0) REVERT: B 8 HIS cc_start: 0.8109 (m90) cc_final: 0.7888 (m90) REVERT: B 15 TYR cc_start: 0.8437 (t80) cc_final: 0.8094 (t80) REVERT: B 36 THR cc_start: 0.8528 (m) cc_final: 0.8276 (p) REVERT: B 41 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8394 (ttmt) REVERT: B 43 HIS cc_start: 0.8758 (t-90) cc_final: 0.8440 (t-170) REVERT: B 47 TYR cc_start: 0.8560 (m-80) cc_final: 0.7466 (m-10) REVERT: B 54 ASN cc_start: 0.8563 (m-40) cc_final: 0.8327 (m-40) REVERT: B 79 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8403 (ttmm) REVERT: B 103 MET cc_start: 0.7797 (mmm) cc_final: 0.7494 (mmm) REVERT: B 109 LYS cc_start: 0.9222 (tptt) cc_final: 0.8990 (ttmm) REVERT: B 139 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: B 145 SER cc_start: 0.8509 (p) cc_final: 0.7805 (p) REVERT: B 147 ASP cc_start: 0.7024 (m-30) cc_final: 0.6666 (m-30) REVERT: B 155 MET cc_start: 0.7810 (tpp) cc_final: 0.7276 (tpp) REVERT: B 159 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7643 (mm-30) REVERT: B 166 MET cc_start: 0.7355 (ppp) cc_final: 0.7016 (ppp) REVERT: B 167 ASN cc_start: 0.8564 (m-40) cc_final: 0.8193 (m-40) REVERT: B 213 ASP cc_start: 0.7818 (m-30) cc_final: 0.7521 (m-30) REVERT: B 226 MET cc_start: 0.8261 (mmm) cc_final: 0.7593 (mmp) REVERT: B 231 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 236 ARG cc_start: 0.7831 (ttm110) cc_final: 0.6928 (ttm110) REVERT: B 243 ASP cc_start: 0.7206 (t0) cc_final: 0.6902 (t0) REVERT: B 245 SER cc_start: 0.8384 (t) cc_final: 0.7250 (p) REVERT: B 248 ASP cc_start: 0.7459 (m-30) cc_final: 0.7203 (m-30) REVERT: B 258 GLU cc_start: 0.8367 (pt0) cc_final: 0.8073 (pt0) REVERT: B 260 LYS cc_start: 0.8754 (tttp) cc_final: 0.8442 (tttp) REVERT: B 274 ARG cc_start: 0.7672 (mtp85) cc_final: 0.7421 (mtm-85) REVERT: B 278 LYS cc_start: 0.8459 (tptp) cc_final: 0.8250 (tptp) REVERT: B 279 GLN cc_start: 0.8542 (tt0) cc_final: 0.7931 (tt0) REVERT: B 318 SER cc_start: 0.8154 (m) cc_final: 0.7359 (t) REVERT: B 324 TYR cc_start: 0.7498 (t80) cc_final: 0.7272 (t80) REVERT: B 368 MET cc_start: 0.8292 (tpp) cc_final: 0.8045 (ttt) REVERT: B 384 MET cc_start: 0.8197 (mmm) cc_final: 0.7798 (mmm) REVERT: B 392 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 403 GLN cc_start: 0.7360 (tt0) cc_final: 0.6547 (pt0) REVERT: B 413 LYS cc_start: 0.8432 (tppt) cc_final: 0.7842 (tppt) REVERT: C 13 GLN cc_start: 0.7671 (tp40) cc_final: 0.7183 (tp40) REVERT: C 26 GLU cc_start: 0.8063 (pt0) cc_final: 0.7733 (pt0) REVERT: C 39 LEU cc_start: 0.8620 (mt) cc_final: 0.8329 (mt) REVERT: C 41 LYS cc_start: 0.8791 (tttt) cc_final: 0.8326 (tttt) REVERT: C 85 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 103 MET cc_start: 0.8167 (mmt) cc_final: 0.7949 (mmt) REVERT: C 113 ILE cc_start: 0.8906 (mt) cc_final: 0.8230 (mm) REVERT: C 128 MET cc_start: 0.7917 (mmm) cc_final: 0.7646 (mmm) REVERT: C 140 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7806 (tm-30) REVERT: C 166 MET cc_start: 0.7270 (tpt) cc_final: 0.6562 (tpt) REVERT: C 178 ILE cc_start: 0.8075 (tp) cc_final: 0.7690 (mm) REVERT: C 213 ASP cc_start: 0.8046 (m-30) cc_final: 0.7736 (m-30) REVERT: C 224 ILE cc_start: 0.8057 (mt) cc_final: 0.7823 (tp) REVERT: C 226 MET cc_start: 0.8511 (mmm) cc_final: 0.8304 (mmp) REVERT: C 241 MET cc_start: 0.8140 (mmm) cc_final: 0.7552 (mmm) REVERT: C 243 ASP cc_start: 0.7739 (t0) cc_final: 0.7470 (t0) REVERT: C 247 ASP cc_start: 0.7947 (m-30) cc_final: 0.7634 (m-30) REVERT: C 263 MET cc_start: 0.7455 (mmm) cc_final: 0.7169 (mmm) REVERT: C 279 GLN cc_start: 0.8151 (tt0) cc_final: 0.7779 (tt0) REVERT: C 280 TYR cc_start: 0.8649 (m-80) cc_final: 0.7752 (m-80) REVERT: C 292 SER cc_start: 0.9069 (m) cc_final: 0.8718 (t) REVERT: C 293 LEU cc_start: 0.8550 (tp) cc_final: 0.8236 (tp) REVERT: C 318 SER cc_start: 0.7927 (t) cc_final: 0.7540 (p) REVERT: C 342 LEU cc_start: 0.8678 (tp) cc_final: 0.8432 (tp) REVERT: C 345 GLU cc_start: 0.8250 (tt0) cc_final: 0.7895 (tt0) REVERT: C 393 LEU cc_start: 0.8856 (mt) cc_final: 0.8628 (mt) REVERT: C 423 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8574 (mmmm) REVERT: D 41 LYS cc_start: 0.8682 (ttpp) cc_final: 0.8147 (ttpp) REVERT: D 47 TYR cc_start: 0.9013 (m-80) cc_final: 0.8110 (m-80) REVERT: D 67 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 74 LYS cc_start: 0.9000 (tttp) cc_final: 0.8708 (mmmm) REVERT: D 90 LEU cc_start: 0.8394 (mm) cc_final: 0.8185 (mm) REVERT: D 93 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7337 (mm-30) REVERT: D 96 LYS cc_start: 0.8508 (ttpp) cc_final: 0.7860 (ttpp) REVERT: D 109 LYS cc_start: 0.8237 (tttp) cc_final: 0.7872 (ttmm) REVERT: D 118 GLU cc_start: 0.7349 (tp30) cc_final: 0.6909 (tp30) REVERT: D 128 MET cc_start: 0.8654 (tpp) cc_final: 0.8384 (tpp) REVERT: D 140 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7888 (mm110) REVERT: D 143 SER cc_start: 0.9018 (m) cc_final: 0.8211 (t) REVERT: D 147 ASP cc_start: 0.7451 (p0) cc_final: 0.7100 (p0) REVERT: D 154 TRP cc_start: 0.8765 (t60) cc_final: 0.8488 (t60) REVERT: D 155 MET cc_start: 0.7848 (tpt) cc_final: 0.7307 (tpt) REVERT: D 189 THR cc_start: 0.8656 (p) cc_final: 0.6888 (p) REVERT: D 196 MET cc_start: 0.7536 (mtp) cc_final: 0.7262 (mtp) REVERT: D 226 MET cc_start: 0.7103 (mmm) cc_final: 0.6730 (mmm) REVERT: D 235 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8599 (ttpp) REVERT: D 263 MET cc_start: 0.7928 (mmm) cc_final: 0.7689 (mmm) REVERT: D 264 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8155 (mm-30) REVERT: D 267 ARG cc_start: 0.8175 (ttm110) cc_final: 0.7951 (ttp-110) REVERT: D 280 TYR cc_start: 0.8452 (m-80) cc_final: 0.8028 (m-80) REVERT: D 300 LYS cc_start: 0.8500 (mttm) cc_final: 0.7720 (mttm) REVERT: D 307 ILE cc_start: 0.8203 (mm) cc_final: 0.7998 (mm) REVERT: D 324 TYR cc_start: 0.7705 (m-80) cc_final: 0.7383 (m-80) REVERT: D 326 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7131 (mm-30) REVERT: D 338 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6888 (mt-10) REVERT: D 347 GLU cc_start: 0.7814 (tp30) cc_final: 0.7155 (tp30) REVERT: E 12 ASP cc_start: 0.8632 (t0) cc_final: 0.8427 (t70) REVERT: E 18 LYS cc_start: 0.9162 (tppt) cc_final: 0.8839 (tppt) REVERT: E 34 LYS cc_start: 0.8802 (tttp) cc_final: 0.8157 (tttp) REVERT: E 35 ASN cc_start: 0.8403 (m-40) cc_final: 0.7762 (m-40) REVERT: E 38 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8438 (mtpt) REVERT: E 39 LEU cc_start: 0.8766 (mt) cc_final: 0.8463 (mt) REVERT: E 41 LYS cc_start: 0.8956 (ttpt) cc_final: 0.8734 (ttpt) REVERT: E 47 TYR cc_start: 0.6310 (t80) cc_final: 0.6010 (t80) REVERT: E 53 ILE cc_start: 0.8986 (mm) cc_final: 0.8730 (tp) REVERT: E 79 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8043 (tttt) REVERT: E 86 ASP cc_start: 0.8421 (t0) cc_final: 0.8195 (t70) REVERT: E 95 GLU cc_start: 0.8517 (tt0) cc_final: 0.7938 (tt0) REVERT: E 103 MET cc_start: 0.7719 (mmp) cc_final: 0.7205 (mmt) REVERT: E 104 PHE cc_start: 0.8594 (t80) cc_final: 0.8119 (t80) REVERT: E 146 PHE cc_start: 0.7545 (m-10) cc_final: 0.7169 (m-10) REVERT: E 181 LYS cc_start: 0.8466 (tmmt) cc_final: 0.7913 (tmmt) REVERT: E 182 ILE cc_start: 0.7903 (pt) cc_final: 0.7668 (pt) REVERT: E 215 LEU cc_start: 0.9074 (tp) cc_final: 0.8795 (tp) REVERT: E 228 MET cc_start: 0.7213 (ptm) cc_final: 0.6881 (ptm) REVERT: E 238 ASP cc_start: 0.8570 (m-30) cc_final: 0.8369 (m-30) REVERT: E 241 MET cc_start: 0.7931 (mmm) cc_final: 0.7496 (mmm) REVERT: E 248 ASP cc_start: 0.7907 (m-30) cc_final: 0.7618 (m-30) REVERT: E 258 GLU cc_start: 0.8194 (mp0) cc_final: 0.7753 (mp0) REVERT: E 259 TYR cc_start: 0.9204 (t80) cc_final: 0.8864 (t80) REVERT: E 263 MET cc_start: 0.8709 (mmp) cc_final: 0.8383 (tpp) REVERT: E 265 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8663 (mtpt) REVERT: E 271 THR cc_start: 0.9223 (p) cc_final: 0.8841 (t) REVERT: E 301 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7698 (ptpt) REVERT: E 326 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7633 (mt-10) REVERT: E 333 LYS cc_start: 0.7860 (tttp) cc_final: 0.7422 (tttp) REVERT: E 416 LYS cc_start: 0.7975 (mttp) cc_final: 0.7712 (mttp) REVERT: F 13 GLN cc_start: 0.8126 (tp-100) cc_final: 0.7864 (tm-30) REVERT: F 22 TYR cc_start: 0.8457 (m-80) cc_final: 0.8229 (m-10) REVERT: F 29 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7564 (mm-30) REVERT: F 34 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8108 (ttmm) REVERT: F 38 LYS cc_start: 0.9098 (mmtp) cc_final: 0.8711 (mmtp) REVERT: F 43 HIS cc_start: 0.8507 (t-90) cc_final: 0.7848 (t-90) REVERT: F 60 LEU cc_start: 0.8755 (tp) cc_final: 0.8553 (tp) REVERT: F 61 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7303 (mm-30) REVERT: F 82 ASP cc_start: 0.7571 (t0) cc_final: 0.7275 (t0) REVERT: F 93 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7539 (mt-10) REVERT: F 95 GLU cc_start: 0.8132 (tt0) cc_final: 0.7689 (tt0) REVERT: F 96 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8276 (ttpp) REVERT: F 116 ASN cc_start: 0.8634 (t0) cc_final: 0.8207 (t0) REVERT: F 119 LEU cc_start: 0.8618 (mt) cc_final: 0.8186 (mt) REVERT: F 123 LYS cc_start: 0.8655 (tppt) cc_final: 0.8382 (tppt) REVERT: F 155 MET cc_start: 0.6767 (tpp) cc_final: 0.6381 (tpp) REVERT: F 157 ASP cc_start: 0.7964 (m-30) cc_final: 0.7402 (m-30) REVERT: F 158 TYR cc_start: 0.7586 (p90) cc_final: 0.7199 (p90) REVERT: F 183 THR cc_start: 0.7909 (p) cc_final: 0.7352 (t) REVERT: F 184 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7706 (mmmt) REVERT: F 189 THR cc_start: 0.8102 (p) cc_final: 0.7552 (t) REVERT: F 237 ILE cc_start: 0.9172 (mm) cc_final: 0.8473 (mt) REVERT: F 246 LEU cc_start: 0.7929 (mt) cc_final: 0.7687 (mt) REVERT: F 265 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8590 (mmtm) REVERT: F 268 GLU cc_start: 0.8079 (pt0) cc_final: 0.7839 (pt0) REVERT: F 296 GLU cc_start: 0.7584 (pt0) cc_final: 0.7373 (pt0) REVERT: F 326 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7702 (mm-30) REVERT: F 333 LYS cc_start: 0.8579 (ttpp) cc_final: 0.8348 (ttpp) REVERT: F 338 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7080 (mm-30) REVERT: F 340 ARG cc_start: 0.9072 (ttt-90) cc_final: 0.8788 (ttt-90) REVERT: F 355 GLN cc_start: 0.7602 (mt0) cc_final: 0.7370 (mt0) REVERT: F 370 ASP cc_start: 0.7215 (m-30) cc_final: 0.6882 (m-30) REVERT: F 384 MET cc_start: 0.7148 (mtm) cc_final: 0.6796 (mtm) REVERT: F 404 ILE cc_start: 0.8524 (mt) cc_final: 0.8007 (mt) REVERT: F 405 LYS cc_start: 0.6942 (tptp) cc_final: 0.6280 (tptp) REVERT: F 407 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7972 (ttp80) REVERT: F 411 LYS cc_start: 0.6934 (mtmm) cc_final: 0.6597 (mtpp) REVERT: F 430 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6889 (mm-30) REVERT: G 8 ASP cc_start: 0.8681 (m-30) cc_final: 0.8227 (m-30) REVERT: G 19 LEU cc_start: 0.8272 (mt) cc_final: 0.8007 (tt) REVERT: G 63 ILE cc_start: 0.8638 (mp) cc_final: 0.8371 (mm) REVERT: G 77 TYR cc_start: 0.8407 (t80) cc_final: 0.7898 (t80) REVERT: G 78 LEU cc_start: 0.9465 (mt) cc_final: 0.9181 (mt) REVERT: G 85 LEU cc_start: 0.9288 (mt) cc_final: 0.8486 (mt) REVERT: G 89 TYR cc_start: 0.8100 (t80) cc_final: 0.7623 (t80) REVERT: G 95 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8603 (mtpp) REVERT: G 97 LYS cc_start: 0.8166 (tppp) cc_final: 0.7284 (tppp) REVERT: G 100 SER cc_start: 0.8765 (p) cc_final: 0.8356 (p) REVERT: G 238 ASP cc_start: 0.8494 (m-30) cc_final: 0.7985 (m-30) REVERT: G 240 LEU cc_start: 0.9029 (mt) cc_final: 0.8800 (mt) REVERT: G 276 ASP cc_start: 0.8636 (p0) cc_final: 0.8088 (p0) REVERT: G 278 ILE cc_start: 0.9103 (mp) cc_final: 0.8861 (mp) REVERT: G 279 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8848 (mttm) REVERT: G 283 LYS cc_start: 0.9171 (pttm) cc_final: 0.8927 (ptpp) REVERT: G 305 ASN cc_start: 0.8059 (t0) cc_final: 0.7847 (t0) REVERT: G 307 MET cc_start: 0.8914 (mmt) cc_final: 0.8536 (mmm) REVERT: G 328 GLN cc_start: 0.7725 (tp40) cc_final: 0.7354 (tp40) REVERT: G 333 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8749 (mmtt) REVERT: G 334 MET cc_start: 0.7960 (tpp) cc_final: 0.7717 (tpp) outliers start: 1 outliers final: 0 residues processed: 1159 average time/residue: 0.1810 time to fit residues: 316.1798 Evaluate side-chains 1081 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1081 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 250 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 282 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN A 219 HIS A 220 ASN A 240 ASN B 99 GLN B 403 GLN C 114 GLN D 100 GLN D 114 GLN D 422 GLN E 219 HIS F 48 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104273 restraints weight = 48803.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107863 restraints weight = 25477.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.110282 restraints weight = 15607.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111833 restraints weight = 10710.