Starting phenix.real_space_refine on Sat Jul 4 22:28:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gao_29902/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gao_29902/07_2026/8gao_29902.map" } 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-dev-6108/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: {'RNA': 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: 5.88, per 1000 atoms: 0.25 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: 2.03 Conformation dependent library (CDL) restraints added in 975.2 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: 0.76 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: 4.56 Time building geometry restraints manager: 2.67 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: 32877 2.27 - 4.55: 351 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: 14546 35.94 - 71.87: 200 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=" 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 dihedral pdb=" C5' GTP P 1 " pdb=" O5' GTP P 1 " pdb=" PA GTP P 1 " pdb=" O3A GTP P 1 " ideal model delta sinusoidal sigma weight residual 69.27 143.57 -74.30 1 2.00e+01 2.50e-03 1.75e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2786 0.042 - 0.083: 647 0.083 - 0.125: 232 0.125 - 0.167: 28 0.167 - 0.209: 4 Chirality restraints: 3697 Sorted by residual: chirality pdb=" CA VAL E 244 " pdb=" N VAL E 244 " pdb=" C VAL E 244 " pdb=" CB VAL E 244 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE F 321 " pdb=" N ILE F 321 " pdb=" C ILE F 321 " pdb=" CB ILE F 321 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA LEU A 210 " pdb=" N LEU A 210 " pdb=" C LEU A 210 " pdb=" CB LEU A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.85e-01 ... (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: 0.630 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.610 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- 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 : 0.602 11.371 33269 Z= 0.382 Chirality : 0.042 0.209 3697 Planarity : 0.003 0.044 4105 Dihedral : 12.214 179.685 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 0.60064 / 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 : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1622 time to fit residues: 326.4872 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 : 0.598 ------------------------------------------------------------------------------- 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 = 0.3646 r_free = 0.3646 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101804 restraints weight = 48882.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105371 restraints weight = 25563.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.107803 restraints weight = 15700.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109331 restraints weight = 10773.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110503 restraints weight = 8254.905| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 24515 Z= 0.208 Angle : 0.679 9.679 33269 Z= 0.355 Chirality : 0.046 0.330 3697 Planarity : 0.005 0.171 4105 Dihedral : 10.357 178.910 3441 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.12 % Allowed : 3.27 % Favored : 96.61 % 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: 0.02 (0.16), residues: 2917 helix: 1.27 (0.14), residues: 1446 sheet: -1.26 (0.26), residues: 387 loop : -1.17 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 36 TYR 0.035 0.002 TYR G 54 PHE 0.038 0.002 PHE G 293 TRP 0.021 0.002 TRP F 89 HIS 0.008 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (24510) covalent geometry : angle 0.67462 / 0.36 (33263) hydrogen bonds : bond 0.04455 / 2.95 ( 1174) hydrogen bonds : angle 5.27752 / 3.76 ( 3363) metal coordination : bond 0.01024 / 0.51 ( 4) metal coordination : angle 6.00266 / 2.95 ( 6) Misc. bond : bond 0.00669 / 0.35 ( 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 1214 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1211 time to evaluate : 0.617 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: 0.8411 (tpp) cc_final: 0.7682 (tpp) REVERT: A 3 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7521 (mm-30) REVERT: A 11 PHE cc_start: 0.7823 (m-80) cc_final: 0.7343 (m-10) REVERT: A 19 VAL cc_start: 0.8180 (m) cc_final: 0.7863 (p) REVERT: A 26 GLU cc_start: 0.7918 (pm20) cc_final: 0.7442 (pm20) REVERT: A 29 GLU cc_start: 0.7668 (tt0) cc_final: 0.7326 (tt0) REVERT: A 35 ASN cc_start: 0.8557 (m-40) cc_final: 0.8184 (m110) REVERT: A 42 SER cc_start: 0.8576 (m) cc_final: 0.8138 (p) REVERT: A 47 TYR cc_start: 0.6374 (m-80) cc_final: 0.6061 (m-80) REVERT: A 60 LEU cc_start: 0.9160 (tp) cc_final: 0.8881 (tp) REVERT: A 66 THR cc_start: 0.8691 (p) cc_final: 0.8296 (p) REVERT: A 73 VAL cc_start: 0.8875 (t) cc_final: 0.8120 (p) REVERT: A 79 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8049 (ttmt) REVERT: A 93 GLU cc_start: 0.8088 (tp30) cc_final: 0.7613 (tp30) REVERT: A 103 MET cc_start: 0.7749 (mmm) cc_final: 0.7394 (mmp) REVERT: A 113 ILE cc_start: 0.9049 (mt) cc_final: 0.8794 (mt) REVERT: A 123 LYS cc_start: 0.8229 (mmmm) cc_final: 0.8014 (mmmm) REVERT: A 131 VAL cc_start: 0.9031 (t) cc_final: 0.8664 (m) REVERT: A 146 PHE cc_start: 0.8382 (m-10) cc_final: 0.7871 (m-10) REVERT: A 163 LEU cc_start: 0.8822 (tp) cc_final: 0.8559 (tt) REVERT: A 166 MET cc_start: 0.7638 (mtm) cc_final: 0.7391 (mtm) REVERT: A 171 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7497 (mmtm) REVERT: A 174 PHE cc_start: 0.8648 (m-80) cc_final: 0.8207 (m-10) REVERT: A 184 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8317 (mmtp) REVERT: A 188 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7261 (mt-10) REVERT: A 189 THR cc_start: 0.8389 (p) cc_final: 0.8148 (m) REVERT: A 214 TYR cc_start: 0.8544 (m-80) cc_final: 0.7673 (m-10) REVERT: A 215 LEU cc_start: 0.8597 (tp) cc_final: 0.8354 (tp) REVERT: A 235 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8087 (ttpt) REVERT: A 241 MET cc_start: 0.8150 (mmm) cc_final: 0.7632 (mmm) REVERT: A 260 LYS cc_start: 0.8749 (tppt) cc_final: 0.8547 (mmmm) REVERT: A 265 LYS cc_start: 0.8990 (ttpp) cc_final: 0.8616 (ttpp) REVERT: A 267 ARG cc_start: 0.6931 (ttm-80) cc_final: 0.5500 (ttm-80) REVERT: A 313 LEU cc_start: 0.7030 (tt) cc_final: 0.6794 (tt) REVERT: A 316 CYS cc_start: 0.8113 (m) cc_final: 0.7644 (m) REVERT: A 347 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 384 MET cc_start: 0.8369 (ttt) cc_final: 0.7994 (ttm) REVERT: A 403 GLN cc_start: 0.8209 (tt0) cc_final: 0.7938 (tt0) REVERT: A 408 TYR cc_start: 0.8632 (m-80) cc_final: 0.8399 (m-80) REVERT: A 416 LYS cc_start: 0.8937 (mptt) cc_final: 0.8713 (mptt) REVERT: A 426 GLN cc_start: 0.8029 (mt0) cc_final: 0.7651 (mt0) REVERT: B 3 GLU cc_start: 0.7535 (tt0) cc_final: 0.6856 (tt0) REVERT: B 15 TYR cc_start: 0.8225 (t80) cc_final: 0.7721 (t80) REVERT: B 64 SER cc_start: 0.8656 (t) cc_final: 0.8387 (p) REVERT: B 79 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8079 (ttmm) REVERT: B 95 GLU cc_start: 0.8148 (tt0) cc_final: 0.7880 (tt0) REVERT: B 103 MET cc_start: 0.7951 (mmm) cc_final: 0.7731 (mmm) REVERT: B 139 ARG cc_start: 0.7898 (ttp-170) cc_final: 0.7646 (ttp-170) REVERT: B 144 ILE cc_start: 0.8921 (tt) cc_final: 0.8670 (tt) REVERT: B 145 SER cc_start: 0.8410 (p) cc_final: 0.7905 (p) REVERT: B 147 ASP cc_start: 0.7176 (m-30) cc_final: 0.6882 (m-30) REVERT: B 194 VAL cc_start: 0.8625 (t) cc_final: 0.8020 (t) REVERT: B 213 ASP cc_start: 0.7854 (m-30) cc_final: 0.7520 (m-30) REVERT: B 226 MET cc_start: 0.8177 (mmm) cc_final: 0.7504 (mmp) REVERT: B 231 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 243 ASP cc_start: 0.7331 (t0) cc_final: 0.6937 (t0) REVERT: B 245 SER cc_start: 0.8430 (t) cc_final: 0.7689 (p) REVERT: B 258 GLU cc_start: 0.8311 (pt0) cc_final: 0.8064 (pt0) REVERT: B 260 LYS cc_start: 0.8818 (tttp) cc_final: 0.8516 (tttp) REVERT: B 263 MET cc_start: 0.8013 (mmm) cc_final: 0.7723 (mmt) REVERT: B 265 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8615 (ttmt) REVERT: B 278 LYS cc_start: 0.8455 (tptp) cc_final: 0.8248 (tptp) REVERT: B 279 GLN cc_start: 0.8478 (tt0) cc_final: 0.8045 (tt0) REVERT: B 298 LYS cc_start: 0.8816 (ttpp) cc_final: 0.8541 (ttpp) REVERT: B 300 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8011 (mtpt) REVERT: B 318 SER cc_start: 0.8169 (m) cc_final: 0.7450 (t) REVERT: B 324 TYR cc_start: 0.7497 (t80) cc_final: 0.7267 (t80) REVERT: B 368 MET cc_start: 0.8345 (tpp) cc_final: 0.7898 (ttt) REVERT: B 391 GLU cc_start: 0.7397 (tp30) cc_final: 0.7149 (tp30) REVERT: B 392 GLU cc_start: 0.7323 (tm-30) cc_final: 0.6929 (tm-30) REVERT: B 413 LYS cc_start: 0.8730 (tppt) cc_final: 0.8169 (tppt) REVERT: C 3 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7980 (mm-30) REVERT: C 26 GLU cc_start: 0.8070 (pt0) cc_final: 0.7764 (pt0) REVERT: C 39 LEU cc_start: 0.8764 (mt) cc_final: 0.8427 (mt) REVERT: C 41 LYS cc_start: 0.8825 (tttt) cc_final: 0.8587 (tttt) REVERT: C 85 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7743 (mm-30) REVERT: C 155 MET cc_start: 0.7483 (tpt) cc_final: 0.7242 (tpt) REVERT: C 181 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8095 (ttpp) REVERT: C 203 LYS cc_start: 0.7939 (mtmm) cc_final: 0.7665 (mtmm) REVERT: C 241 MET cc_start: 0.8178 (mmm) cc_final: 0.7460 (mmm) REVERT: C 263 MET cc_start: 0.7497 (mmm) cc_final: 0.7101 (mmm) REVERT: C 269 LYS cc_start: 0.7683 (mmtp) cc_final: 0.7415 (mttm) REVERT: C 272 LEU cc_start: 0.8801 (tp) cc_final: 0.8599 (tt) REVERT: C 279 GLN cc_start: 0.8203 (tt0) cc_final: 0.7793 (tt0) REVERT: C 292 SER cc_start: 0.9094 (m) cc_final: 0.8745 (t) REVERT: C 312 TYR cc_start: 0.6538 (t80) cc_final: 0.6002 (t80) REVERT: C 318 SER cc_start: 0.8037 (t) cc_final: 0.7768 (t) REVERT: C 333 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7592 (ttmt) REVERT: C 342 LEU cc_start: 0.9035 (tp) cc_final: 0.8751 (tp) REVERT: C 345 GLU cc_start: 0.8171 (tt0) cc_final: 0.7801 (tt0) REVERT: C 393 LEU cc_start: 0.8861 (mt) cc_final: 0.8597 (mt) REVERT: D 1 MET cc_start: 0.8023 (ppp) cc_final: 0.7337 (ppp) REVERT: D 29 GLU cc_start: 0.7168 (tt0) cc_final: 0.6967 (tt0) REVERT: D 35 ASN cc_start: 0.8676 (m110) cc_final: 0.8329 (m110) REVERT: D 41 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8132 (ttmm) REVERT: D 47 TYR cc_start: 0.9011 (m-80) cc_final: 0.8108 (m-80) REVERT: D 66 THR cc_start: 0.8081 (p) cc_final: 0.7649 (p) REVERT: D 67 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7679 (tm-30) REVERT: D 89 TRP cc_start: 0.8099 (t60) cc_final: 0.7243 (t60) REVERT: D 93 GLU cc_start: 0.7872 (mm-30) cc_final: 0.6834 (mm-30) REVERT: D 96 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7892 (ttpp) REVERT: D 103 MET cc_start: 0.8000 (mmm) cc_final: 0.7457 (mmm) REVERT: D 109 LYS cc_start: 0.8236 (tttp) cc_final: 0.7914 (ttmm) REVERT: D 118 GLU cc_start: 0.7478 (tp30) cc_final: 0.6877 (tp30) REVERT: D 128 MET cc_start: 0.8702 (tpp) cc_final: 0.8403 (tpp) REVERT: D 139 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.7674 (ttp-170) REVERT: D 143 SER cc_start: 0.8944 (m) cc_final: 0.8115 (t) REVERT: D 147 ASP cc_start: 0.7490 (p0) cc_final: 0.7239 (p0) REVERT: D 154 TRP cc_start: 0.8810 (t60) cc_final: 0.8391 (t60) REVERT: D 155 MET cc_start: 0.8066 (tpt) cc_final: 0.7124 (tpt) REVERT: D 189 THR cc_start: 0.8618 (p) cc_final: 0.6935 (p) REVERT: D 196 MET cc_start: 0.7540 (mtp) cc_final: 0.7259 (mtp) REVERT: D 226 MET cc_start: 0.7282 (mmm) cc_final: 0.6692 (mmm) REVERT: D 263 MET cc_start: 0.7949 (mmm) cc_final: 0.7673 (mmm) REVERT: D 280 TYR cc_start: 0.8449 (m-80) cc_final: 0.7957 (m-80) REVERT: D 293 LEU cc_start: 0.8708 (tp) cc_final: 0.8465 (tp) REVERT: D 324 TYR cc_start: 0.7749 (m-80) cc_final: 0.7343 (m-80) REVERT: D 326 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 329 TYR cc_start: 0.6162 (t80) cc_final: 0.5548 (t80) REVERT: D 333 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7707 (ttmt) REVERT: D 347 GLU cc_start: 0.7699 (tp30) cc_final: 0.6922 (tp30) REVERT: D 392 GLU cc_start: 0.7688 (tp30) cc_final: 0.7207 (tp30) REVERT: D 393 LEU cc_start: 0.8229 (mt) cc_final: 0.7995 (mm) REVERT: D 397 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7857 (mt-10) REVERT: D 416 LYS cc_start: 0.8205 (mppt) cc_final: 0.7395 (mppt) REVERT: E 1 MET cc_start: 0.7945 (ptm) cc_final: 0.6569 (ptm) REVERT: E 4 ILE cc_start: 0.8941 (mt) cc_final: 0.8726 (mt) REVERT: E 12 ASP cc_start: 0.8389 (t0) cc_final: 0.8045 (t70) REVERT: E 23 MET cc_start: 0.8199 (mmt) cc_final: 0.7995 (tpp) REVERT: E 34 LYS cc_start: 0.8845 (tttp) cc_final: 0.8356 (tttp) REVERT: E 38 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8452 (mtpt) REVERT: E 39 LEU cc_start: 0.8869 (mt) cc_final: 0.8623 (mt) REVERT: E 47 TYR cc_start: 0.6369 (t80) cc_final: 0.6045 (t80) REVERT: E 79 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7840 (mtmt) REVERT: E 85 GLU cc_start: 0.7225 (mp0) cc_final: 0.6693 (mp0) REVERT: E 86 ASP cc_start: 0.8465 (t0) cc_final: 0.8035 (t70) REVERT: E 93 GLU cc_start: 0.7991 (tp30) cc_final: 0.7083 (tp30) REVERT: E 104 PHE cc_start: 0.8641 (t80) cc_final: 0.8164 (t80) REVERT: E 113 ILE cc_start: 0.9322 (mm) cc_final: 0.8061 (mm) REVERT: E 118 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7827 (mt-10) REVERT: E 216 GLN cc_start: 0.8031 (mt0) cc_final: 0.7676 (mt0) REVERT: E 226 MET cc_start: 0.5890 (mmm) cc_final: 0.5492 (mmm) REVERT: E 228 MET cc_start: 0.7128 (ptm) cc_final: 0.6927 (ptm) REVERT: E 237 ILE cc_start: 0.8718 (mt) cc_final: 0.8514 (mt) REVERT: E 241 MET cc_start: 0.7913 (mmm) cc_final: 0.7493 (mmm) REVERT: E 247 ASP cc_start: 0.8107 (p0) cc_final: 0.7872 (p0) REVERT: E 269 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8584 (ttmm) REVERT: E 271 THR cc_start: 0.9175 (p) cc_final: 0.8891 (t) REVERT: E 296 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7254 (mt-10) REVERT: E 326 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7533 (mt-10) REVERT: E 333 LYS cc_start: 0.7907 (tttp) cc_final: 0.7469 (tttp) REVERT: E 345 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8137 (tt0) REVERT: E 347 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7261 (mt-10) REVERT: E 402 LYS cc_start: 0.7704 (ttmm) cc_final: 0.7384 (ttpp) REVERT: E 404 ILE cc_start: 0.7908 (mm) cc_final: 0.7349 (mm) REVERT: E 411 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7777 (mtpp) REVERT: E 423 LYS cc_start: 0.9020 (mttm) cc_final: 0.8734 (mtpp) REVERT: F 5 ILE cc_start: 0.9007 (mt) cc_final: 0.8573 (mt) REVERT: F 15 TYR cc_start: 0.8623 (t80) cc_final: 0.7302 (t80) REVERT: F 22 TYR cc_start: 0.8193 (m-80) cc_final: 0.7965 (m-80) REVERT: F 24 ASP cc_start: 0.8510 (t70) cc_final: 0.8226 (t70) REVERT: F 29 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7558 (mm-30) REVERT: F 34 LYS cc_start: 0.9004 (ttmt) cc_final: 0.8610 (ttmm) REVERT: F 38 LYS cc_start: 0.9120 (mmtp) cc_final: 0.8835 (mmtp) REVERT: F 43 HIS cc_start: 0.8481 (t-90) cc_final: 0.7844 (t-90) REVERT: F 60 LEU cc_start: 0.8644 (tp) cc_final: 0.8383 (tp) REVERT: F 61 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7385 (mm-30) REVERT: F 62 ASN cc_start: 0.8440 (m-40) cc_final: 0.8194 (t0) REVERT: F 74 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8777 (ttmm) REVERT: F 93 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8014 (mm-30) REVERT: F 95 GLU cc_start: 0.8129 (tt0) cc_final: 0.7879 (tt0) REVERT: F 96 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8220 (ttpp) REVERT: F 116 ASN cc_start: 0.8700 (t0) cc_final: 0.8192 (t0) REVERT: F 119 LEU cc_start: 0.8630 (mt) cc_final: 0.8252 (mt) REVERT: F 123 LYS cc_start: 0.8772 (tptt) cc_final: 0.8458 (tptt) REVERT: F 155 MET cc_start: 0.6995 (tpp) cc_final: 0.5401 (tpp) REVERT: F 157 ASP cc_start: 0.8233 (m-30) cc_final: 0.7548 (m-30) REVERT: F 158 TYR cc_start: 0.7409 (p90) cc_final: 0.6859 (p90) REVERT: F 183 THR cc_start: 0.7962 (p) cc_final: 0.7395 (t) REVERT: F 189 THR cc_start: 0.8304 (p) cc_final: 0.7780 (t) REVERT: F 235 