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112948 restraints weight = 8143.912| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24515 Z= 0.156 Angle : 0.648 12.837 33269 Z= 0.339 Chirality : 0.045 0.261 3697 Planarity : 0.004 0.066 4105 Dihedral : 10.238 162.942 3441 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.23 (0.16), residues: 2917 helix: 1.06 (0.14), residues: 1448 sheet: -1.24 (0.27), residues: 384 loop : -1.36 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 267 TYR 0.039 0.002 TYR G 54 PHE 0.021 0.002 PHE G 91 TRP 0.039 0.002 TRP E 414 HIS 0.005 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (24510) covalent geometry : angle 0.64460 / 0.34 (33263) hydrogen bonds : bond 0.03558 / 2.41 ( 1174) hydrogen bonds : angle 4.93830 / 3.55 ( 3363) metal coordination : bond 0.00989 / 0.49 ( 4) metal coordination : angle 5.13015 / 2.66 ( 6) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1138 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8119 (tpp) cc_final: 0.7844 (tpp) REVERT: A 3 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 11 PHE cc_start: 0.7814 (m-80) cc_final: 0.7476 (m-10) REVERT: A 19 VAL cc_start: 0.8236 (m) cc_final: 0.7943 (p) REVERT: A 26 GLU cc_start: 0.7824 (pm20) cc_final: 0.7154 (pm20) REVERT: A 29 GLU cc_start: 0.7591 (tt0) cc_final: 0.7336 (tt0) REVERT: A 35 ASN cc_start: 0.8518 (m-40) cc_final: 0.8138 (m110) REVERT: A 39 LEU cc_start: 0.9064 (mt) cc_final: 0.8832 (mt) REVERT: A 42 SER cc_start: 0.8523 (m) cc_final: 0.8249 (p) REVERT: A 47 TYR cc_start: 0.6334 (m-10) cc_final: 0.6130 (m-80) REVERT: A 73 VAL cc_start: 0.8917 (t) cc_final: 0.8236 (p) REVERT: A 83 SER cc_start: 0.8443 (m) cc_final: 0.8196 (m) REVERT: A 85 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7053 (mm-30) REVERT: A 93 GLU cc_start: 0.8064 (tp30) cc_final: 0.7508 (tp30) REVERT: A 104 PHE cc_start: 0.7950 (t80) cc_final: 0.7539 (t80) REVERT: A 123 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7875 (mmmm) REVERT: A 131 VAL cc_start: 0.8789 (m) cc_final: 0.8549 (p) REVERT: A 139 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7218 (ttm-80) REVERT: A 146 PHE cc_start: 0.8295 (m-10) cc_final: 0.7928 (m-10) REVERT: A 171 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7796 (mmtm) REVERT: A 184 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8268 (mmtp) REVERT: A 214 TYR cc_start: 0.8544 (m-80) cc_final: 0.8036 (m-10) REVERT: A 235 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8094 (ttpt) REVERT: A 241 MET cc_start: 0.8092 (mmm) cc_final: 0.7523 (mmm) REVERT: A 248 ASP cc_start: 0.7711 (m-30) cc_final: 0.7341 (m-30) REVERT: A 263 MET cc_start: 0.7650 (mmp) cc_final: 0.7397 (mmp) REVERT: A 265 LYS cc_start: 0.8944 (ttpp) cc_final: 0.8490 (ttpp) REVERT: A 268 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7750 (mt-10) REVERT: A 278 LYS cc_start: 0.8304 (tptm) cc_final: 0.7898 (mtpp) REVERT: A 279 GLN cc_start: 0.8675 (tt0) cc_final: 0.8435 (tt0) REVERT: A 313 LEU cc_start: 0.6901 (tt) cc_final: 0.6660 (tt) REVERT: A 316 CYS cc_start: 0.7931 (m) cc_final: 0.7434 (m) REVERT: A 345 GLU cc_start: 0.7129 (pp20) cc_final: 0.6891 (pp20) REVERT: A 384 MET cc_start: 0.8208 (ttt) cc_final: 0.7647 (ttm) REVERT: A 426 GLN cc_start: 0.8138 (mt0) cc_final: 0.7758 (mt0) REVERT: B 15 TYR cc_start: 0.8556 (t80) cc_final: 0.8292 (t80) REVERT: B 26 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7060 (mt-10) REVERT: B 36 THR cc_start: 0.8601 (m) cc_final: 0.8328 (p) REVERT: B 41 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8470 (ttmt) REVERT: B 43 HIS cc_start: 0.8757 (t-90) cc_final: 0.8429 (t-170) REVERT: B 47 TYR cc_start: 0.8492 (m-80) cc_final: 0.7397 (m-10) REVERT: B 54 ASN cc_start: 0.8553 (m-40) cc_final: 0.8293 (m-40) REVERT: B 103 MET cc_start: 0.7782 (mmm) cc_final: 0.7546 (mmm) REVERT: B 109 LYS cc_start: 0.9230 (tptt) cc_final: 0.8707 (ttmm) REVERT: B 139 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7614 (ttp-170) REVERT: B 145 SER cc_start: 0.8588 (p) cc_final: 0.8097 (t) REVERT: B 155 MET cc_start: 0.7726 (tpp) cc_final: 0.7252 (tpp) REVERT: B 166 MET cc_start: 0.7318 (ppp) cc_final: 0.7009 (ppp) REVERT: B 191 THR cc_start: 0.8421 (p) cc_final: 0.8215 (p) REVERT: B 213 ASP cc_start: 0.7706 (m-30) cc_final: 0.7431 (m-30) REVERT: B 226 MET cc_start: 0.8268 (mmm) cc_final: 0.7627 (mmp) REVERT: B 231 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 236 ARG cc_start: 0.7834 (ttm110) cc_final: 0.6860 (ttm110) REVERT: B 243 ASP cc_start: 0.7148 (t0) cc_final: 0.6839 (t0) REVERT: B 245 SER cc_start: 0.8411 (t) cc_final: 0.7232 (p) REVERT: B 248 ASP cc_start: 0.7465 (m-30) cc_final: 0.7192 (m-30) REVERT: B 258 GLU cc_start: 0.8388 (pt0) cc_final: 0.8079 (pt0) REVERT: B 260 LYS cc_start: 0.8713 (tttp) cc_final: 0.8435 (tppt) REVERT: B 265 LYS cc_start: 0.8949 (ttpp) cc_final: 0.8657 (ttpp) REVERT: B 266 TRP cc_start: 0.8559 (m100) cc_final: 0.8278 (m100) REVERT: B 274 ARG cc_start: 0.7675 (mtp85) cc_final: 0.7418 (mtm-85) REVERT: B 278 LYS cc_start: 0.8519 (tptp) cc_final: 0.8312 (tptp) REVERT: B 279 GLN cc_start: 0.8545 (tt0) cc_final: 0.7940 (tt0) REVERT: B 298 LYS cc_start: 0.8786 (pttp) cc_final: 0.8386 (pttp) REVERT: B 318 SER cc_start: 0.8118 (m) cc_final: 0.7354 (t) REVERT: B 324 TYR cc_start: 0.7481 (t80) cc_final: 0.7262 (t80) REVERT: B 392 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7035 (tm-30) REVERT: B 403 GLN cc_start: 0.7169 (tt0) cc_final: 0.6492 (pt0) REVERT: B 413 LYS cc_start: 0.8427 (tppt) cc_final: 0.7312 (tppt) REVERT: B 414 TRP cc_start: 0.7019 (m-90) cc_final: 0.6570 (m-90) REVERT: B 428 TRP cc_start: 0.8255 (m-10) cc_final: 0.8011 (m-10) REVERT: C 13 GLN cc_start: 0.7633 (tp40) cc_final: 0.7082 (tp40) REVERT: C 26 GLU cc_start: 0.8024 (pt0) cc_final: 0.7700 (pt0) REVERT: C 41 LYS cc_start: 0.8757 (tttt) cc_final: 0.8315 (tttt) REVERT: C 56 LEU cc_start: 0.8873 (mm) cc_final: 0.8651 (mm) REVERT: C 85 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7697 (mm-30) REVERT: C 113 ILE cc_start: 0.8933 (mt) cc_final: 0.8277 (mm) REVERT: C 128 MET cc_start: 0.7894 (mmm) cc_final: 0.7608 (mmm) REVERT: C 140 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 166 MET cc_start: 0.7271 (tpt) cc_final: 0.6693 (tpt) REVERT: C 184 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8251 (mtmm) REVERT: C 213 ASP cc_start: 0.8042 (m-30) cc_final: 0.7745 (m-30) REVERT: C 224 ILE cc_start: 0.7990 (mt) cc_final: 0.7755 (tt) REVERT: C 226 MET cc_start: 0.8541 (mmm) cc_final: 0.8341 (mmp) REVERT: C 240 ASN cc_start: 0.8250 (t0) cc_final: 0.7987 (t0) REVERT: C 241 MET cc_start: 0.8125 (mmm) cc_final: 0.7529 (mmm) REVERT: C 243 ASP cc_start: 0.7732 (t0) cc_final: 0.7458 (t0) REVERT: C 263 MET cc_start: 0.7441 (mmm) cc_final: 0.7147 (mmm) REVERT: C 279 GLN cc_start: 0.8138 (tt0) cc_final: 0.7778 (tt0) REVERT: C 292 SER cc_start: 0.9051 (m) cc_final: 0.8679 (t) REVERT: C 318 SER cc_start: 0.7701 (t) cc_final: 0.7361 (p) REVERT: C 342 LEU cc_start: 0.8649 (tp) cc_final: 0.8435 (tp) REVERT: C 345 GLU cc_start: 0.8247 (tt0) cc_final: 0.7851 (tt0) REVERT: C 356 VAL cc_start: 0.8381 (m) cc_final: 0.8076 (p) REVERT: C 367 ASN cc_start: 0.7846 (m110) cc_final: 0.7590 (m110) REVERT: C 393 LEU cc_start: 0.8855 (mt) cc_final: 0.8644 (mt) REVERT: D 24 ASP cc_start: 0.7605 (t70) cc_final: 0.7203 (t0) REVERT: D 37 PHE cc_start: 0.8937 (t80) cc_final: 0.8737 (t80) REVERT: D 38 LYS cc_start: 0.9121 (mttm) cc_final: 0.8794 (mttm) REVERT: D 41 LYS cc_start: 0.8652 (ttpp) cc_final: 0.7981 (ttpp) REVERT: D 46 GLU cc_start: 0.8115 (tt0) cc_final: 0.7601 (tt0) REVERT: D 47 TYR cc_start: 0.8974 (m-80) cc_final: 0.7941 (m-80) REVERT: D 62 ASN cc_start: 0.8336 (t0) cc_final: 0.8055 (t0) REVERT: D 74 LYS cc_start: 0.9007 (tttp) cc_final: 0.8706 (mmmm) REVERT: D 90 LEU cc_start: 0.8343 (mm) cc_final: 0.7705 (mm) REVERT: D 93 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7378 (mm-30) REVERT: D 96 LYS cc_start: 0.8521 (ttpp) cc_final: 0.7961 (ttpp) REVERT: D 118 GLU cc_start: 0.7148 (tp30) cc_final: 0.6841 (tp30) REVERT: D 143 SER cc_start: 0.9028 (m) cc_final: 0.8302 (t) REVERT: D 147 ASP cc_start: 0.7410 (p0) cc_final: 0.7135 (p0) REVERT: D 154 TRP cc_start: 0.8718 (t60) cc_final: 0.8443 (t60) REVERT: D 155 MET cc_start: 0.7861 (tpt) cc_final: 0.7267 (tpt) REVERT: D 159 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7761 (tp30) REVERT: D 189 THR cc_start: 0.8644 (p) cc_final: 0.6914 (p) REVERT: D 196 MET cc_start: 0.7545 (mtp) cc_final: 0.7233 (mtp) REVERT: D 223 TYR cc_start: 0.8160 (t80) cc_final: 0.6948 (t80) REVERT: D 226 MET cc_start: 0.6996 (mmm) cc_final: 0.6204 (mmm) REVERT: D 233 CYS cc_start: 0.7595 (m) cc_final: 0.7040 (m) REVERT: D 235 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8538 (ttpp) REVERT: D 263 MET cc_start: 0.7868 (mmm) cc_final: 0.7625 (mmm) REVERT: D 264 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8149 (mm-30) REVERT: D 280 TYR cc_start: 0.8460 (m-80) cc_final: 0.7980 (m-80) REVERT: D 296 GLU cc_start: 0.7530 (pt0) cc_final: 0.7146 (pt0) REVERT: D 324 TYR cc_start: 0.7707 (m-80) cc_final: 0.7375 (m-80) REVERT: D 326 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7119 (mm-30) REVERT: D 347 GLU cc_start: 0.7738 (tp30) cc_final: 0.7263 (tp30) REVERT: D 392 GLU cc_start: 0.7692 (tp30) cc_final: 0.7068 (tp30) REVERT: E 1 MET cc_start: 0.7854 (ptm) cc_final: 0.6684 (ptm) REVERT: E 12 ASP cc_start: 0.8723 (t0) cc_final: 0.8509 (t70) REVERT: E 18 LYS cc_start: 0.9139 (tppt) cc_final: 0.8922 (tppt) REVERT: E 23 MET cc_start: 0.8401 (mmt) cc_final: 0.8065 (mmt) REVERT: E 34 LYS cc_start: 0.8783 (tttp) cc_final: 0.8196 (tttp) REVERT: E 35 ASN cc_start: 0.8383 (m-40) cc_final: 0.7793 (m-40) REVERT: E 38 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8462 (mtpt) REVERT: E 39 LEU cc_start: 0.8753 (mt) cc_final: 0.8436 (mt) REVERT: E 41 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8680 (ttpt) REVERT: E 47 TYR cc_start: 0.6239 (t80) cc_final: 0.5963 (t80) REVERT: E 53 ILE cc_start: 0.8951 (mm) cc_final: 0.8681 (tp) REVERT: E 86 ASP cc_start: 0.8486 (t0) cc_final: 0.8228 (t0) REVERT: E 93 GLU cc_start: 0.7955 (tp30) cc_final: 0.7085 (tp30) REVERT: E 95 GLU cc_start: 0.8631 (tt0) cc_final: 0.7974 (tt0) REVERT: E 96 LYS cc_start: 0.8579 (tttp) cc_final: 0.8274 (ttpp) REVERT: E 103 MET cc_start: 0.7762 (mmp) cc_final: 0.7342 (mmp) REVERT: E 104 PHE cc_start: 0.8602 (t80) cc_final: 0.8270 (t80) REVERT: E 118 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8034 (mt-10) REVERT: E 146 PHE cc_start: 0.7577 (m-10) cc_final: 0.7143 (m-10) REVERT: E 181 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8025 (tmmt) REVERT: E 215 LEU cc_start: 0.9102 (tp) cc_final: 0.8807 (tp) REVERT: E 228 MET cc_start: 0.6979 (ptm) cc_final: 0.6744 (ptt) REVERT: E 237 ILE cc_start: 0.8915 (mt) cc_final: 0.8662 (mt) REVERT: E 238 ASP cc_start: 0.8547 (m-30) cc_final: 0.8307 (m-30) REVERT: E 241 MET cc_start: 0.7903 (mmm) cc_final: 0.7532 (mmm) REVERT: E 243 ASP cc_start: 0.8057 (t0) cc_final: 0.7851 (t0) REVERT: E 248 ASP cc_start: 0.7722 (m-30) cc_final: 0.7399 (m-30) REVERT: E 253 HIS cc_start: 0.7452 (m90) cc_final: 0.7093 (m90) REVERT: E 258 GLU cc_start: 0.8134 (mp0) cc_final: 0.7905 (mp0) REVERT: E 271 THR cc_start: 0.9187 (p) cc_final: 0.8812 (t) REVERT: E 296 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7167 (mt-10) REVERT: E 301 LYS cc_start: 0.8121 (ptpt) cc_final: 0.7668 (ptpt) REVERT: E 333 LYS cc_start: 0.7839 (tttp) cc_final: 0.7454 (tttp) REVERT: F 5 ILE cc_start: 0.8935 (mt) cc_final: 0.8585 (mt) REVERT: F 13 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7888 (tp40) REVERT: F 15 TYR cc_start: 0.8570 (t80) cc_final: 0.7216 (t80) REVERT: F 18 LYS cc_start: 0.8675 (tppt) cc_final: 0.8429 (tppt) REVERT: F 22 TYR cc_start: 0.8399 (m-80) cc_final: 0.8098 (m-10) REVERT: F 29 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7571 (mm-30) REVERT: F 34 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8074 (ttmm) REVERT: F 38 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8772 (mmtp) REVERT: F 43 HIS cc_start: 0.8499 (t-90) cc_final: 0.7869 (t-90) REVERT: F 60 LEU cc_start: 0.8786 (tp) cc_final: 0.8557 (tp) REVERT: F 61 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7290 (mm-30) REVERT: F 82 ASP cc_start: 0.7582 (t0) cc_final: 0.7282 (t0) REVERT: F 93 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7814 (mm-30) REVERT: F 95 GLU cc_start: 0.8105 (tt0) cc_final: 0.7611 (tt0) REVERT: F 96 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8323 (ttpp) REVERT: F 116 ASN cc_start: 0.8706 (t0) cc_final: 0.7078 (t0) REVERT: F 119 LEU cc_start: 0.8622 (mt) cc_final: 0.8192 (mt) REVERT: F 123 LYS cc_start: 0.8628 (tppt) cc_final: 0.8361 (tppt) REVERT: F 158 TYR cc_start: 0.7708 (p90) cc_final: 0.7207 (p90) REVERT: F 183 THR cc_start: 0.7948 (p) cc_final: 0.7428 (t) REVERT: F 184 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7742 (mmmt) REVERT: F 189 THR cc_start: 0.8080 (p) cc_final: 0.7631 (t) REVERT: F 191 THR cc_start: 0.8678 (p) cc_final: 0.7381 (m) REVERT: F 237 ILE cc_start: 0.9195 (mm) cc_final: 0.8456 (mt) REVERT: F 246 LEU cc_start: 0.7993 (mt) cc_final: 0.7702 (mt) REVERT: F 263 MET cc_start: 0.8554 (mmm) cc_final: 0.7848 (tpt) REVERT: F 265 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8458 (mmtm) REVERT: F 296 GLU cc_start: 0.7644 (pt0) cc_final: 0.7319 (pt0) REVERT: F 326 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7685 (mm-30) REVERT: F 333 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8390 (ttpp) REVERT: F 338 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7104 (mm-30) REVERT: F 340 ARG cc_start: 0.9078 (ttt-90) cc_final: 0.8746 (tpt-90) REVERT: F 384 MET cc_start: 0.7224 (mtm) cc_final: 0.6690 (mtm) REVERT: F 404 ILE cc_start: 0.8527 (mt) cc_final: 0.7971 (mt) REVERT: F 405 LYS cc_start: 0.7016 (tptp) cc_final: 0.6461 (tppp) REVERT: G 8 ASP cc_start: 0.8689 (m-30) cc_final: 0.8276 (m-30) REVERT: G 55 TYR cc_start: 0.7901 (m-80) cc_final: 0.7509 (m-80) REVERT: G 77 TYR cc_start: 0.8384 (t80) cc_final: 0.7981 (t80) REVERT: G 78 LEU cc_start: 0.9395 (mt) cc_final: 0.9156 (mt) REVERT: G 82 GLU cc_start: 0.8404 (tp30) cc_final: 0.8033 (tp30) REVERT: G 85 LEU cc_start: 0.9293 (mt) cc_final: 0.8553 (mt) REVERT: G 89 TYR cc_start: 0.8101 (t80) cc_final: 0.7706 (t80) REVERT: G 95 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8344 (mtpp) REVERT: G 100 SER cc_start: 0.8661 (p) cc_final: 0.8031 (p) REVERT: G 151 LYS cc_start: 0.8724 (ptpp) cc_final: 0.8505 (pttp) REVERT: G 238 ASP cc_start: 0.8436 (m-30) cc_final: 0.7914 (m-30) REVERT: G 240 LEU cc_start: 0.9067 (mt) cc_final: 0.8846 (mt) REVERT: G 276 ASP cc_start: 0.8605 (p0) cc_final: 0.8101 (p0) REVERT: G 279 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8863 (mttm) REVERT: G 283 LYS cc_start: 0.9127 (pttm) cc_final: 0.8857 (pttm) REVERT: G 295 ASP cc_start: 0.8514 (p0) cc_final: 0.7836 (p0) REVERT: G 296 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8551 (mmmt) REVERT: G 307 MET cc_start: 0.8848 (mmt) cc_final: 0.8457 (mmm) REVERT: G 328 GLN cc_start: 0.7816 (tp40) cc_final: 0.7313 (tp40) REVERT: G 333 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8814 (mmtt) REVERT: G 338 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8741 (mmtt) outliers start: 1 outliers final: 0 residues processed: 1138 average time/residue: 0.1863 time to fit residues: 319.7996 Evaluate side-chains 1052 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1052 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 191 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 32 optimal weight: 0.0970 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 219 HIS A 240 ASN B 99 GLN B 193 ASN D 100 GLN D 114 GLN F 48 HIS F 422 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.129502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.107956 restraints weight = 48691.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111731 restraints weight = 25176.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114278 restraints weight = 15376.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115916 restraints weight = 10546.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117034 restraints weight = 7995.167| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 24515 Z= 0.143 Angle : 0.647 10.420 33269 Z= 0.336 Chirality : 0.045 0.232 3697 Planarity : 0.004 0.063 4105 Dihedral : 10.169 156.364 3441 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.28 (0.16), residues: 2917 helix: 1.02 (0.14), residues: 1445 sheet: -1.27 (0.27), residues: 381 loop : -1.38 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 236 TYR 0.036 0.002 TYR B 165 PHE 0.021 0.002 PHE E 28 TRP 0.047 0.002 TRP G 266 HIS 0.014 0.001 HIS G 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24510) covalent geometry : angle 0.64417 / 0.34 (33263) hydrogen bonds : bond 0.03449 / 2.34 ( 1174) hydrogen bonds : angle 4.84268 / 3.47 ( 3363) metal coordination : bond 0.00914 / 0.46 ( 4) metal coordination : angle 4.78022 / 2.49 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1127 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 11 PHE cc_start: 0.7850 (m-80) cc_final: 0.7398 (m-10) REVERT: A 19 VAL cc_start: 0.8159 (m) cc_final: 0.7881 (p) REVERT: A 26 GLU cc_start: 0.7872 (pm20) cc_final: 0.7185 (pm20) REVERT: A 29 GLU cc_start: 0.7618 (tt0) cc_final: 0.7319 (tt0) REVERT: A 35 ASN cc_start: 0.8535 (m-40) cc_final: 0.8166 (m110) REVERT: A 39 LEU cc_start: 0.9063 (mt) cc_final: 0.8844 (mt) REVERT: A 42 SER cc_start: 0.8521 (m) cc_final: 0.8261 (p) REVERT: A 47 TYR cc_start: 0.6397 (m-10) cc_final: 0.6157 (m-80) REVERT: A 61 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6668 (tm-30) REVERT: A 73 VAL cc_start: 0.8954 (t) cc_final: 0.8435 (p) REVERT: A 85 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 93 GLU cc_start: 0.8106 (tp30) cc_final: 0.7515 (tp30) REVERT: A 104 PHE cc_start: 0.7794 (t80) cc_final: 0.7432 (t80) REVERT: A 123 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7923 (mmmm) REVERT: A 131 VAL cc_start: 0.8794 (m) cc_final: 0.8493 (p) REVERT: A 146 PHE cc_start: 0.8317 (m-10) cc_final: 0.7822 (m-10) REVERT: A 149 TYR cc_start: 0.6268 (t80) cc_final: 0.6046 (t80) REVERT: A 150 VAL cc_start: 0.8787 (p) cc_final: 0.8501 (m) REVERT: A 171 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7796 (mmtm) REVERT: A 174 PHE cc_start: 0.8839 (m-80) cc_final: 0.8514 (m-80) REVERT: A 184 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8380 (mmtp) REVERT: A 214 TYR cc_start: 0.8467 (m-80) cc_final: 0.8026 (m-10) REVERT: A 235 LYS cc_start: 0.8676 (ttpt) cc_final: 0.8095 (ttpt) REVERT: A 241 MET cc_start: 0.8122 (mmm) cc_final: 0.7539 (mmm) REVERT: A 248 ASP cc_start: 0.7629 (m-30) cc_final: 0.7270 (m-30) REVERT: A 263 MET cc_start: 0.7770 (mmp) cc_final: 0.7532 (mmp) REVERT: A 265 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8652 (ttpp) REVERT: A 268 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 278 LYS cc_start: 0.8154 (tptm) cc_final: 0.7734 (mtpp) REVERT: A 279 GLN cc_start: 0.8677 (tt0) cc_final: 0.8356 (tt0) REVERT: A 313 LEU cc_start: 0.6839 (tt) cc_final: 0.6500 (tt) REVERT: A 316 CYS cc_start: 0.8157 (m) cc_final: 0.7572 (m) REVERT: A 340 ARG cc_start: 0.6985 (ttt-90) cc_final: 0.6621 (ttt-90) REVERT: A 345 GLU cc_start: 0.7077 (pp20) cc_final: 0.6814 (pp20) REVERT: A 355 GLN cc_start: 0.7662 (mm110) cc_final: 0.7441 (mm110) REVERT: A 382 ASP cc_start: 0.7901 (m-30) cc_final: 0.7649 (m-30) REVERT: A 384 MET cc_start: 0.8345 (ttt) cc_final: 0.7748 (ttm) REVERT: A 426 GLN cc_start: 0.8161 (mt0) cc_final: 0.7775 (mt0) REVERT: B 4 ILE cc_start: 0.8495 (tp) cc_final: 0.8087 (tp) REVERT: B 15 TYR cc_start: 0.8573 (t80) cc_final: 0.8263 (t80) REVERT: B 36 THR cc_start: 0.8498 (m) cc_final: 0.8272 (p) REVERT: B 41 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8386 (ttmt) REVERT: B 43 HIS cc_start: 0.8756 (t-90) cc_final: 0.8420 (t-170) REVERT: B 47 TYR cc_start: 0.8495 (m-80) cc_final: 0.7387 (m-10) REVERT: B 54 ASN cc_start: 0.8539 (m-40) cc_final: 0.8308 (m-40) REVERT: B 79 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8536 (ttmm) REVERT: B 103 MET cc_start: 0.7921 (mmm) cc_final: 0.7655 (mmm) REVERT: B 139 ARG cc_start: 0.7900 (ttp-170) cc_final: 0.7663 (ttp-170) REVERT: B 145 SER cc_start: 0.8708 (p) cc_final: 0.8011 (t) REVERT: B 155 MET cc_start: 0.7771 (tpp) cc_final: 0.7316 (tpp) REVERT: B 191 THR cc_start: 0.8387 (p) cc_final: 0.8173 (p) REVERT: B 213 ASP cc_start: 0.7750 (m-30) cc_final: 0.7443 (m-30) REVERT: B 226 MET cc_start: 0.8206 (mmm) cc_final: 0.7500 (mmp) REVERT: B 231 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 243 ASP cc_start: 0.7210 (t0) cc_final: 0.6911 (t0) REVERT: B 245 SER cc_start: 0.8316 (t) cc_final: 0.7172 (p) REVERT: B 248 ASP cc_start: 0.7447 (m-30) cc_final: 0.7194 (m-30) REVERT: B 258 GLU cc_start: 0.8449 (pt0) cc_final: 0.8052 (pt0) REVERT: B 260 LYS cc_start: 0.8797 (tttp) cc_final: 0.8541 (tttp) REVERT: B 264 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8362 (mm-30) REVERT: B 274 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7406 (mtm-85) REVERT: B 278 LYS cc_start: 0.8445 (tptp) cc_final: 0.8189 (tptp) REVERT: B 279 GLN cc_start: 0.8461 (tt0) cc_final: 0.7815 (tt0) REVERT: B 291 ARG cc_start: 0.8824 (ttm170) cc_final: 0.8611 (ttm-80) REVERT: B 318 SER cc_start: 0.8018 (m) cc_final: 0.7298 (t) REVERT: B 324 TYR cc_start: 0.7525 (t80) cc_final: 0.7246 (t80) REVERT: B 392 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 403 GLN cc_start: 0.7019 (tt0) cc_final: 0.6478 (pt0) REVERT: B 413 LYS cc_start: 0.8513 (tppt) cc_final: 0.7445 (tppt) REVERT: B 414 TRP cc_start: 0.7024 (m-90) cc_final: 0.6673 (m-90) REVERT: B 428 TRP cc_start: 0.8257 (m-10) cc_final: 0.8035 (m-10) REVERT: C 3 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8113 (mm-30) REVERT: C 13 GLN cc_start: 0.7648 (tp40) cc_final: 0.7041 (tp40) REVERT: C 26 GLU cc_start: 0.8142 (pt0) cc_final: 0.7808 (pt0) REVERT: C 41 LYS cc_start: 0.8764 (tttt) cc_final: 0.8420 (tttt) REVERT: C 85 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7711 (mm-30) REVERT: C 109 LYS cc_start: 0.8784 (tppt) cc_final: 0.8441 (mmmm) REVERT: C 113 ILE cc_start: 0.8859 (mt) cc_final: 0.8280 (mm) REVERT: C 128 MET cc_start: 0.8042 (mmm) cc_final: 0.7681 (mmm) REVERT: C 140 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 161 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8147 (ttp80) REVERT: C 166 MET cc_start: 0.7392 (tpt) cc_final: 0.6855 (tpt) REVERT: C 178 ILE cc_start: 0.7962 (tp) cc_final: 0.7481 (mm) REVERT: C 213 ASP cc_start: 0.8082 (m-30) cc_final: 0.7715 (m-30) REVERT: C 224 ILE cc_start: 0.7983 (mt) cc_final: 0.7611 (tt) REVERT: C 226 MET cc_start: 0.8500 (mmm) cc_final: 0.7822 (mmp) REVERT: C 235 LYS cc_start: 0.8828 (ttpp) cc_final: 0.8601 (ttpp) REVERT: C 241 MET cc_start: 0.8171 (mmm) cc_final: 0.7499 (mmm) REVERT: C 263 MET cc_start: 0.7473 (mmm) cc_final: 0.7234 (mmm) REVERT: C 279 GLN cc_start: 0.8161 (tt0) cc_final: 0.7696 (tt0) REVERT: C 280 TYR cc_start: 0.8749 (m-80) cc_final: 0.7580 (m-80) REVERT: C 292 SER cc_start: 0.9054 (m) cc_final: 0.8703 (t) REVERT: C 318 SER cc_start: 0.7665 (t) cc_final: 0.7227 (p) REVERT: C 345 GLU cc_start: 0.8359 (tt0) cc_final: 0.8049 (tt0) REVERT: C 367 ASN cc_start: 0.7858 (m110) cc_final: 0.7654 (m110) REVERT: C 393 LEU cc_start: 0.8899 (mt) cc_final: 0.8677 (mt) REVERT: C 410 ASP cc_start: 0.7873 (t0) cc_final: 0.7658 (t0) REVERT: D 38 LYS cc_start: 0.9164 (mttm) cc_final: 0.8917 (mttm) REVERT: D 41 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8117 (ttmm) REVERT: D 46 GLU cc_start: 0.8183 (tt0) cc_final: 0.7696 (tt0) REVERT: D 47 TYR cc_start: 0.8992 (m-80) cc_final: 0.7923 (m-80) REVERT: D 74 LYS cc_start: 0.9010 (tttp) cc_final: 0.8706 (mmmm) REVERT: D 90 LEU cc_start: 0.8458 (mm) cc_final: 0.8108 (mm) REVERT: D 93 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7429 (mm-30) REVERT: D 96 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8014 (ttpp) REVERT: D 109 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7664 (ttmm) REVERT: D 114 GLN cc_start: 0.7371 (mt0) cc_final: 0.7168 (mt0) REVERT: D 118 GLU cc_start: 0.7199 (tp30) cc_final: 0.6862 (tp30) REVERT: D 128 MET cc_start: 0.8820 (tpp) cc_final: 0.8554 (tpp) REVERT: D 143 SER cc_start: 0.9021 (m) cc_final: 0.8334 (t) REVERT: D 147 ASP cc_start: 0.7379 (p0) cc_final: 0.7114 (p0) REVERT: D 154 TRP cc_start: 0.8665 (t60) cc_final: 0.8444 (t60) REVERT: D 155 MET cc_start: 0.7946 (tpt) cc_final: 0.7330 (tpt) REVERT: D 189 THR cc_start: 0.8558 (p) cc_final: 0.6917 (p) REVERT: D 196 MET cc_start: 0.7595 (mtp) cc_final: 0.7251 (mtp) REVERT: D 223 TYR cc_start: 0.8225 (t80) cc_final: 0.6925 (t80) REVERT: D 226 MET cc_start: 0.7087 (mmm) cc_final: 0.6214 (mmm) REVERT: D 235 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8316 (ttpp) REVERT: D 238 ASP cc_start: 0.8920 (m-30) cc_final: 0.8050 (m-30) REVERT: D 280 TYR cc_start: 0.8508 (m-80) cc_final: 0.8017 (m-80) REVERT: D 296 GLU cc_start: 0.7748 (pt0) cc_final: 0.6409 (pt0) REVERT: D 301 LYS cc_start: 0.8616 (mppt) cc_final: 0.8344 (mppt) REVERT: D 324 TYR cc_start: 0.7734 (m-80) cc_final: 0.7345 (m-80) REVERT: D 326 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7114 (mm-30) REVERT: D 333 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7589 (ttmt) REVERT: D 347 GLU cc_start: 0.7960 (tp30) cc_final: 0.7389 (tp30) REVERT: D 368 MET cc_start: 0.7772 (ttp) cc_final: 0.7520 (ttm) REVERT: D 392 GLU cc_start: 0.7730 (tp30) cc_final: 0.7335 (tp30) REVERT: D 397 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7758 (mt-10) REVERT: D 423 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8590 (mtmm) REVERT: E 12 ASP cc_start: 0.8744 (t0) cc_final: 0.8507 (t70) REVERT: E 18 LYS cc_start: 0.9146 (tppt) cc_final: 0.8940 (tppt) REVERT: E 23 MET cc_start: 0.8472 (mmt) cc_final: 0.8158 (mmt) REVERT: E 34 LYS cc_start: 0.8828 (tttp) cc_final: 0.8189 (tttp) REVERT: E 38 LYS cc_start: 0.8939 (mtpt) cc_final: 0.8364 (mtpt) REVERT: E 41 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8648 (ttpt) REVERT: E 47 TYR cc_start: 0.6344 (t80) cc_final: 0.6039 (t80) REVERT: E 53 ILE cc_start: 0.9014 (mm) cc_final: 0.8757 (tp) REVERT: E 79 LYS cc_start: 0.8321 (mttt) cc_final: 0.8113 (tttt) REVERT: E 86 ASP cc_start: 0.8460 (t0) cc_final: 0.8207 (t0) REVERT: E 95 GLU cc_start: 0.8675 (tt0) cc_final: 0.8028 (tt0) REVERT: E 103 MET cc_start: 0.7707 (mmp) cc_final: 0.7174 (mmt) REVERT: E 104 PHE cc_start: 0.8639 (t80) cc_final: 0.8152 (t80) REVERT: E 118 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8014 (mt-10) REVERT: E 146 PHE cc_start: 0.7601 (m-10) cc_final: 0.7168 (m-10) REVERT: E 177 