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8207 (tttm) REVERT: F 236 ARG cc_start: 0.8507 (ttm170) cc_final: 0.7913 (tpp80) REVERT: F 237 ILE cc_start: 0.8934 (mm) cc_final: 0.7137 (mt) REVERT: F 256 TYR cc_start: 0.7608 (t80) cc_final: 0.6772 (t80) REVERT: F 260 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7842 (ttmm) REVERT: F 280 TYR cc_start: 0.8023 (m-80) cc_final: 0.7698 (m-80) REVERT: F 291 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7189 (mtt90) REVERT: F 326 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7627 (mm-30) REVERT: F 333 LYS cc_start: 0.8548 (ttpp) cc_final: 0.8338 (ttpp) REVERT: F 338 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6997 (mm-30) REVERT: F 345 GLU cc_start: 0.7464 (tt0) cc_final: 0.7054 (tt0) REVERT: F 370 ASP cc_start: 0.7248 (m-30) cc_final: 0.6947 (m-30) REVERT: F 422 GLN cc_start: 0.7373 (mt0) cc_final: 0.7142 (mt0) REVERT: G 4 ILE cc_start: 0.8951 (mm) cc_final: 0.8235 (mm) REVERT: G 8 ASP cc_start: 0.8857 (m-30) cc_final: 0.8325 (m-30) REVERT: G 19 LEU cc_start: 0.8204 (mt) cc_final: 0.7912 (tt) REVERT: G 77 TYR cc_start: 0.8443 (t80) cc_final: 0.7889 (t80) REVERT: G 78 LEU cc_start: 0.9499 (mt) cc_final: 0.9214 (mt) REVERT: G 89 TYR cc_start: 0.8131 (t80) cc_final: 0.7859 (t80) REVERT: G 93 ILE cc_start: 0.9183 (tt) cc_final: 0.8688 (tt) REVERT: G 100 SER cc_start: 0.8618 (p) cc_final: 0.8196 (p) REVERT: G 147 LYS cc_start: 0.8974 (mmtm) cc_final: 0.8654 (mmmt) REVERT: G 157 THR cc_start: 0.8477 (p) cc_final: 0.8026 (m) REVERT: G 238 ASP cc_start: 0.8712 (m-30) cc_final: 0.8255 (m-30) REVERT: G 278 ILE cc_start: 0.9182 (mp) cc_final: 0.8958 (mp) REVERT: G 307 MET cc_start: 0.8970 (mmt) cc_final: 0.8605 (mmt) REVERT: G 323 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8920 (pttm) REVERT: G 328 GLN cc_start: 0.6660 (tp40) cc_final: 0.6351 (tp40) REVERT: G 333 LYS cc_start: 0.9175 (tttp) cc_final: 0.8917 (tttp) REVERT: G 334 MET cc_start: 0.7908 (tpp) cc_final: 0.7409 (tpp) outliers start: 3 outliers final: 1 residues processed: 1212 average time/residue: 0.1610 time to fit residues: 294.5368 Evaluate side-chains 1079 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1078 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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: 9.9990 chunk 56 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 226 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 114 GLN D 422 GLN E 105 ASN F 48 HIS F 105 ASN F 114 GLN ** 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** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.124633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103232 restraints weight = 48972.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106862 restraints weight = 25451.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109311 restraints weight = 15619.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.110917 restraints weight = 10765.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112055 restraints weight = 8182.122| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24515 Z= 0.159 Angle : 0.651 9.879 33269 Z= 0.344 Chirality : 0.045 0.275 3697 Planarity : 0.005 0.086 4105 Dihedral : 10.370 174.425 3441 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.12 % Allowed : 2.80 % Favored : 97.09 % 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: -0.09 (0.16), residues: 2917 helix: 1.20 (0.14), residues: 1445 sheet: -1.25 (0.27), residues: 388 loop : -1.28 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 139 TYR 0.034 0.002 TYR A 165 PHE 0.030 0.002 PHE A 417 TRP 0.022 0.002 TRP G 294 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (24510) covalent geometry : angle 0.64656 / 0.34 (33263) hydrogen bonds : bond 0.03844 / 2.58 ( 1174) hydrogen bonds : angle 5.08210 / 3.63 ( 3363) metal coordination : bond 0.01088 / 0.54 ( 4) metal coordination : angle 5.73859 / 2.96 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 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 