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7420 (mtt90) REVERT: E 215 LEU cc_start: 0.9074 (tp) cc_final: 0.8785 (tp) REVERT: E 228 MET cc_start: 0.7173 (ptm) cc_final: 0.6819 (ptt) REVERT: E 237 ILE cc_start: 0.8871 (mt) cc_final: 0.8669 (mt) REVERT: E 241 MET cc_start: 0.7814 (mmm) cc_final: 0.7435 (mmm) REVERT: E 248 ASP cc_start: 0.7677 (m-30) cc_final: 0.7341 (m-30) REVERT: E 253 HIS cc_start: 0.7509 (m90) cc_final: 0.7133 (m90) REVERT: E 258 GLU cc_start: 0.8221 (mp0) cc_final: 0.7794 (mp0) REVERT: E 271 THR cc_start: 0.9165 (p) cc_final: 0.8788 (t) REVERT: E 301 LYS cc_start: 0.8203 (ptpt) cc_final: 0.7715 (ptpt) REVERT: E 333 LYS cc_start: 0.7772 (tttp) cc_final: 0.7261 (tttp) REVERT: E 416 LYS cc_start: 0.8210 (mttp) cc_final: 0.7996 (mttp) REVERT: E 419 MET cc_start: 0.6393 (mtm) cc_final: 0.6124 (ttp) REVERT: E 423 LYS cc_start: 0.8867 (mttm) cc_final: 0.8643 (mtpp) REVERT: F 5 ILE cc_start: 0.8909 (mt) cc_final: 0.8572 (mt) REVERT: F 13 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7935 (tp40) REVERT: F 15 TYR cc_start: 0.8595 (t80) cc_final: 0.7238 (t80) REVERT: F 18 LYS cc_start: 0.8732 (tppt) cc_final: 0.8296 (tppt) REVERT: F 22 TYR cc_start: 0.8437 (m-80) cc_final: 0.8162 (m-10) REVERT: F 29 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7590 (mm-30) REVERT: F 34 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8114 (ttmm) REVERT: F 43 HIS cc_start: 0.8432 (t-90) cc_final: 0.7778 (t-90) REVERT: F 60 LEU cc_start: 0.8823 (tp) cc_final: 0.8609 (tp) REVERT: F 61 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7306 (mm-30) REVERT: F 82 ASP cc_start: 0.7654 (t0) cc_final: 0.7339 (t0) REVERT: F 93 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7826 (mm-30) REVERT: F 95 GLU cc_start: 0.8113 (tt0) cc_final: 0.7664 (tt0) REVERT: F 96 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8307 (ttpp) REVERT: F 116 ASN cc_start: 0.8455 (t0) cc_final: 0.8026 (t0) REVERT: F 119 LEU cc_start: 0.8552 (mt) cc_final: 0.8107 (mt) REVERT: F 123 LYS cc_start: 0.8644 (tppt) cc_final: 0.8284 (tppt) REVERT: F 157 ASP cc_start: 0.7865 (m-30) cc_final: 0.7444 (m-30) REVERT: F 158 TYR cc_start: 0.7759 (p90) cc_final: 0.7169 (p90) REVERT: F 183 THR cc_start: 0.7986 (p) cc_final: 0.7478 (t) REVERT: F 184 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7757 (mmmt) REVERT: F 189 THR cc_start: 0.7921 (p) cc_final: 0.7344 (t) REVERT: F 265 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8523 (mmtm) REVERT: F 296 GLU cc_start: 0.7719 (pt0) cc_final: 0.7324 (pt0) REVERT: F 326 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7680 (mm-30) REVERT: F 338 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7202 (mm-30) REVERT: F 340 ARG cc_start: 0.9039 (ttt-90) cc_final: 0.8769 (tpt-90) REVERT: F 404 ILE cc_start: 0.8330 (mt) cc_final: 0.8058 (mt) REVERT: F 405 LYS cc_start: 0.6796 (tptp) cc_final: 0.6380 (tppp) REVERT: G 8 ASP cc_start: 0.8710 (m-30) cc_final: 0.8337 (m-30) REVERT: G 77 TYR cc_start: 0.8464 (t80) cc_final: 0.8124 (t80) REVERT: G 78 LEU cc_start: 0.9448 (mt) cc_final: 0.9179 (mt) REVERT: G 82 GLU cc_start: 0.8496 (tp30) cc_final: 0.8096 (tp30) REVERT: G 84 ASP cc_start: 0.8817 (p0) cc_final: 0.8529 (p0) REVERT: G 89 TYR cc_start: 0.8160 (t80) cc_final: 0.7772 (t80) REVERT: G 95 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8510 (mtpp) REVERT: G 151 LYS cc_start: 0.8747 (ptpp) cc_final: 0.8508 (pttm) REVERT: G 238 ASP cc_start: 0.8447 (m-30) cc_final: 0.7899 (m-30) REVERT: G 240 LEU cc_start: 0.9124 (mt) cc_final: 0.8880 (mt) REVERT: G 276 ASP cc_start: 0.8571 (p0) cc_final: 0.8260 (p0) REVERT: G 279 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8661 (mttm) REVERT: G 283 LYS cc_start: 0.9132 (pttm) cc_final: 0.8852 (ptpt) REVERT: G 295 ASP cc_start: 0.8484 (p0) cc_final: 0.8206 (p0) REVERT: G 296 LYS cc_start: 0.9112 (mmmt) cc_final: 0.8762 (mmmt) REVERT: G 306 ASP cc_start: 0.8241 (t0) cc_final: 0.8033 (t0) REVERT: G 307 MET cc_start: 0.8810 (mmt) cc_final: 0.8459 (mmm) REVERT: G 309 ARG cc_start: 0.8632 (mtp180) cc_final: 0.8332 (mtp180) REVERT: G 323 LYS cc_start: 0.9321 (pttm) cc_final: 0.9084 (ptpp) REVERT: G 328 GLN cc_start: 0.7972 (tp40) cc_final: 0.7478 (tp40) REVERT: G 333 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8718 (mmtt) REVERT: G 334 MET cc_start: 0.8037 (tpp) cc_final: 0.7729 (tpp) REVERT: G 338 LYS cc_start: 0.9028 (mmtt) cc_final: 0.8666 (mmtt) outliers start: 0 outliers final: 0 residues processed: 1127 average time/residue: 0.1702 time to fit residues: 288.3399 Evaluate side-chains 1039 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1039 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 148 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 280 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN A 116 ASN A 219 HIS A 220 ASN A 240 ASN B 99 GLN B 403 GLN D 100 GLN D 240 ASN E 426 GLN F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104897 restraints weight = 48759.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108818 restraints weight = 24711.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111418 restraints weight = 14896.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113182 restraints weight = 10151.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114246 restraints weight = 7617.253| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24515 Z= 0.191 Angle : 0.663 9.508 33269 Z= 0.346 Chirality : 0.045 0.227 3697 Planarity : 0.004 0.062 4105 Dihedral : 10.216 154.341 3441 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.30 (0.16), residues: 2917 helix: 0.99 (0.14), residues: 1445 sheet: -1.31 (0.27), residues: 370 loop : -1.34 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 139 TYR 0.031 0.002 TYR B 165 PHE 0.023 0.002 PHE E 16 TRP 0.045 0.002 TRP G 266 HIS 0.013 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (24510) covalent geometry : angle 0.66016 / 0.35 (33263) hydrogen bonds : bond 0.03491 / 2.40 ( 1174) hydrogen bonds : angle 4.85921 / 3.49 ( 3363) metal coordination : bond 0.01249 / 0.63 ( 4) metal coordination : angle 4.80023 / 2.42 ( 6) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1128 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 11 PHE cc_start: 0.7944 (m-80) cc_final: 0.7490 (m-10) REVERT: A 19 VAL cc_start: 0.8214 (m) cc_final: 0.7886 (p) REVERT: A 26 GLU cc_start: 0.7930 (pm20) cc_final: 0.7291 (pm20) REVERT: A 29 GLU cc_start: 0.7599 (tt0) cc_final: 0.7394 (tt0) REVERT: A 35 ASN cc_start: 0.8551 (m-40) cc_final: 0.8220 (m110) REVERT: A 39 LEU cc_start: 0.9086 (mt) cc_final: 0.8865 (mt) REVERT: A 47 TYR cc_start: 0.6467 (m-10) cc_final: 0.6259 (m-80) REVERT: A 61 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6651 (tm-30) REVERT: A 73 VAL cc_start: 0.9000 (t) cc_final: 0.8485 (p) REVERT: A 79 LYS cc_start: 0.8738 (ttmt) cc_final: 0.7883 (ttmt) REVERT: A 104 PHE cc_start: 0.7940 (t80) cc_final: 0.7485 (t80) REVERT: A 112 GLU cc_start: 0.8162 (tt0) cc_final: 0.7849 (tt0) REVERT: A 113 ILE cc_start: 0.8982 (mt) cc_final: 0.8726 (mt) REVERT: A 123 LYS cc_start: 0.8190 (mmmm) cc_final: 0.7823 (mmmm) REVERT: A 136 ASP cc_start: 0.7557 (m-30) cc_final: 0.7353 (m-30) REVERT: A 139 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7097 (ttm-80) REVERT: A 146 PHE cc_start: 0.8446 (m-10) cc_final: 0.7993 (m-10) REVERT: A 148 SER cc_start: 0.8145 (t) cc_final: 0.7933 (t) REVERT: A 150 VAL cc_start: 0.8731 (p) cc_final: 0.8436 (m) REVERT: A 171 LYS cc_start: 0.8217 (mmtp) cc_final: 0.7732 (mmtm) REVERT: A 184 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8418 (mmtp) REVERT: A 203 LYS cc_start: 0.7968 (pttm) cc_final: 0.7151 (pttm) REVERT: A 207 LEU cc_start: 0.8320 (mt) cc_final: 0.8065 (mp) REVERT: A 214 TYR cc_start: 0.8536 (m-80) cc_final: 0.8113 (m-10) REVERT: A 235 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8137 (ttpt) REVERT: A 241 MET cc_start: 0.8069 (mmm) cc_final: 0.7519 (mmm) REVERT: A 248 ASP cc_start: 0.7364 (m-30) cc_final: 0.6994 (m-30) REVERT: A 263 MET cc_start: 0.7877 (mmp) cc_final: 0.7664 (mmp) REVERT: A 265 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8648 (ttpp) REVERT: A 268 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 278 LYS cc_start: 0.8261 (tptm) cc_final: 0.7966 (mtpp) REVERT: A 279 GLN cc_start: 0.8741 (tt0) cc_final: 0.8415 (tt0) REVERT: A 313 LEU cc_start: 0.6761 (tt) cc_final: 0.6500 (tt) REVERT: A 316 CYS cc_start: 0.8300 (m) cc_final: 0.7661 (m) REVERT: A 342 LEU cc_start: 0.8710 (tp) cc_final: 0.7862 (tp) REVERT: A 382 ASP cc_start: 0.7996 (m-30) cc_final: 0.7738 (m-30) REVERT: A 384 MET cc_start: 0.8388 (ttt) cc_final: 0.7766 (ttm) REVERT: A 426 GLN cc_start: 0.8203 (mt0) cc_final: 0.7749 (mt0) REVERT: B 15 TYR cc_start: 0.8720 (t80) cc_final: 0.8136 (t80) REVERT: B 41 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8385 (ttmt) REVERT: B 47 TYR cc_start: 0.8451 (m-80) cc_final: 0.8206 (m-80) REVERT: B 54 ASN cc_start: 0.8662 (m-40) cc_final: 0.8390 (m-40) REVERT: B 79 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8481 (ttmm) REVERT: B 86 ASP cc_start: 0.7514 (t70) cc_final: 0.7284 (t0) REVERT: B 87 HIS cc_start: 0.7842 (t-90) cc_final: 0.7508 (t70) REVERT: B 103 MET cc_start: 0.7850 (mmm) cc_final: 0.7558 (mmm) REVERT: B 109 LYS cc_start: 0.9276 (tptt) cc_final: 0.8613 (tptt) REVERT: B 139 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7659 (ttp-170) REVERT: B 145 SER cc_start: 0.8687 (p) cc_final: 0.8052 (t) REVERT: B 155 MET cc_start: 0.7859 (tpp) cc_final: 0.7384 (tpp) REVERT: B 213 ASP cc_start: 0.7783 (m-30) cc_final: 0.7534 (m-30) REVERT: B 226 MET cc_start: 0.8215 (mmm) cc_final: 0.7469 (mmp) REVERT: B 243 ASP cc_start: 0.7262 (t0) cc_final: 0.6866 (t0) REVERT: B 245 SER cc_start: 0.8388 (t) cc_final: 0.7161 (p) REVERT: B 248 ASP cc_start: 0.7527 (m-30) cc_final: 0.7232 (m-30) REVERT: B 258 GLU cc_start: 0.8409 (pt0) cc_final: 0.8128 (pt0) REVERT: B 272 LEU cc_start: 0.9163 (tp) cc_final: 0.8920 (tp) REVERT: B 274 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7503 (mtm-85) REVERT: B 278 LYS cc_start: 0.8503 (tptp) cc_final: 0.8285 (tptp) REVERT: B 279 GLN cc_start: 0.8478 (tt0) cc_final: 0.7887 (tt0) REVERT: B 291 ARG cc_start: 0.8834 (ttm170) cc_final: 0.8587 (ttm-80) REVERT: B 318 SER cc_start: 0.8051 (m) cc_final: 0.7337 (t) REVERT: B 324 TYR cc_start: 0.7462 (t80) cc_final: 0.7218 (t80) REVERT: B 392 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 403 GLN cc_start: 0.7287 (tt0) cc_final: 0.6593 (pt0) REVERT: B 413 LYS cc_start: 0.8608 (tppt) cc_final: 0.8061 (tppt) REVERT: B 419 MET cc_start: 0.4599 (tpp) cc_final: 0.3626 (ttt) REVERT: C 3 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 13 GLN cc_start: 0.7753 (tp40) cc_final: 0.7173 (tp40) REVERT: C 26 GLU cc_start: 0.8096 (pt0) cc_final: 0.7772 (pt0) REVERT: C 41 LYS cc_start: 0.8758 (tttt) cc_final: 0.8369 (tttt) REVERT: C 85 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7702 (mm-30) REVERT: C 113 ILE cc_start: 0.9020 (mt) cc_final: 0.8397 (mm) REVERT: C 128 MET cc_start: 0.7948 (mmm) cc_final: 0.7617 (mmm) REVERT: C 161 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8230 (ttp80) REVERT: C 166 MET cc_start: 0.7386 (tpt) cc_final: 0.6774 (tpt) REVERT: C 213 ASP cc_start: 0.8098 (m-30) cc_final: 0.7724 (m-30) REVERT: C 224 ILE cc_start: 0.8040 (mt) cc_final: 0.7758 (tt) REVERT: C 226 MET cc_start: 0.8483 (mmm) cc_final: 0.7818 (mmp) REVERT: C 241 MET cc_start: 0.8178 (mmm) cc_final: 0.7694 (mmm) REVERT: C 243 ASP cc_start: 0.7767 (t0) cc_final: 0.7522 (t0) REVERT: C 263 MET cc_start: 0.7393 (mmm) cc_final: 0.7030 (mmm) REVERT: C 279 GLN cc_start: 0.8254 (tt0) cc_final: 0.7815 (tt0) REVERT: C 292 SER cc_start: 0.9078 (m) cc_final: 0.8730 (t) REVERT: C 318 SER cc_start: 0.7806 (t) cc_final: 0.7395 (p) REVERT: C 342 LEU cc_start: 0.8853 (tp) cc_final: 0.8652 (tp) REVERT: C 345 GLU cc_start: 0.8313 (tt0) cc_final: 0.7968 (tt0) REVERT: C 367 ASN cc_start: 0.7717 (m110) cc_final: 0.7494 (m110) REVERT: C 393 LEU cc_start: 0.8866 (mt) cc_final: 0.8642 (mt) REVERT: D 15 TYR cc_start: 0.8143 (t80) cc_final: 0.7536 (t80) REVERT: D 38 LYS cc_start: 0.9134 (mttm) cc_final: 0.8900 (mttm) REVERT: D 41 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8199 (ttpp) REVERT: D 46 GLU cc_start: 0.8159 (tt0) cc_final: 0.7659 (tt0) REVERT: D 47 TYR cc_start: 0.8966 (m-80) cc_final: 0.7910 (m-80) REVERT: D 74 LYS cc_start: 0.9042 (tttp) cc_final: 0.8734 (mmmm) REVERT: D 90 LEU cc_start: 0.8455 (mm) cc_final: 0.8034 (mm) REVERT: D 93 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7415 (mm-30) REVERT: D 96 LYS cc_start: 0.8631 (ttpp) cc_final: 0.8221 (ttpp) REVERT: D 109 LYS cc_start: 0.8221 (ttmm) cc_final: 0.7856 (ttmm) REVERT: D 118 GLU cc_start: 0.7155 (tp30) cc_final: 0.6812 (tp30) REVERT: D 128 MET cc_start: 0.8842 (tpp) cc_final: 0.8526 (tpp) REVERT: D 143 SER cc_start: 0.9016 (m) cc_final: 0.8364 (t) REVERT: D 147 ASP cc_start: 0.7456 (p0) cc_final: 0.7180 (p0) REVERT: D 168 LYS cc_start: 0.7984 (mttt) cc_final: 0.7739 (mttt) REVERT: D 189 THR cc_start: 0.8660 (p) cc_final: 0.7081 (p) REVERT: D 196 MET cc_start: 0.7559 (mtp) cc_final: 0.7255 (mtp) REVERT: D 222 LEU cc_start: 0.8880 (tp) cc_final: 0.8641 (tt) REVERT: D 223 TYR cc_start: 0.8398 (t80) cc_final: 0.7181 (t80) REVERT: D 226 MET cc_start: 0.7194 (mmm) cc_final: 0.6364 (mmm) REVERT: D 235 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8396 (ttpp) REVERT: D 238 ASP cc_start: 0.8964 (m-30) cc_final: 0.8220 (m-30) REVERT: D 278 LYS cc_start: 0.8129 (tptp) cc_final: 0.7920 (tptp) REVERT: D 280 TYR cc_start: 0.8499 (m-80) cc_final: 0.7964 (m-80) REVERT: D 296 GLU cc_start: 0.7749 (pt0) cc_final: 0.6638 (pt0) REVERT: D 301 LYS cc_start: 0.8630 (mppt) cc_final: 0.8417 (mppt) REVERT: D 324 TYR cc_start: 0.7730 (m-80) cc_final: 0.7350 (m-80) REVERT: D 326 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7117 (mm-30) REVERT: D 329 TYR cc_start: 0.6020 (t80) cc_final: 0.5376 (t80) REVERT: D 333 LYS cc_start: 0.8092 (ttmt) cc_final: 0.7601 (ttmt) REVERT: D 338 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6971 (mt-10) REVERT: D 347 GLU cc_start: 0.7910 (tp30) cc_final: 0.7358 (tp30) REVERT: D 392 GLU cc_start: 0.7670 (tp30) cc_final: 0.7129 (tp30) REVERT: E 23 MET cc_start: 0.8465 (mmt) cc_final: 0.8114 (mmt) REVERT: E 34 LYS cc_start: 0.8833 (tttp) cc_final: 0.8254 (tttp) REVERT: E 38 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8432 (mtpt) REVERT: E 39 LEU cc_start: 0.8768 (mt) cc_final: 0.8463 (mt) REVERT: E 41 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8605 (ttpt) REVERT: E 47 TYR cc_start: 0.6362 (t80) cc_final: 0.6104 (t80) REVERT: E 86 ASP cc_start: 0.8533 (t0) cc_final: 0.8237 (t0) REVERT: E 93 GLU cc_start: 0.8023 (tp30) cc_final: 0.7355 (tp30) REVERT: E 95 GLU cc_start: 0.8657 (tt0) cc_final: 0.8070 (tt0) REVERT: E 104 PHE cc_start: 0.8693 (t80) cc_final: 0.8356 (t80) REVERT: E 118 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 139 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7751 (ttp80) REVERT: E 146 PHE cc_start: 0.7713 (m-10) cc_final: 0.7191 (m-10) REVERT: E 215 LEU cc_start: 0.9099 (tp) cc_final: 0.8838 (tp) REVERT: E 238 ASP cc_start: 0.8680 (m-30) cc_final: 0.8309 (m-30) REVERT: E 241 MET cc_start: 0.7820 (mmm) cc_final: 0.7285 (mmm) REVERT: E 245 SER cc_start: 0.8736 (m) cc_final: 0.8226 (p) REVERT: E 258 GLU cc_start: 0.8195 (mp0) cc_final: 0.7961 (mp0) REVERT: E 265 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8592 (mtmt) REVERT: E 271 THR cc_start: 0.9198 (p) cc_final: 0.8829 (t) REVERT: E 301 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7725 (ptpt) REVERT: E 333 LYS cc_start: 0.7844 (tttp) cc_final: 0.7482 (tttp) REVERT: E 397 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7968 (mt-10) REVERT: E 419 MET cc_start: 0.6661 (mtm) cc_final: 0.6419 (ttp) REVERT: F 5 ILE cc_start: 0.8941 (mt) cc_final: 0.8667 (mt) REVERT: F 13 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7931 (tp40) REVERT: F 15 TYR cc_start: 0.8567 (t80) cc_final: 0.7221 (t80) REVERT: F 18 LYS cc_start: 0.8753 (tppt) cc_final: 0.8457 (tppt) REVERT: F 22 TYR cc_start: 0.8424 (m-80) cc_final: 0.8194 (m-10) REVERT: F 24 ASP cc_start: 0.8496 (t0) cc_final: 0.8107 (t70) REVERT: F 29 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7645 (mm-30) REVERT: F 34 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8063 (ttmm) REVERT: F 38 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8803 (mmtp) REVERT: F 43 HIS cc_start: 0.8522 (t-90) cc_final: 0.7852 (t-90) REVERT: F 61 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7390 (mm-30) REVERT: F 82 ASP cc_start: 0.7677 (t0) cc_final: 0.7365 (t0) REVERT: F 95 GLU cc_start: 0.8117 (tt0) cc_final: 0.7691 (tt0) REVERT: F 96 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8325 (ttpp) REVERT: F 116 ASN cc_start: 0.8478 (t0) cc_final: 0.7813 (t0) REVERT: F 119 LEU cc_start: 0.8587 (mt) cc_final: 0.8135 (mt) REVERT: F 123 LYS cc_start: 0.8609 (tppt) cc_final: 0.8308 (tppt) REVERT: F 149 TYR cc_start: 0.6349 (t80) cc_final: 0.6048 (t80) REVERT: F 157 ASP cc_start: 0.7662 (m-30) cc_final: 0.7257 (m-30) REVERT: F 158 TYR cc_start: 0.7777 (p90) cc_final: 0.7230 (p90) REVERT: F 183 THR cc_start: 0.8103 (p) cc_final: 0.7611 (t) REVERT: F 184 LYS cc_start: 0.8151 (mmtp) cc_final: 0.7878 (mmmt) REVERT: F 189 THR cc_start: 0.8038 (p) cc_final: 0.7446 (t) REVERT: F 258 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7845 (mt-10) REVERT: F 265 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8497 (mmtm) REVERT: F 296 GLU cc_start: 0.7592 (pt0) cc_final: 0.7390 (pt0) REVERT: F 326 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7703 (mm-30) REVERT: F 333 LYS cc_start: 0.8643 (ttpp) cc_final: 0.8412 (ttpp) REVERT: F 338 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7256 (mm-30) REVERT: F 340 ARG cc_start: 0.9052 (ttt-90) cc_final: 0.8506 (tpt-90) REVERT: F 404 ILE cc_start: 0.8343 (mt) cc_final: 0.8103 (mt) REVERT: F 405 LYS cc_start: 0.7007 (tptp) cc_final: 0.6538 (tppp) REVERT: F 426 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7012 (mm-40) REVERT: G 8 ASP cc_start: 0.8715 (m-30) cc_final: 0.8367 (m-30) REVERT: G 78 LEU cc_start: 0.9402 (mt) cc_final: 0.9146 (mt) REVERT: G 82 GLU cc_start: 0.8390 (tp30) cc_final: 0.8052 (tp30) REVERT: G 89 TYR cc_start: 0.8168 (t80) cc_final: 0.7797 (t80) REVERT: G 95 LYS cc_start: 0.9098 (mtpt) cc_final: 0.8486 (mtpp) REVERT: G 97 LYS cc_start: 0.8215 (ptpt) cc_final: 0.7995 (ptpt) REVERT: G 100 SER cc_start: 0.8507 (p) cc_final: 0.7475 (p) REVERT: G 151 LYS cc_start: 0.8752 (ptpp) cc_final: 0.8474 (pttm) REVERT: G 238 ASP cc_start: 0.8450 (m-30) cc_final: 0.7912 (m-30) REVERT: G 240 LEU cc_start: 0.9095 (mt) cc_final: 0.8873 (mt) REVERT: G 276 ASP cc_start: 0.8296 (p0) cc_final: 0.7963 (p0) REVERT: G 279 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8595 (mttm) REVERT: G 283 LYS cc_start: 0.9118 (pttm) cc_final: 0.8819 (ptpt) REVERT: G 295 ASP cc_start: 0.8461 (p0) cc_final: 0.8208 (p0) REVERT: G 296 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8756 (mmmt) REVERT: G 306 ASP cc_start: 0.8197 (t0) cc_final: 0.7990 (t0) REVERT: G 307 MET cc_start: 0.8818 (mmt) cc_final: 0.8471 (mmm) REVERT: G 323 LYS cc_start: 0.9302 (pttm) cc_final: 0.8995 (pttp) REVERT: G 324 ASN cc_start: 0.8966 (m-40) cc_final: 0.8759 (m-40) REVERT: G 328 GLN cc_start: 0.7989 (tp40) cc_final: 0.7493 (tp40) REVERT: G 333 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8816 (mmtt) REVERT: G 338 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8676 (mmtt) outliers start: 0 outliers final: 0 residues processed: 1128 average time/residue: 0.1737 time to fit residues: 294.4216 Evaluate side-chains 1045 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1045 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 274 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 219 HIS A 220 ASN A 240 ASN B 99 GLN B 114 GLN B 193 ASN B 403 GLN C 288 ASN C 412 ASN D 62 ASN D 100 GLN D 114 GLN F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.127648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.106123 restraints weight = 48517.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109894 restraints weight = 25120.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112417 restraints weight = 15305.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113967 restraints weight = 10470.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115228 restraints weight = 8010.132| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24515 Z= 0.165 Angle : 0.671 10.365 33269 Z= 0.348 Chirality : 0.045 0.207 3697 Planarity : 0.005 0.135 4105 Dihedral : 10.196 152.701 3441 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.04 % Allowed : 0.87 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.32 (0.16), residues: 2917 helix: 0.95 (0.14), residues: 1443 sheet: -1.31 (0.28), residues: 350 loop : -1.34 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 340 TYR 0.033 0.002 TYR B 165 PHE 0.023 0.002 PHE A 16 TRP 0.044 0.002 TRP E 414 HIS 0.014 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (24510) covalent geometry : angle 0.66778 / 0.35 (33263) hydrogen bonds : bond 0.03390 / 2.32 ( 1174) hydrogen bonds : angle 4.86237 / 3.49 ( 3363) metal coordination : bond 0.01072 / 0.54 ( 4) metal coordination : angle 4.61159 / 2.36 ( 6) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1124 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7776 (tpp) cc_final: 0.7272 (tpt) REVERT: A 3 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7382 (mm-30) REVERT: A 11 PHE cc_start: 0.7871 (m-80) cc_final: 0.7376 (m-10) REVERT: A 19 VAL cc_start: 0.8149 (m) cc_final: 0.7885 (p) REVERT: A 26 GLU cc_start: 0.7873 (pm20) cc_final: 0.7333 (pm20) REVERT: A 29 GLU cc_start: 0.7654 (tt0) cc_final: 0.7354 (tt0) REVERT: A 35 ASN cc_start: 0.8554 (m-40) cc_final: 0.8199 (m110) REVERT: A 47 TYR cc_start: 0.6468 (m-10) cc_final: 0.6262 (m-80) REVERT: A 65 PHE cc_start: 0.7816 (m-10) cc_final: 0.7591 (m-10) REVERT: A 73 VAL cc_start: 0.9022 (t) cc_final: 0.8536 (p) REVERT: A 79 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8004 (ttmt) REVERT: A 85 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7277 (mm-30) REVERT: A 93 GLU cc_start: 0.8184 (tp30) cc_final: 0.7550 (tp30) REVERT: A 104 PHE cc_start: 0.7806 (t80) cc_final: 0.7383 (t80) REVERT: A 123 LYS cc_start: 0.8222 (mmmm) cc_final: 0.7943 (mmmm) REVERT: A 146 PHE cc_start: 0.8386 (m-10) cc_final: 0.7965 (m-10) REVERT: A 150 VAL cc_start: 0.8818 (p) cc_final: 0.8479 (m) REVERT: A 153 ASP cc_start: 0.8360 (t0) cc_final: 0.8033 (t0) REVERT: A 171 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7703 (mmtm) REVERT: A 214 TYR cc_start: 0.8523 (m-80) cc_final: 0.8094 (m-10) REVERT: A 235 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8167 (ttpt) REVERT: A 238 ASP cc_start: 0.8702 (m-30) cc_final: 0.8479 (m-30) REVERT: A 241 MET cc_start: 0.8087 (mmm) cc_final: 0.7530 (mmm) REVERT: A 248 ASP cc_start: 0.7210 (m-30) cc_final: 0.6829 (m-30) REVERT: A 263 MET cc_start: 0.7916 (mmp) cc_final: 0.7691 (mmp) REVERT: A 265 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8641 (ttpp) REVERT: A 268 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 278 LYS cc_start: 0.8024 (tptm) cc_final: 0.7651 (mtpp) REVERT: A 279 GLN cc_start: 0.8681 (tt0) cc_final: 0.8328 (tt0) REVERT: A 293 LEU cc_start: 0.9062 (tt) cc_final: 0.8855 (tp) REVERT: A 313 LEU cc_start: 0.6741 (tt) cc_final: 0.6503 (tt) REVERT: A 316 CYS cc_start: 0.8255 (m) cc_final: 0.7646 (m) REVERT: A 384 MET cc_start: 0.8441 (ttt) cc_final: 0.7769 (ttm) REVERT: A 398 GLN cc_start: 0.6992 (mt0) cc_final: 0.6740 (mt0) REVERT: A 426 GLN cc_start: 0.8187 (mt0) cc_final: 0.7662 (mt0) REVERT: B 4 ILE cc_start: 0.8536 (tp) cc_final: 0.8207 (tp) REVERT: B 13 GLN cc_start: 0.7829 (tp40) cc_final: 0.7464 (tp40) REVERT: B 15 TYR cc_start: 0.8715 (t80) cc_final: 0.8018 (t80) REVERT: B 23 MET cc_start: 0.8322 (tpp) cc_final: 0.7751 (mmm) REVERT: B 41 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8413 (ttmt) REVERT: B 79 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8485 (ttmm) REVERT: B 86 ASP cc_start: 0.7545 (t70) cc_final: 0.7270 (t0) REVERT: B 87 HIS cc_start: 0.7944 (t-90) cc_final: 0.7607 (t70) REVERT: B 103 MET cc_start: 0.7916 (mmm) cc_final: 0.7623 (mmm) REVERT: B 109 LYS cc_start: 0.9320 (tptt) cc_final: 0.8643 (tptt) REVERT: B 139 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7702 (ttp-170) REVERT: B 145 SER cc_start: 0.8729 (p) cc_final: 0.7878 (t) REVERT: B 155 MET cc_start: 0.7933 (tpp) cc_final: 0.7440 (tpp) REVERT: B 191 THR cc_start: 0.8385 (p) cc_final: 0.8149 (p) REVERT: B 213 ASP cc_start: 0.7924 (m-30) cc_final: 0.7314 (m-30) REVERT: B 226 MET cc_start: 0.8176 (mmm) cc_final: 0.7403 (mmp) REVERT: B 243 ASP cc_start: 0.7233 (t0) cc_final: 0.6952 (t0) REVERT: B 245 SER cc_start: 0.8332 (t) cc_final: 0.7038 (p) REVERT: B 248 ASP cc_start: 0.7489 (m-30) cc_final: 0.7218 (m-30) REVERT: B 258 GLU cc_start: 0.8441 (pt0) cc_final: 0.8157 (pt0) REVERT: B 260 LYS cc_start: 0.8918 (tttp) cc_final: 0.8690 (tppt) REVERT: B 263 MET cc_start: 0.7659 (tpt) cc_final: 0.7284 (tpt) REVERT: B 265 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8557 (ttpp) REVERT: B 269 LYS cc_start: 0.7975 (mtmm) cc_final: 0.6996 (mtmm) REVERT: B 274 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7529 (mtm-85) REVERT: B 278 LYS cc_start: 0.8470 (tptp) cc_final: 0.8208 (tptp) REVERT: B 279 GLN cc_start: 0.8447 (tt0) cc_final: 0.7825 (tt0) REVERT: B 291 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8555 (ttm-80) REVERT: B 318 SER cc_start: 0.8042 (m) cc_final: 0.7338 (t) REVERT: B 324 TYR cc_start: 0.7481 (t80) cc_final: 0.7209 (t80) REVERT: B 392 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7138 (tm-30) REVERT: B 403 GLN cc_start: 0.7032 (tt0) cc_final: 0.6494 (pt0) REVERT: B 413 LYS cc_start: 0.8775 (tppt) cc_final: 0.8130 (tppt) REVERT: B 414 TRP cc_start: 0.7996 (m100) cc_final: 0.7628 (m100) REVERT: C 3 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8088 (mm-30) REVERT: C 13 GLN cc_start: 0.7747 (tp40) cc_final: 0.7100 (tp40) REVERT: C 26 GLU cc_start: 0.8183 (pt0) cc_final: 0.7858 (pt0) REVERT: C 41 LYS cc_start: 0.8736 (tttt) cc_final: 0.8356 (tttt) REVERT: C 56 LEU cc_start: 0.9140 (mm) cc_final: 0.8897 (mm) REVERT: C 60 LEU cc_start: 0.8716 (mm) cc_final: 0.8306 (tp) REVERT: C 85 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 113 ILE cc_start: 0.9067 (mt) cc_final: 0.8449 (mm) REVERT: C 128 MET cc_start: 0.7989 (mmm) cc_final: 0.7740 (mmm) REVERT: C 166 MET cc_start: 0.7403 (tpt) cc_final: 0.6750 (tpt) REVERT: C 213 ASP cc_start: 0.8067 (m-30) cc_final: 0.7749 (m-30) REVERT: C 224 ILE cc_start: 0.8012 (mt) cc_final: 0.7699 (tt) REVERT: C 226 MET cc_start: 0.8484 (mmm) cc_final: 0.7864 (mmp) REVERT: C 241 MET cc_start: 0.8180 (mmm) cc_final: 0.7754 (mmm) REVERT: C 243 ASP cc_start: 0.7921 (t0) cc_final: 0.7624 (t0) REVERT: C 292 SER cc_start: 0.9059 (m) cc_final: 0.8729 (t) REVERT: C 312 TYR cc_start: 0.6329 (t80) cc_final: 0.6017 (t80) REVERT: C 315 ILE cc_start: 0.8358 (pt) cc_final: 0.8017 (pt) REVERT: C 318 SER cc_start: 0.7770 (t) cc_final: 0.7408 (p) REVERT: C 322 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7463 (ttm170) REVERT: C 335 ILE cc_start: 0.8410 (tp) cc_final: 0.8141 (tp) REVERT: C 345 GLU cc_start: 0.8295 (tt0) cc_final: 0.8043 (tt0) REVERT: C 367 ASN cc_start: 0.7716 (m110) cc_final: 0.7514 (m110) REVERT: C 393 LEU cc_start: 0.8880 (mt) cc_final: 0.8652 (mt) REVERT: C 426 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7314 (mm-40) REVERT: D 2 VAL cc_start: 0.9127 (m) cc_final: 0.8916 (p) REVERT: D 38 LYS cc_start: 0.9160 (mttm) cc_final: 0.8926 (mttm) REVERT: D 41 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8210 (ttpp) REVERT: D 46 GLU cc_start: 0.8220 (tt0) cc_final: 0.7704 (tt0) REVERT: D 47 TYR cc_start: 0.8979 (m-80) cc_final: 0.7851 (m-80) REVERT: D 90 LEU cc_start: 0.8418 (mm) cc_final: 0.8123 (mm) REVERT: D 93 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 96 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8037 (ttpp) REVERT: D 109 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7785 (ttmm) REVERT: D 114 GLN cc_start: 0.7496 (mt0) cc_final: 0.7224 (mt0) REVERT: D 118 GLU cc_start: 0.7142 (tp30) cc_final: 0.6796 (tp30) REVERT: D 128 MET cc_start: 0.8899 (tpp) cc_final: 0.8602 (tpp) REVERT: D 143 SER cc_start: 0.9033 (m) cc_final: 0.8414 (t) REVERT: D 147 ASP cc_start: 0.7436 (p0) cc_final: 0.7207 (p0) REVERT: D 189 THR cc_start: 0.8635 (p) cc_final: 0.7011 (p) REVERT: D 196 MET cc_start: 0.7633 (mtp) cc_final: 0.7241 (mtp) REVERT: D 222 LEU cc_start: 0.8882 (tp) cc_final: 0.8636 (tt) REVERT: D 223 TYR cc_start: 0.8557 (t80) cc_final: 0.7020 (t80) REVERT: D 235 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8413 (ttpp) REVERT: D 267 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7825 (ttm-80) REVERT: D 280 TYR cc_start: 0.8514 (m-80) cc_final: 0.8242 (m-80) REVERT: D 296 GLU cc_start: 0.7765 (pt0) cc_final: 0.6537 (pt0) REVERT: D 300 LYS cc_start: 0.8417 (mtmm) cc_final: 0.8134 (mtmm) REVERT: D 301 LYS cc_start: 0.8713 (mppt) cc_final: 0.8437 (mppt) REVERT: D 324 TYR cc_start: 0.7743 (m-80) cc_final: 0.7344 (m-80) REVERT: D 326 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7103 (mm-30) REVERT: D 329 TYR cc_start: 0.5950 (t80) cc_final: 0.5262 (t80) REVERT: D 333 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7555 (ttmt) REVERT: D 338 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7006 (mt-10) REVERT: D 347 GLU cc_start: 0.8000 (tp30) cc_final: 0.7387 (tp30) REVERT: D 392 GLU cc_start: 0.7731 (tp30) cc_final: 0.7182 (tp30) REVERT: D 397 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7769 (mt-10) REVERT: E 1 MET cc_start: 0.8014 (ptm) cc_final: 0.7721 (ppp) REVERT: E 23 MET cc_start: 0.8530 (mmt) cc_final: 0.8238 (mmt) REVERT: E 34 LYS cc_start: 0.8870 (tttp) cc_final: 0.8272 (tttp) REVERT: E 38 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8409 (mtpt) REVERT: E 39 LEU cc_start: 0.8767 (mt) cc_final: 0.8457 (mt) REVERT: E 41 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8621 (ttpt) REVERT: E 47 TYR cc_start: 0.6410 (t80) cc_final: 0.6128 (t80) REVERT: E 79 LYS cc_start: 0.8241 (mttp) cc_final: 0.7975 (mttp) REVERT: E 86 ASP cc_start: 0.8476 (t0) cc_final: 0.8182 (t0) REVERT: E 93 GLU cc_start: 0.8053 (tp30) cc_final: 0.7554 (tp30) REVERT: E 95 GLU cc_start: 0.8677 (tt0) cc_final: 0.8087 (tt0) REVERT: E 96 LYS cc_start: 0.8597 (tttp) cc_final: 0.8331 (tttp) REVERT: E 118 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8102 (mt-10) REVERT: E 146 PHE cc_start: 0.7686 (m-10) cc_final: 0.7183 (m-10) REVERT: E 215 LEU cc_start: 0.9093 (tp) cc_final: 0.8793 (tp) REVERT: E 241 MET cc_start: 0.7649 (mmm) cc_final: 0.7155 (mmm) REVERT: E 265 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8574 (mtmt) REVERT: E 271 THR cc_start: 0.9193 (p) cc_final: 0.8813 (t) REVERT: E 301 LYS cc_start: 0.8246 (ptpt) cc_final: 0.7744 (ptpt) REVERT: E 333 LYS cc_start: 0.7826 (tttp) cc_final: 0.7382 (tttp) REVERT: E 397 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7875 (mt-10) REVERT: E 419 MET cc_start: 0.6275 (mtm) cc_final: 0.6075 (ttp) REVERT: F 5 ILE cc_start: 0.8899 (mt) cc_final: 0.8528 (mt) REVERT: F 13 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7951 (tp40) REVERT: F 15 TYR cc_start: 0.8631 (t80) cc_final: 0.7199 (t80) REVERT: F 18 LYS cc_start: 0.8809 (tppt) cc_final: 0.8414 (tppt) REVERT: F 22 TYR cc_start: 0.8445 (m-80) cc_final: 0.8159 (m-10) REVERT: F 29 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 34 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8061 (ttmm) REVERT: F 38 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8895 (mmtp) REVERT: F 43 HIS cc_start: 0.8419 (t-90) cc_final: 0.7801 (t-90) REVERT: F 60 LEU cc_start: 0.8844 (tp) cc_final: 0.8642 (tp) REVERT: F 61 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7430 (mm-30) REVERT: F 62 ASN cc_start: 0.8490 (m-40) cc_final: 0.7952 (t0) REVERT: F 79 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8680 (mtpt) REVERT: F 82 ASP cc_start: 0.7748 (t0) cc_final: 0.7424 (t0) REVERT: F 93 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 95 GLU cc_start: 0.8092 (tt0) cc_final: 0.7647 (tt0) REVERT: F 96 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8457 (ttpp) REVERT: F 116 ASN cc_start: 0.8496 (t0) cc_final: 0.7819 (t0) REVERT: F 119 LEU cc_start: 0.8604 (mt) cc_final: 0.8148 (mt) REVERT: F 123 LYS cc_start: 0.8652 (tppt) cc_final: 0.8309 (tppt) REVERT: F 149 TYR cc_start: 0.6393 (t80) cc_final: 0.6115 (t80) REVERT: F 155 MET cc_start: 0.6881 (tpp) cc_final: 0.6357 (tpp) REVERT: F 157 ASP cc_start: 0.7647 (m-30) cc_final: 0.7279 (m-30) REVERT: F 158 TYR cc_start: 0.7783 (p90) cc_final: 0.7323 (p90) REVERT: F 183 THR cc_start: 0.8029 (p) cc_final: 0.7519 (t) REVERT: F 184 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7906 (mmmt) REVERT: F 195 LEU cc_start: 0.8500 (tp) cc_final: 0.8272 (tt) REVERT: F 258 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7650 (mt-10) REVERT: F 265 LYS cc_start: 0.8871 (mmtm) cc_final: 0.8468 (mmtm) REVERT: F 296 GLU cc_start: 0.7617 (pt0) cc_final: 0.7307 (pt0) REVERT: F 326 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7451 (mm-30) REVERT: F 333 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8423 (ttpp) REVERT: F 338 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7254 (mm-30) REVERT: F 370 ASP cc_start: 0.7324 (m-30) cc_final: 0.6975 (m-30) REVERT: F 404 ILE cc_start: 0.8301 (mt) cc_final: 0.8092 (mt) REVERT: F 405 LYS cc_start: 0.7037 (tptp) cc_final: 0.6705 (tppp) REVERT: F 418 LEU cc_start: 0.7847 (mp) cc_final: 0.7597 (mp) REVERT: F 419 MET cc_start: 0.4114 (tpt) cc_final: 0.3778 (tpp) REVERT: G 8 ASP cc_start: 0.8760 (m-30) cc_final: 0.8490 (m-30) REVERT: G 78 LEU cc_start: 0.9444 (mt) cc_final: 0.9204 (mt) REVERT: G 82 GLU cc_start: 0.8524 (tp30) cc_final: 0.8136 (tp30) REVERT: G 89 TYR cc_start: 0.8244 (t80) cc_final: 0.7881 (t80) REVERT: G 95 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8472 (mtpp) REVERT: G 100 SER cc_start: 0.8615 (p) cc_final: 0.8326 (p) REVERT: G 238 ASP cc_start: 0.8474 (m-30) cc_final: 0.7940 (m-30) REVERT: G 240 LEU cc_start: 0.9112 (mt) cc_final: 0.8900 (mt) REVERT: G 276 ASP cc_start: 0.8490 (p0) cc_final: 0.8012 (p0) REVERT: G 279 LYS cc_start: 0.9224 (mtmm) cc_final: 0.8559 (mttm) REVERT: G 280 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8444 (ptp-110) REVERT: G 283 LYS cc_start: 0.9058 (pttm) cc_final: 0.8781 (ptpt) REVERT: G 284 LEU cc_start: 0.8950 (pp) cc_final: 0.8741 (mt) REVERT: G 296 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8825 (mmmt) REVERT: G 307 MET cc_start: 0.8859 (mmt) cc_final: 0.8470 (mmm) REVERT: G 323 LYS cc_start: 0.9324 (pttm) cc_final: 0.9092 (pttt) REVERT: G 324 ASN cc_start: 0.8975 (m-40) cc_final: 0.8742 (m-40) REVERT: G 328 GLN cc_start: 0.8205 (tp40) cc_final: 0.7967 (tp40) REVERT: G 330 LEU cc_start: 0.9112 (mm) cc_final: 0.7899 (mm) REVERT: G 331 MET cc_start: 0.8330 (mmp) cc_final: 0.7413 (mmm) outliers start: 1 outliers final: 0 residues processed: 1125 average time/residue: 0.1657 time to fit residues: 280.6937 Evaluate side-chains 1047 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1047 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 134 optimal weight: 0.7980 chunk 257 optimal weight: 0.3980 chunk 239 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 55 optimal weight: 0.0970 chunk 139 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 219 HIS A 240 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN E 398 GLN F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.130026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108007 restraints weight = 48271.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111983 restraints weight = 24135.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114632 restraints weight = 14421.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116451 restraints weight = 9758.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117491 restraints weight = 7251.837| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24515 Z= 0.136 Angle : 0.676 12.255 33269 Z= 0.348 Chirality : 0.045 0.274 3697 Planarity : 0.005 0.093 4105 Dihedral : 10.132 151.350 3441 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.16), residues: 2917 helix: 0.93 (0.14), residues: 1451 sheet: -1.39 (0.27), residues: 373 loop : -1.33 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 139 TYR 0.033 0.002 TYR B 165 PHE 0.022 0.002 PHE D 417 TRP 0.037 0.002 TRP E 414 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (24510) covalent geometry : angle 0.67324 / 0.35 (33263) hydrogen bonds : bond 0.03250 / 2.22 ( 1174) hydrogen bonds : angle 4.79846 / 3.44 ( 3363) metal coordination : bond 0.00761 / 0.38 ( 4) metal coordination : angle 4.39336 / 2.29 ( 6) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1118 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7558 (tpp) cc_final: 0.7344 (tpp) REVERT: A 3 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 11 PHE cc_start: 0.7849 (m-80) cc_final: 0.7364 (m-10) REVERT: A 19 VAL cc_start: 0.8176 (m) cc_final: 0.7915 (p) REVERT: A 26 GLU cc_start: 0.7831 (pm20) cc_final: 0.7249 (pm20) REVERT: A 29 GLU cc_start: 0.7695 (tt0) cc_final: 0.7417 (tt0) REVERT: A 35 ASN cc_start: 0.8530 (m-40) cc_final: 0.8161 (m110) REVERT: A 73 VAL cc_start: 0.9026 (t) cc_final: 0.8549 (p) REVERT: A 85 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7304 (mm-30) REVERT: A 93 GLU cc_start: 0.8076 (tp30) cc_final: 0.7552 (tp30) REVERT: A 95 GLU cc_start: 0.8652 (tt0) cc_final: 0.7809 (tt0) REVERT: A 104 PHE cc_start: 0.7898 (t80) cc_final: 0.7434 (t80) REVERT: A 123 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7813 (mmmm) REVERT: A 139 ARG cc_start: 0.7534 (ttm-80) cc_final: 0.6489 (ttm-80) REVERT: A 146 PHE cc_start: 0.8337 (m-10) cc_final: 0.7977 (m-10) REVERT: A 150 VAL cc_start: 0.8558 (p) cc_final: 0.8279 (m) REVERT: A 171 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7760 (mmtm) REVERT: A 184 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8432 (mmtp) REVERT: A 203 LYS cc_start: 0.7979 (pttm) cc_final: 0.7235 (pttm) REVERT: A 214 TYR cc_start: 0.8510 (m-80) cc_final: 0.8125 (m-10) REVERT: A 235 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8061 (ttpt) REVERT: A 241 MET cc_start: 0.8005 (mmm) cc_final: 0.7460 (mmm) REVERT: A 248 ASP cc_start: 0.7097 (m-30) cc_final: 0.6694 (m-30) REVERT: A 265 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8578 (ttpp) REVERT: A 268 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 269 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7685 (mtmm) REVERT: A 313 LEU cc_start: 0.6753 (tt) cc_final: 0.6505 (tt) REVERT: A 316 CYS cc_start: 0.8243 (m) cc_final: 0.7659 (m) REVERT: A 345 GLU cc_start: 0.6961 (pp20) cc_final: 0.6733 (pp20) REVERT: A 384 MET cc_start: 0.8399 (ttt) cc_final: 0.7743 (ttm) REVERT: A 398 GLN cc_start: 0.6974 (mt0) cc_final: 0.6770 (mt0) REVERT: A 426 GLN cc_start: 0.8169 (mt0) cc_final: 0.7666 (mt0) REVERT: B 4 ILE cc_start: 0.8533 (tp) cc_final: 0.8198 (tp) REVERT: B 13 GLN cc_start: 0.7779 (tp40) cc_final: 0.7405 (tp40) REVERT: B 15 TYR cc_start: 0.8633 (t80) cc_final: 0.7935 (t80) REVERT: B 23 MET cc_start: 0.8195 (tpp) cc_final: 0.7664 (mmm) REVERT: B 41 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8366 (ttmt) REVERT: B 43 HIS cc_start: 0.8705 (t-170) cc_final: 0.8344 (t-170) REVERT: B 47 TYR cc_start: 0.8530 (m-80) cc_final: 0.8130 (m-10) REVERT: B 54 ASN cc_start: 0.8530 (m-40) cc_final: 0.8291 (m-40) REVERT: B 75 THR cc_start: 0.9044 (p) cc_final: 0.8552 (t) REVERT: B 79 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8270 (ttmm) REVERT: B 87 HIS cc_start: 0.7866 (t-90) cc_final: 0.7519 (t-90) REVERT: B 103 MET cc_start: 0.7918 (mmm) cc_final: 0.7621 (mmm) REVERT: B 109 LYS cc_start: 0.9282 (tptt) cc_final: 0.8613 (tptt) REVERT: B 139 ARG cc_start: 0.7901 (ttp-170) cc_final: 0.7625 (ttp-170) REVERT: B 145 SER cc_start: 0.8788 (p) cc_final: 0.8180 (t) REVERT: B 194 VAL cc_start: 0.8245 (t) cc_final: 0.7906 (t) REVERT: B 213 ASP cc_start: 0.7824 (m-30) cc_final: 0.7549 (m-30) REVERT: B 226 MET cc_start: 0.8152 (mmm) cc_final: 0.7446 (mmp) REVERT: B 238 ASP cc_start: 0.8668 (m-30) cc_final: 0.8443 (m-30) REVERT: B 243 ASP cc_start: 0.7172 (t0) cc_final: 0.6938 (t0) REVERT: B 245 SER cc_start: 0.8304 (t) cc_final: 0.6989 (p) REVERT: B 248 ASP cc_start: 0.7474 (m-30) cc_final: 0.6871 (m-30) REVERT: B 258 GLU cc_start: 0.8433 (pt0) cc_final: 0.8156 (pt0) REVERT: B 264 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8343 (mm-30) REVERT: B 274 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7524 (mtm-85) REVERT: B 278 LYS cc_start: 0.8441 (tptp) cc_final: 0.8209 (tptp) REVERT: B 279 GLN cc_start: 0.8426 (tt0) cc_final: 0.7811 (tt0) REVERT: B 298 LYS cc_start: 0.8570 (pttp) cc_final: 0.7894 (pttp) REVERT: B 316 CYS cc_start: 0.7965 (m) cc_final: 0.7297 (m) REVERT: B 318 SER cc_start: 0.7959 (m) cc_final: 0.7271 (t) REVERT: B 324 TYR cc_start: 0.7485 (t80) cc_final: 0.7220 (t80) REVERT: B 384 MET cc_start: 0.8384 (mmm) cc_final: 0.8137 (mmm) REVERT: B 392 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7158 (tm-30) REVERT: B 403 GLN cc_start: 0.7007 (tt0) cc_final: 0.6476 (pt0) REVERT: B 413 LYS cc_start: 0.8667 (tppt) cc_final: 0.8014 (tppt) REVERT: B 414 TRP cc_start: 0.7892 (m100) cc_final: 0.7526 (m100) REVERT: B 427 LYS cc_start: 0.8165 (tttm) cc_final: 0.7671 (ttmm) REVERT: C 3 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 13 GLN cc_start: 0.7703 (tp40) cc_final: 0.7050 (tp40) REVERT: C 26 GLU cc_start: 0.8124 (pt0) cc_final: 0.7794 (pt0) REVERT: C 41 LYS cc_start: 0.8688 (tttt) cc_final: 0.8394 (tttt) REVERT: C 56 LEU cc_start: 0.9119 (mm) cc_final: 0.8915 (mm) REVERT: C 85 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7699 (mm-30) REVERT: C 113 ILE cc_start: 0.8981 (mt) cc_final: 0.8363 (mm) REVERT: C 128 MET cc_start: 0.7949 (mmm) cc_final: 0.7726 (mmm) REVERT: C 154 TRP cc_start: 0.8463 (t60) cc_final: 0.8206 (t60) REVERT: C 166 MET cc_start: 0.7340 (tpt) cc_final: 0.6922 (tpt) REVERT: C 224 ILE cc_start: 0.8004 (mt) cc_final: 0.7689 (tt) REVERT: C 226 MET cc_start: 0.8455 (mmm) cc_final: 0.7909 (mmp) REVERT: C 241 MET cc_start: 0.8073 (mmm) cc_final: 0.7734 (mmm) REVERT: C 279 GLN cc_start: 0.8268 (tt0) cc_final: 0.7772 (tt0) REVERT: C 292 SER cc_start: 0.9051 (m) cc_final: 0.8726 (t) REVERT: C 318 SER cc_start: 0.7739 (t) cc_final: 0.7286 (p) REVERT: C 322 ARG cc_start: 0.7719 (ttm170) cc_final: 0.7512 (ttm170) REVERT: C 329 TYR cc_start: 0.8035 (t80) cc_final: 0.7684 (t80) REVERT: C 333 LYS cc_start: 0.7777 (ttmt) cc_final: 0.7454 (ttpt) REVERT: C 367 ASN cc_start: 0.7716 (m110) cc_final: 0.7485 (m110) REVERT: C 393 LEU cc_start: 0.8842 (mt) cc_final: 0.8603 (mt) REVERT: C 426 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7252 (mm-40) REVERT: D 2 VAL cc_start: 0.9084 (m) cc_final: 0.8868 (p) REVERT: D 15 TYR cc_start: 0.8120 (t80) cc_final: 0.7462 (t80) REVERT: D 24 ASP cc_start: 0.7814 (t0) cc_final: 0.7422 (t0) REVERT: D 38 LYS cc_start: 0.9114 (mttm) cc_final: 0.8830 (mttm) REVERT: D 41 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8016 (ttpp) REVERT: D 46 GLU cc_start: 0.8171 (tt0) cc_final: 0.7707 (tt0) REVERT: D 47 TYR cc_start: 0.8947 (m-80) cc_final: 0.7791 (m-80) REVERT: D 93 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7430 (mm-30) REVERT: D 96 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8102 (ttpp) REVERT: D 109 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7741 (ttmm) REVERT: D 128 MET cc_start: 0.8844 (tpp) cc_final: 0.8516 (tpp) REVERT: D 143 SER cc_start: 0.9027 (m) cc_final: 0.8375 (t) REVERT: D 189 THR cc_start: 0.8592 (p) cc_final: 0.6986 (p) REVERT: D 196 MET cc_start: 0.7625 (mtp) cc_final: 0.7253 (mtp) REVERT: D 222 LEU cc_start: 0.8773 (tp) cc_final: 0.8564 (tt) REVERT: D 223 TYR cc_start: 0.8539 (t80) cc_final: 0.7108 (t80) REVERT: D 235 LYS cc_start: 0.8782 (ttpt) cc_final: 0.8370 (ttpp) REVERT: D 280 TYR cc_start: 0.8364 (m-80) cc_final: 0.8053 (m-80) REVERT: D 296 GLU cc_start: 0.7670 (pt0) cc_final: 0.6479 (pt0) REVERT: D 301 LYS cc_start: 0.8725 (mppt) cc_final: 0.8485 (mppt) REVERT: D 324 TYR cc_start: 0.7742 (m-80) cc_final: 0.7331 (m-80) REVERT: D 329 TYR cc_start: 0.5756 (t80) cc_final: 0.5024 (t80) REVERT: D 333 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7462 (ttmt) REVERT: D 338 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7008 (mt-10) REVERT: D 347 GLU cc_start: 0.7972 (tp30) cc_final: 0.7335 (tp30) REVERT: D 397 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7759 (mt-10) REVERT: E 23 MET cc_start: 0.8547 (mmt) cc_final: 0.8241 (mmt) REVERT: E 34 LYS cc_start: 0.8828 (tttp) cc_final: 0.8161 (tttp) REVERT: E 35 ASN cc_start: 0.8438 (m-40) cc_final: 0.7938 (m-40) REVERT: E 38 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8392 (mtpt) REVERT: E 39 LEU cc_start: 0.8707 (mt) cc_final: 0.8398 (mt) REVERT: E 41 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8580 (ttpt) REVERT: E 47 TYR cc_start: 0.6365 (t80) cc_final: 0.6089 (t80) REVERT: E 79 LYS cc_start: 0.8179 (mttp) cc_final: 0.7938 (mttp) REVERT: E 86 ASP cc_start: 0.8478 (t0) cc_final: 0.8198 (t0) REVERT: E 95 GLU cc_start: 0.8651 (tt0) cc_final: 0.7995 (tt0) REVERT: E 103 MET cc_start: 0.7687 (mmp) cc_final: 0.7107 (mmt) REVERT: E 119 LEU cc_start: 0.8968 (mt) cc_final: 0.8494 (mt) REVERT: E 139 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7712 (ttp80) REVERT: E 146 PHE cc_start: 0.7723 (m-10) cc_final: 0.7156 (m-10) REVERT: E 181 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8422 (tmmt) REVERT: E 215 LEU cc_start: 0.9106 (tp) cc_final: 0.8816 (tp) REVERT: E 238 ASP cc_start: 0.8594 (m-30) cc_final: 0.8334 (m-30) REVERT: E 241 MET cc_start: 0.7623 (mmm) cc_final: 0.7151 (mmm) REVERT: E 271 THR cc_start: 0.9135 (p) cc_final: 0.8757 (t) REVERT: E 301 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7700 (ptpt) REVERT: E 333 LYS cc_start: 0.7820 (tttp) cc_final: 0.7380 (tttp) REVERT: E 397 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7901 (mt-10) REVERT: E 423 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8425 (mtpp) REVERT: F 5 ILE cc_start: 0.8903 (mt) cc_final: 0.8505 (mt) REVERT: F 13 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7944 (tp40) REVERT: F 15 TYR cc_start: 0.8578 (t80) cc_final: 0.7189 (t80) REVERT: F 22 TYR cc_start: 0.8401 (m-80) cc_final: 0.8077 (m-10) REVERT: F 29 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7584 (mm-30) REVERT: F 34 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8075 (ttmm) REVERT: F 41 LYS cc_start: 0.8860 (tttp) cc_final: 0.8636 (tttp) REVERT: F 43 HIS cc_start: 0.8318 (t-90) cc_final: 0.7737 (t-90) REVERT: F 61 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7398 (mm-30) REVERT: F 62 ASN cc_start: 0.8423 (m-40) cc_final: 0.7903 (t0) REVERT: F 82 ASP cc_start: 0.7540 (t0) cc_final: 0.7247 (t0) REVERT: F 95 GLU cc_start: 0.8044 (tt0) cc_final: 0.7568 (tt0) REVERT: F 96 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8303 (ttpp) REVERT: F 109 LYS cc_start: 0.8678 (tttp) cc_final: 0.8475 (tttp) REVERT: F 116 ASN cc_start: 0.8518 (t0) cc_final: 0.7744 (t0) REVERT: F 119 LEU cc_start: 0.8584 (mt) cc_final: 0.8123 (mt) REVERT: F 123 LYS cc_start: 0.8616 (tppt) cc_final: 0.8388 (tppt) REVERT: F 128 MET cc_start: 0.7574 (ptp) cc_final: 0.7330 (ptt) REVERT: F 155 MET cc_start: 0.6863 (tpp) cc_final: 0.6468 (tpp) REVERT: F 157 ASP cc_start: 0.7529 (m-30) cc_final: 0.6425 (p0) REVERT: F 158 TYR cc_start: 0.7575 (p90) cc_final: 0.6873 (p90) REVERT: F 183 THR cc_start: 0.8048 (p) cc_final: 0.7499 (t) REVERT: F 184 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7883 (mmmt) REVERT: F 189 THR cc_start: 0.7816 (p) cc_final: 0.7199 (t) REVERT: F 191 THR cc_start: 0.8691 (p) cc_final: 0.8053 (t) REVERT: F 258 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7758 (mt-10) REVERT: F 265 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8512 (mmtm) REVERT: F 296 GLU cc_start: 0.7608 (pt0) cc_final: 0.7395 (pt0) REVERT: F 326 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7421 (mm-30) REVERT: F 333 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8422 (ttpp) REVERT: F 338 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7265 (mm-30) REVERT: F 370 ASP cc_start: 0.7154 (m-30) cc_final: 0.6824 (m-30) REVERT: F 404 ILE cc_start: 0.8300 (mt) cc_final: 0.8044 (mt) REVERT: F 405 LYS cc_start: 0.6803 (tptp) cc_final: 0.6429 (tppp) REVERT: F 418 LEU cc_start: 0.7838 (mp) cc_final: 0.7495 (mp) REVERT: G 8 ASP cc_start: 0.8716 (m-30) cc_final: 0.8441 (m-30) REVERT: G 78 LEU cc_start: 0.9420 (mt) cc_final: 0.9176 (mt) REVERT: G 82 GLU cc_start: 0.8523 (tp30) cc_final: 0.8156 (tp30) REVERT: G 89 TYR cc_start: 0.8182 (t80) cc_final: 0.7846 (t80) REVERT: G 95 LYS cc_start: 0.9120 (mtpt) cc_final: 0.8391 (mtpp) REVERT: G 96 GLU cc_start: 0.7619 (pp20) cc_final: 0.7366 (pp20) REVERT: G 97 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7437 (mtmt) REVERT: G 238 ASP cc_start: 0.8395 (m-30) cc_final: 0.7862 (m-30) REVERT: G 240 LEU cc_start: 0.9080 (mt) cc_final: 0.8856 (mt) REVERT: G 276 ASP cc_start: 0.8489 (p0) cc_final: 0.7999 (p0) REVERT: G 279 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8497 (mttm) REVERT: G 280 ARG cc_start: 0.8718 (mtm-85) cc_final: 0.8454 (ptp-110) REVERT: G 283 LYS cc_start: 0.9032 (pttm) cc_final: 0.8714 (ptpt) REVERT: G 284 LEU cc_start: 0.8938 (pp) cc_final: 0.8562 (mp) REVERT: G 307 MET cc_start: 0.8816 (mmt) cc_final: 0.8373 (mmm) REVERT: G 323 LYS cc_start: 0.9320 (pttm) cc_final: 0.9107 (pttp) REVERT: G 324 ASN cc_start: 0.8850 (m-40) cc_final: 0.8625 (m-40) REVERT: G 334 MET cc_start: 0.7968 (mtm) cc_final: 0.7606 (mtm) outliers start: 0 outliers final: 0 residues processed: 1118 average time/residue: 0.1775 time to fit residues: 299.8230 Evaluate side-chains 1048 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1048 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 129 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 227 optimal weight: 0.1980 chunk 290 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN A 116 ASN A 220 ASN A 240 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN D 62 ASN D 100 GLN D 114 GLN ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 422 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.123493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.102246 restraints weight = 49477.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105705 restraints weight = 26138.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108007 restraints weight = 16209.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109562 restraints weight = 11338.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110528 restraints weight = 8708.890| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 24515 Z= 0.271 Angle : 0.751 14.841 33269 Z= 0.391 Chirality : 0.048 0.288 3697 Planarity : 0.005 0.062 4105 Dihedral : 10.322 153.435 3441 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.04 % Allowed : 0.35 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.53 (0.16), residues: 2917 helix: 0.77 (0.14), residues: 1446 sheet: -1.51 (0.27), residues: 362 loop : -1.38 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 124 TYR 0.036 0.002 TYR B 165 PHE 0.032 0.003 PHE E 174 TRP 0.055 0.003 TRP G 266 HIS 0.011 0.002 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (24510) covalent geometry : angle 0.74772 / 0.39 (33263) hydrogen bonds : bond 0.03602 / 2.48 ( 1174) hydrogen bonds : angle 5.02540 / 3.59 ( 3363) metal coordination : bond 0.01646 / 0.83 ( 4) metal coordination : angle 4.97466 / 2.41 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1122 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7390 (mm-30) REVERT: A 11 PHE cc_start: 0.7994 (m-80) cc_final: 0.7560 (m-10) REVERT: A 19 VAL cc_start: 0.8191 (m) cc_final: 0.7947 (p) REVERT: A 26 GLU cc_start: 0.7842 (pm20) cc_final: 0.7290 (pm20) REVERT: A 29 GLU cc_start: 0.7658 (tt0) cc_final: 0.7452 (tt0) REVERT: A 39 LEU cc_start: 0.9085 (mt) cc_final: 0.8863 (mt) REVERT: A 47 TYR cc_start: 0.6289 (m-80) cc_final: 0.6078 (m-80) REVERT: A 73 VAL cc_start: 0.8941 (t) cc_final: 0.8467 (p) REVERT: A 79 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8033 (ttmt) REVERT: A 123 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7961 (mmmm) REVERT: A 128 MET cc_start: 0.8362 (tpt) cc_final: 0.8092 (tpt) REVERT: A 136 ASP cc_start: 0.7500 (m-30) cc_final: 0.7265 (m-30) REVERT: A 146 PHE cc_start: 0.8509 (m-10) cc_final: 0.8068 (m-80) REVERT: A 150 VAL cc_start: 0.8874 (p) cc_final: 0.8501 (m) REVERT: A 171 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7643 (mmtm) REVERT: A 214 TYR cc_start: 0.8636 (m-80) cc_final: 0.8244 (m-10) REVERT: A 235 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8115 (ttpt) REVERT: A 238 ASP cc_start: 0.8671 (m-30) cc_final: 0.8425 (m-30) REVERT: A 241 MET cc_start: 0.7914 (mmm) cc_final: 0.7427 (mmm) REVERT: A 248 ASP cc_start: 0.7141 (m-30) cc_final: 0.6644 (m-30) REVERT: A 265 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8564 (ttpp) REVERT: A 268 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7697 (mt-10) REVERT: A 316 CYS cc_start: 0.8330 (m) cc_final: 0.7743 (m) REVERT: A 384 MET cc_start: 0.8491 (ttt) cc_final: 0.8028 (ttm) REVERT: A 403 GLN cc_start: 0.7736 (tt0) cc_final: 0.7378 (tt0) REVERT: A 426 GLN cc_start: 0.8107 (mt0) cc_final: 0.7605 (mt0) REVERT: B 4 ILE cc_start: 0.8708 (tp) cc_final: 0.8451 (tp) REVERT: B 13 GLN cc_start: 0.7735 (tp40) cc_final: 0.7326 (tp40) REVERT: B 15 TYR cc_start: 0.8690 (t80) cc_final: 0.7986 (t80) REVERT: B 41 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8453 (ttmt) REVERT: B 43 HIS cc_start: 0.8857 (t-170) cc_final: 0.8564 (t-170) REVERT: B 47 TYR cc_start: 0.8572 (m-80) cc_final: 0.8041 (m-80) REVERT: B 87 HIS cc_start: 0.8039 (t-90) cc_final: 0.7715 (t-90) REVERT: B 103 MET cc_start: 0.7869 (mmm) cc_final: 0.7579 (mmm) REVERT: B 109 LYS cc_start: 0.9224 (tptt) cc_final: 0.8598 (tptt) REVERT: B 114 GLN cc_start: 0.8817 (tt0) cc_final: 0.8448 (tt0) REVERT: B 145 SER cc_start: 0.8665 (p) cc_final: 0.8291 (t) REVERT: B 155 MET cc_start: 0.7962 (tpp) cc_final: 0.7466 (tpp) REVERT: B 184 LYS cc_start: 0.8649 (mmtm) cc_final: 0.8133 (mmmt) REVERT: B 213 ASP cc_start: 0.7854 (m-30) cc_final: 0.7614 (m-30) REVERT: B 226 MET cc_start: 0.8246 (mmm) cc_final: 0.7496 (mmp) REVERT: B 231 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 243 ASP cc_start: 0.7156 (t0) cc_final: 0.6898 (t0) REVERT: B 245 SER cc_start: 0.8559 (t) cc_final: 0.7106 (p) REVERT: B 248 ASP cc_start: 0.7906 (m-30) cc_final: 0.7171 (m-30) REVERT: B 253 HIS cc_start: 0.7603 (m90) cc_final: 0.7280 (m90) REVERT: B 258 GLU cc_start: 0.8313 (pt0) cc_final: 0.8046 (pt0) REVERT: B 265 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8396 (ttpp) REVERT: B 269 LYS cc_start: 0.7772 (mtmm) cc_final: 0.6908 (mtmm) REVERT: B 272 LEU cc_start: 0.9161 (tp) cc_final: 0.8900 (tp) REVERT: B 274 ARG cc_start: 0.8001 (mtp85) cc_final: 0.7678 (mtm-85) REVERT: B 278 LYS cc_start: 0.8549 (tptp) cc_final: 0.8317 (tptp) REVERT: B 279 GLN cc_start: 0.8493 (tt0) cc_final: 0.7926 (tt0) REVERT: B 300 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8180 (mtpt) REVERT: B 318 SER cc_start: 0.8059 (m) cc_final: 0.7371 (t) REVERT: B 392 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7299 (tm-30) REVERT: B 403 GLN cc_start: 0.7426 (tt0) cc_final: 0.6758 (pt0) REVERT: B 413 LYS cc_start: 0.8692 (tppt) cc_final: 0.8154 (tppt) REVERT: B 414 TRP cc_start: 0.7979 (m100) cc_final: 0.7606 (m100) REVERT: B 419 MET cc_start: 0.4647 (tpp) cc_final: 0.4288 (ttm) REVERT: B 427 LYS cc_start: 0.8220 (tttm) cc_final: 0.7765 (ttmm) REVERT: C 13 GLN cc_start: 0.7807 (tp40) cc_final: 0.7301 (tp40) REVERT: C 26 GLU cc_start: 0.7933 (pt0) cc_final: 0.7612 (pt0) REVERT: C 56 LEU cc_start: 0.9094 (mm) cc_final: 0.8876 (mm) REVERT: C 60 LEU cc_start: 0.8739 (mm) cc_final: 0.8375 (tp) REVERT: C 85 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7806 (mm-30) REVERT: C 113 ILE cc_start: 0.9069 (mt) cc_final: 0.8657 (mm) REVERT: C 166 MET cc_start: 0.7309 (tpt) cc_final: 0.6753 (tpt) REVERT: C 178 ILE cc_start: 0.8178 (tp) cc_final: 0.7770 (mm) REVERT: C 200 ASN cc_start: 0.7478 (t0) cc_final: 0.7131 (t0) REVERT: C 213 ASP cc_start: 0.8072 (m-30) cc_final: 0.7722 (m-30) REVERT: C 224 ILE cc_start: 0.8106 (mt) cc_final: 0.7823 (tt) REVERT: C 226 MET cc_start: 0.8419 (mmm) cc_final: 0.8001 (mmp) REVERT: C 241 MET cc_start: 0.7989 (mmm) cc_final: 0.7692 (mmm) REVERT: C 243 ASP cc_start: 0.7781 (t0) cc_final: 0.7484 (t0) REVERT: C 279 GLN cc_start: 0.8355 (tt0) cc_final: 0.7897 (tt0) REVERT: C 292 SER cc_start: 0.9025 (m) cc_final: 0.8713 (t) REVERT: C 318 SER cc_start: 0.7818 (t) cc_final: 0.7379 (p) REVERT: C 335 ILE cc_start: 0.8496 (tp) cc_final: 0.8124 (tp) REVERT: C 347 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7565 (mm-30) REVERT: C 426 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7473 (mm-40) REVERT: D 1 MET cc_start: 0.8661 (ppp) cc_final: 0.8385 (ppp) REVERT: D 2 VAL cc_start: 0.9053 (m) cc_final: 0.8842 (p) REVERT: D 15 TYR cc_start: 0.8136 (t80) cc_final: 0.7518 (t80) REVERT: D 38 LYS cc_start: 0.9127 (mttm) cc_final: 0.8924 (mttm) REVERT: D 41 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8186 (ttmm) REVERT: D 90 LEU cc_start: 0.8493 (mm) cc_final: 0.8149 (mm) REVERT: D 93 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 96 LYS cc_start: 0.8654 (ttpp) cc_final: 0.7964 (ttpp) REVERT: D 114 GLN cc_start: 0.7610 (mt0) cc_final: 0.7394 (mt0) REVERT: D 118 GLU cc_start: 0.7053 (tp30) cc_final: 0.6707 (tp30) REVERT: D 143 SER cc_start: 0.8997 (m) cc_final: 0.8315 (t) REVERT: D 147 ASP cc_start: 0.7415 (p0) cc_final: 0.7123 (p0) REVERT: D 154 TRP cc_start: 0.8743 (t60) cc_final: 0.8103 (t60) REVERT: D 155 MET cc_start: 0.7735 (tpt) cc_final: 0.7340 (tpt) REVERT: D 189 THR cc_start: 0.8754 (p) cc_final: 0.7017 (p) REVERT: D 192 LEU cc_start: 0.8944 (tp) cc_final: 0.8731 (tp) REVERT: D 196 MET cc_start: 0.7194 (mtp) cc_final: 0.6706 (mtp) REVERT: D 235 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8435 (ttpp) REVERT: D 238 ASP cc_start: 0.9042 (m-30) cc_final: 0.8392 (m-30) REVERT: D 280 TYR cc_start: 0.8370 (m-80) cc_final: 0.8027 (m-80) REVERT: D 296 GLU cc_start: 0.7673 (pt0) cc_final: 0.6518 (pt0) REVERT: D 324 TYR cc_start: 0.7828 (m-80) cc_final: 0.7457 (m-80) REVERT: D 338 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7038 (mt-10) REVERT: D 347 GLU cc_start: 0.7770 (tp30) cc_final: 0.7265 (tp30) REVERT: D 392 GLU cc_start: 0.7615 (tp30) cc_final: 0.7157 (tp30) REVERT: D 397 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7587 (mt-10) REVERT: E 3 GLU cc_start: 0.7396 (tp30) cc_final: 0.6978 (tp30) REVERT: E 24 ASP cc_start: 0.7629 (t0) cc_final: 0.7208 (t0) REVERT: E 34 LYS cc_start: 0.8830 (tttp) cc_final: 0.8185 (tttp) REVERT: E 35 ASN cc_start: 0.8587 (m-40) cc_final: 0.7832 (m-40) REVERT: E 38 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8481 (mtpt) REVERT: E 39 LEU cc_start: 0.8836 (mt) cc_final: 0.8534 (mt) REVERT: E 41 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8621 (ttpt) REVERT: E 47 TYR cc_start: 0.6462 (t80) cc_final: 0.6189 (t80) REVERT: E 50 VAL cc_start: 0.8027 (t) cc_final: 0.7824 (m) REVERT: E 74 LYS cc_start: 0.8651 (tttt) cc_final: 0.8321 (tttt) REVERT: E 79 LYS cc_start: 0.8200 (mttp) cc_final: 0.7625 (mttp) REVERT: E 103 MET cc_start: 0.7625 (mmp) cc_final: 0.6899 (mmp) REVERT: E 139 ARG cc_start: 0.7701 (ttp80) cc_final: 0.7235 (ttp80) REVERT: E 177 ARG cc_start: 0.7654 (mtt90) cc_final: 0.7439 (mtt90) REVERT: E 181 LYS cc_start: 0.8531 (tmmt) cc_final: 0.8161 (tmmt) REVERT: E 228 MET cc_start: 0.7406 (ptt) cc_final: 0.7166 (ptt) REVERT: E 237 ILE cc_start: 0.8937 (mm) cc_final: 0.8727 (mm) REVERT: E 241 MET cc_start: 0.7618 (mmm) cc_final: 0.7256 (mmm) REVERT: E 271 THR cc_start: 0.9202 (p) cc_final: 0.8813 (t) REVERT: E 296 GLU cc_start: 0.7799 (pt0) cc_final: 0.7573 (pt0) REVERT: E 301 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7693 (ptpt) REVERT: E 333 LYS cc_start: 0.7978 (tttp) cc_final: 0.7531 (tttp) REVERT: E 338 GLU cc_start: 0.6101 (pt0) cc_final: 0.5880 (pt0) REVERT: E 345 GLU cc_start: 0.8567 (tt0) cc_final: 0.8334 (tt0) REVERT: F 7 SER cc_start: 0.8937 (m) cc_final: 0.8389 (p) REVERT: F 13 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7849 (tp40) REVERT: F 22 TYR cc_start: 0.8404 (m-80) cc_final: 0.8175 (m-10) REVERT: F 29 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 34 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8137 (ttmm) REVERT: F 61 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7518 (mm-30) REVERT: F 62 ASN cc_start: 0.8367 (m-40) cc_final: 0.7886 (t0) REVERT: F 67 GLU cc_start: 0.8022 (tp30) cc_final: 0.7726 (tp30) REVERT: F 82 ASP cc_start: 0.7488 (t0) cc_final: 0.7161 (t0) REVERT: F 93 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7667 (mt-10) REVERT: F 95 GLU cc_start: 0.8020 (tt0) cc_final: 0.7665 (tt0) REVERT: F 96 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8391 (ttpp) REVERT: F 114 GLN cc_start: 0.8562 (mt0) cc_final: 0.8222 (mt0) REVERT: F 116 ASN cc_start: 0.8615 (t0) cc_final: 0.7978 (t0) REVERT: F 119 LEU cc_start: 0.8642 (mt) cc_final: 0.8162 (mt) REVERT: F 123 LYS cc_start: 0.8633 (tppt) cc_final: 0.8326 (tppt) REVERT: F 155 MET cc_start: 0.6920 (tpp) cc_final: 0.6499 (tpp) REVERT: F 157 ASP cc_start: 0.7933 (m-30) cc_final: 0.7553 (m-30) REVERT: F 158 TYR cc_start: 0.7750 (p90) cc_final: 0.7336 (p90) REVERT: F 159 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7527 (mm-30) REVERT: F 183 THR cc_start: 0.8079 (p) cc_final: 0.7546 (t) REVERT: F 184 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7985 (mmmt) REVERT: F 216 GLN cc_start: 0.8268 (mt0) cc_final: 0.7882 (mt0) REVERT: F 226 MET cc_start: 0.7402 (mmp) cc_final: 0.6993 (mmp) REVERT: F 258 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7627 (mt-10) REVERT: F 265 LYS cc_start: 0.8862 (mmtm) cc_final: 0.8564 (mmtm) REVERT: F 296 GLU cc_start: 0.7553 (pt0) cc_final: 0.7297 (pt0) REVERT: F 326 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7516 (mm-30) REVERT: F 338 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7296 (mm-30) REVERT: F 355 GLN cc_start: 0.7864 (mt0) cc_final: 0.7608 (mt0) REVERT: F 370 ASP cc_start: 0.7300 (m-30) cc_final: 0.6977 (m-30) REVERT: F 404 ILE cc_start: 0.8372 (mt) cc_final: 0.8097 (mt) REVERT: F 405 LYS cc_start: 0.7269 (tptp) cc_final: 0.6645 (tptp) REVERT: F 419 MET cc_start: 0.4935 (tpt) cc_final: 0.4535 (tpt) REVERT: F 425 ASN cc_start: 0.7972 (m-40) cc_final: 0.7457 (m-40) REVERT: G 77 TYR cc_start: 0.8224 (t80) cc_final: 0.7850 (t80) REVERT: G 78 LEU cc_start: 0.9423 (mt) cc_final: 0.9136 (mt) REVERT: G 82 GLU cc_start: 0.8466 (tp30) cc_final: 0.8114 (tp30) REVERT: G 84 ASP cc_start: 0.8716 (p0) cc_final: 0.8513 (p0) REVERT: G 89 TYR cc_start: 0.8065 (t80) cc_final: 0.7820 (t80) REVERT: G 93 ILE cc_start: 0.9347 (pt) cc_final: 0.9122 (pt) REVERT: G 95 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8578 (mtpp) REVERT: G 100 SER cc_start: 0.8709 (p) cc_final: 0.8471 (p) REVERT: G 238 ASP cc_start: 0.8511 (m-30) cc_final: 0.8027 (m-30) REVERT: G 279 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8558 (mttm) REVERT: G 283 LYS cc_start: 0.8968 (pttm) cc_final: 0.8658 (ptpt) REVERT: G 284 LEU cc_start: 0.8890 (pp) cc_final: 0.8462 (mp) REVERT: G 307 MET cc_start: 0.8845 (mmt) cc_final: 0.8473 (mmm) REVERT: G 323 LYS cc_start: 0.9307 (pttm) cc_final: 0.9069 (pttt) REVERT: G 328 GLN cc_start: 0.8332 (tp40) cc_final: 0.7719 (tp40) outliers start: 1 outliers final: 0 residues processed: 1123 average time/residue: 0.1726 time to fit residues: 291.7409 Evaluate side-chains 1055 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1055 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 210 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 286 optimal weight: 0.0000 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 219 HIS A 240 ASN A 279 GLN A 295 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN D 62 ASN E 200 ASN E 425 ASN ** E 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 ASN F 48 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 GLN G 324 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106268 restraints weight = 48565.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109937 restraints weight = 25098.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112433 restraints weight = 15354.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.113950 restraints weight = 10519.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115144 restraints weight = 8073.404| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24515 Z= 0.158 Angle : 0.714 14.505 33269 Z= 0.366 Chirality : 0.046 0.286 3697 Planarity : 0.005 0.061 4105 Dihedral : 10.237 152.404 3441 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.08 % Allowed : 0.32 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -0.46 (0.16), residues: 2917 helix: 0.85 (0.14), residues: 1449 sheet: -1.52 (0.27), residues: 360 loop : -1.38 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 139 TYR 0.032 0.002 TYR B 165 PHE 0.030 0.002 PHE F 383 TRP 0.054 0.002 TRP G 266 HIS 0.009 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (24510) covalent geometry : angle 0.71120 / 0.37 (33263) hydrogen bonds : bond 0.03331 / 2.30 ( 1174) hydrogen bonds : angle 4.87796 / 3.47 ( 3363) metal coordination : bond 0.00949 / 0.48 ( 4) metal coordination : angle 4.54715 / 2.34 ( 6) Misc. bond : bond 0.00020 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5655.76 seconds wall clock time: 98 minutes 10.74 seconds (5890.74 seconds total)