1154 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1151 time to evaluate : 0.780 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: A 1 MET cc_start: 0.8182 (tpp) cc_final: 0.7726 (tpp) REVERT: A 3 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 19 VAL cc_start: 0.8183 (m) cc_final: 0.7921 (p) REVERT: A 26 GLU cc_start: 0.7880 (pm20) cc_final: 0.7389 (pm20) REVERT: A 29 GLU cc_start: 0.7673 (tt0) cc_final: 0.7356 (tt0) REVERT: A 35 ASN cc_start: 0.8569 (m-40) cc_final: 0.8099 (m110) REVERT: A 42 SER cc_start: 0.8489 (m) cc_final: 0.8129 (p) REVERT: A 47 TYR cc_start: 0.6283 (m-10) cc_final: 0.6037 (m-80) REVERT: A 60 LEU cc_start: 0.9120 (tp) cc_final: 0.8856 (tp) REVERT: A 61 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 73 VAL cc_start: 0.8838 (t) cc_final: 0.8076 (p) REVERT: A 93 GLU cc_start: 0.8086 (tp30) cc_final: 0.7578 (tp30) REVERT: A 113 ILE cc_start: 0.9060 (mt) cc_final: 0.8785 (mt) REVERT: A 146 PHE cc_start: 0.8268 (m-10) cc_final: 0.7826 (m-10) REVERT: A 153 ASP cc_start: 0.8522 (t0) cc_final: 0.8268 (t0) REVERT: A 163 LEU cc_start: 0.8741 (tp) cc_final: 0.8536 (tt) REVERT: A 171 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7696 (mmtm) REVERT: A 174 PHE cc_start: 0.8664 (m-80) cc_final: 0.8269 (m-10) REVERT: A 188 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7273 (mt-10) REVERT: A 189 THR cc_start: 0.8419 (p) cc_final: 0.8176 (m) REVERT: A 203 LYS cc_start: 0.7858 (pttm) cc_final: 0.7102 (pttm) REVERT: A 214 TYR cc_start: 0.8473 (m-80) cc_final: 0.7601 (m-80) REVERT: A 215 LEU cc_start: 0.8583 (tp) cc_final: 0.8352 (tp) REVERT: A 235 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8090 (ttpt) REVERT: A 241 MET cc_start: 0.8108 (mmm) cc_final: 0.7539 (mmm) REVERT: A 248 ASP cc_start: 0.7710 (m-30) cc_final: 0.7338 (m-30) REVERT: A 255 SER cc_start: 0.8872 (p) cc_final: 0.8345 (p) REVERT: A 260 LYS cc_start: 0.8778 (tppp) cc_final: 0.8405 (mmmm) REVERT: A 265 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8534 (ttpp) REVERT: A 267 ARG cc_start: 0.7075 (ttm-80) cc_final: 0.5982 (ttm-80) REVERT: A 268 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 313 LEU cc_start: 0.6991 (tt) cc_final: 0.6755 (tt) REVERT: A 316 CYS cc_start: 0.8069 (m) cc_final: 0.7615 (m) REVERT: A 345 GLU cc_start: 0.7140 (pp20) cc_final: 0.6855 (pp20) REVERT: A 384 MET cc_start: 0.8360 (ttt) cc_final: 0.7981 (ttm) REVERT: A 401 ILE cc_start: 0.7746 (mm) cc_final: 0.7515 (pt) REVERT: A 403 GLN cc_start: 0.7868 (tt0) cc_final: 0.7663 (tt0) REVERT: B 3 GLU cc_start: 0.7473 (tt0) cc_final: 0.6877 (tt0) REVERT: B 15 TYR cc_start: 0.8220 (t80) cc_final: 0.7714 (t80) REVERT: B 43 HIS cc_start: 0.8733 (t-90) cc_final: 0.8433 (t-170) REVERT: B 79 LYS cc_start: 0.8926 (ttmm) cc_final: 0.7926 (ttmm) REVERT: B 86 ASP cc_start: 0.7639 (t70) cc_final: 0.7425 (t0) REVERT: B 103 MET cc_start: 0.7851 (mmm) cc_final: 0.7466 (mmm) REVERT: B 139 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7590 (ttp-170) REVERT: B 145 SER cc_start: 0.8579 (p) cc_final: 0.7738 (p) REVERT: B 147 ASP cc_start: 0.7133 (m-30) cc_final: 0.6776 (m-30) REVERT: B 154 TRP cc_start: 0.8860 (t60) cc_final: 0.8423 (t60) REVERT: B 155 MET cc_start: 0.7729 (tpp) cc_final: 0.7401 (tpp) REVERT: B 191 THR cc_start: 0.8359 (p) cc_final: 0.8117 (p) REVERT: B 194 VAL cc_start: 0.8321 (t) cc_final: 0.8087 (t) REVERT: B 213 ASP cc_start: 0.7840 (m-30) cc_final: 0.7553 (m-30) REVERT: B 226 MET cc_start: 0.8215 (mmm) cc_final: 0.7626 (mmp) REVERT: B 231 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7537 (mm-30) REVERT: B 238 ASP cc_start: 0.8775 (m-30) cc_final: 0.8567 (m-30) REVERT: B 243 ASP cc_start: 0.7201 (t0) cc_final: 0.6867 (t0) REVERT: B 245 SER cc_start: 0.8387 (t) cc_final: 0.7049 (p) REVERT: B 248 ASP cc_start: 0.7427 (m-30) cc_final: 0.7100 (m-30) REVERT: B 258 GLU cc_start: 0.8336 (pt0) cc_final: 0.8041 (pt0) REVERT: B 260 LYS cc_start: 0.8808 (tttp) cc_final: 0.8499 (tttp) REVERT: B 274 ARG cc_start: 0.7723 (mtp85) cc_final: 0.7428 (mtm-85) REVERT: B 279 GLN cc_start: 0.8541 (tt0) cc_final: 0.8028 (tt0) REVERT: B 298 LYS cc_start: 0.8846 (ttpp) cc_final: 0.8480 (ttpp) REVERT: B 318 SER cc_start: 0.8187 (m) cc_final: 0.7422 (t) REVERT: B 345 GLU cc_start: 0.8192 (tt0) cc_final: 0.7958 (tt0) REVERT: B 368 MET cc_start: 0.8295 (tpp) cc_final: 0.7976 (ttt) REVERT: B 392 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6979 (tm-30) REVERT: B 413 LYS cc_start: 0.8545 (tppt) cc_final: 0.7943 (tppt) REVERT: C 13 GLN cc_start: 0.7887 (tp40) cc_final: 0.7337 (tp40) REVERT: C 26 GLU cc_start: 0.8061 (pt0) cc_final: 0.7747 (pt0) REVERT: C 39 LEU cc_start: 0.8623 (mt) cc_final: 0.8326 (mt) REVERT: C 41 LYS cc_start: 0.8792 (tttt) cc_final: 0.8467 (tttt) REVERT: C 85 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7663 (mm-30) REVERT: C 103 MET cc_start: 0.8277 (mmt) cc_final: 0.8008 (mmt) REVERT: C 109 LYS cc_start: 0.8876 (tppt) cc_final: 0.8506 (mmmm) REVERT: C 113 ILE cc_start: 0.8908 (mt) cc_final: 0.8571 (mm) REVERT: C 140 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 166 MET cc_start: 0.7337 (tpt) cc_final: 0.6761 (tpt) REVERT: C 178 ILE cc_start: 0.8105 (tp) cc_final: 0.7607 (mm) REVERT: C 213 ASP cc_start: 0.8259 (m-30) cc_final: 0.8052 (m-30) REVERT: C 226 MET cc_start: 0.8564 (mmm) cc_final: 0.8336 (mmp) REVERT: C 241 MET cc_start: 0.8179 (mmm) cc_final: 0.7480 (mmm) REVERT: C 247 ASP cc_start: 0.8024 (m-30) cc_final: 0.7686 (m-30) REVERT: C 263 MET cc_start: 0.7444 (mmm) cc_final: 0.6723 (mmm) REVERT: C 276 ILE cc_start: 0.8753 (mm) cc_final: 0.8552 (mm) REVERT: C 279 GLN cc_start: 0.8137 (tt0) cc_final: 0.7685 (tt0) REVERT: C 292 SER cc_start: 0.9101 (m) cc_final: 0.8832 (p) REVERT: C 295 ASN cc_start: 0.8123 (t0) cc_final: 0.7863 (t0) REVERT: C 312 TYR cc_start: 0.6099 (t80) cc_final: 0.5487 (t80) REVERT: C 318 SER cc_start: 0.7885 (t) cc_final: 0.7599 (p) REVERT: C 345 GLU cc_start: 0.8236 (tt0) cc_final: 0.7681 (tt0) REVERT: C 367 ASN cc_start: 0.7901 (m-40) cc_final: 0.7665 (m110) REVERT: C 393 LEU cc_start: 0.8860 (mt) cc_final: 0.8597 (mt) REVERT: C 411 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8542 (mtmm) REVERT: C 426 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7510 (mm-40) REVERT: D 41 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8033 (ttmm) REVERT: D 46 GLU cc_start: 0.8176 (tt0) cc_final: 0.7848 (tt0) REVERT: D 47 TYR cc_start: 0.9011 (m-80) cc_final: 0.8097 (m-80) REVERT: D 62 ASN cc_start: 0.8315 (t0) cc_final: 0.8077 (t0) REVERT: D 67 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 89 TRP cc_start: 0.8062 (t60) cc_final: 0.7470 (t60) REVERT: D 93 GLU cc_start: 0.7752 (mm-30) cc_final: 0.6847 (mm-30) REVERT: D 96 LYS cc_start: 0.8384 (ttpp) cc_final: 0.8011 (ttpp) REVERT: D 109 LYS cc_start: 0.8228 (tttp) cc_final: 0.7813 (ttmm) REVERT: D 118 GLU cc_start: 0.7288 (tp30) cc_final: 0.6850 (tp30) REVERT: D 128 MET cc_start: 0.8645 (tpp) cc_final: 0.8212 (tpp) REVERT: D 143 SER cc_start: 0.8933 (m) cc_final: 0.8204 (t) REVERT: D 154 TRP cc_start: 0.8806 (t60) cc_final: 0.8519 (t60) REVERT: D 155 MET cc_start: 0.7767 (tpt) cc_final: 0.6933 (tpt) REVERT: D 189 THR cc_start: 0.8692 (p) cc_final: 0.6896 (p) REVERT: D 196 MET cc_start: 0.7468 (mtp) cc_final: 0.7110 (mtp) REVERT: D 213 ASP cc_start: 0.7814 (m-30) cc_final: 0.7546 (m-30) REVERT: D 226 MET cc_start: 0.7216 (mmm) cc_final: 0.6691 (mmm) REVERT: D 228 MET cc_start: 0.7330 (mtm) cc_final: 0.7062 (ptp) REVERT: D 263 MET cc_start: 0.7930 (mmm) cc_final: 0.7697 (mmm) REVERT: D 280 TYR cc_start: 0.8446 (m-80) cc_final: 0.7931 (m-80) REVERT: D 286 ASP cc_start: 0.7158 (p0) cc_final: 0.6850 (p0) REVERT: D 293 LEU cc_start: 0.8670 (tp) cc_final: 0.8398 (tp) REVERT: D 301 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8354 (mmtt) REVERT: D 307 ILE cc_start: 0.8261 (mm) cc_final: 0.8054 (mm) REVERT: D 324 TYR cc_start: 0.7685 (m-80) cc_final: 0.7381 (m-80) REVERT: D 326 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7178 (mm-30) REVERT: D 338 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6944 (mt-10) REVERT: D 347 GLU cc_start: 0.7727 (tp30) cc_final: 0.6935 (tp30) REVERT: D 349 VAL cc_start: 0.9164 (t) cc_final: 0.8962 (p) REVERT: D 392 GLU cc_start: 0.7728 (tp30) cc_final: 0.7299 (tp30) REVERT: D 397 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7797 (mt-10) REVERT: D 416 LYS cc_start: 0.8121 (mppt) cc_final: 0.7370 (mppt) REVERT: E 12 ASP cc_start: 0.8350 (t0) cc_final: 0.8048 (t70) REVERT: E 18 LYS cc_start: 0.9177 (tppt) cc_final: 0.8901 (tppt) REVERT: E 34 LYS cc_start: 0.8837 (tttp) cc_final: 0.8224 (tttp) REVERT: E 35 ASN cc_start: 0.8376 (m-40) cc_final: 0.7893 (m-40) REVERT: E 38 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8460 (mtpt) REVERT: E 39 LEU cc_start: 0.8840 (mt) cc_final: 0.8507 (mt) REVERT: E 41 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8609 (ttpt) REVERT: E 47 TYR cc_start: 0.6301 (t80) cc_final: 0.6019 (t80) REVERT: E 53 ILE cc_start: 0.8980 (mm) cc_final: 0.8748 (tp) REVERT: E 79 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7896 (mtmt) REVERT: E 85 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: E 86 ASP cc_start: 0.8459 (t0) cc_final: 0.8115 (t70) REVERT: E 95 GLU cc_start: 0.8526 (tt0) cc_final: 0.7887 (tt0) REVERT: E 96 LYS cc_start: 0.8513 (tttp) cc_final: 0.8259 (tttp) REVERT: E 104 PHE cc_start: 0.8616 (t80) cc_final: 0.8263 (t80) REVERT: E 118 GLU cc_start: 0.8228 (mt-10) cc_final: 0.8025 (mt-10) REVERT: E 139 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7569 (ttp80) REVERT: E 146 PHE cc_start: 0.7518 (m-10) cc_final: 0.7119 (m-10) REVERT: E 215 LEU cc_start: 0.9060 (tp) cc_final: 0.8853 (tp) REVERT: E 226 MET cc_start: 0.5824 (mmm) cc_final: 0.5420 (mmm) REVERT: E 235 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8064 (ttmt) REVERT: E 241 MET cc_start: 0.7872 (mmm) cc_final: 0.7515 (mmm) REVERT: E 251 ASP cc_start: 0.8305 (m-30) cc_final: 0.8040 (m-30) REVERT: E 258 GLU cc_start: 0.8213 (mp0) cc_final: 0.7831 (mp0) REVERT: E 259 TYR cc_start: 0.9231 (t80) cc_final: 0.8818 (t80) REVERT: E 263 MET cc_start: 0.8707 (mmp) cc_final: 0.8310 (tpp) REVERT: E 269 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8497 (ttmm) REVERT: E 271 THR cc_start: 0.9227 (p) cc_final: 0.8836 (t) REVERT: E 296 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7228 (mt-10) REVERT: E 300 LYS cc_start: 0.8021 (tttp) cc_final: 0.7689 (tttp) REVERT: E 301 LYS cc_start: 0.8070 (ptpt) cc_final: 0.7608 (ptpt) REVERT: E 326 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 333 LYS cc_start: 0.7864 (tttp) cc_final: 0.7405 (tttp) REVERT: E 404 ILE cc_start: 0.8038 (mm) cc_final: 0.7816 (tp) REVERT: E 416 LYS cc_start: 0.8181 (mttp) cc_final: 0.7946 (mptp) REVERT: F 5 ILE cc_start: 0.9016 (mt) cc_final: 0.8532 (mt) REVERT: F 15 TYR cc_start: 0.8595 (t80) cc_final: 0.7183 (t80) REVERT: F 29 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7581 (mm-30) REVERT: F 34 LYS cc_start: 0.9017 (ttmt) cc_final: 0.8151 (ttmm) REVERT: F 43 HIS cc_start: 0.8458 (t-90) cc_final: 0.7924 (t-90) REVERT: F 60 LEU cc_start: 0.8749 (tp) cc_final: 0.8529 (tp) REVERT: F 61 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7279 (mm-30) REVERT: F 62 ASN cc_start: 0.8494 (m-40) cc_final: 0.8153 (t0) REVERT: F 82 ASP cc_start: 0.7580 (t0) cc_final: 0.7302 (t0) REVERT: F 95 GLU cc_start: 0.8125 (tt0) cc_final: 0.7789 (tt0) REVERT: F 96 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8196 (ttpp) REVERT: F 109 LYS cc_start: 0.8741 (tttm) cc_final: 0.8501 (tttm) REVERT: F 116 ASN cc_start: 0.8623 (t0) cc_final: 0.8116 (t0) REVERT: F 119 LEU cc_start: 0.8565 (mt) cc_final: 0.8201 (mt) REVERT: F 123 LYS cc_start: 0.8739 (tptt) cc_final: 0.8529 (tptt) REVERT: F 155 MET cc_start: 0.7063 (tpp) cc_final: 0.5331 (tpp) REVERT: F 156 ASP cc_start: 0.8262 (t0) cc_final: 0.7852 (t0) REVERT: F 157 ASP cc_start: 0.7867 (m-30) cc_final: 0.7259 (m-30) REVERT: F 158 TYR cc_start: 0.7473 (p90) cc_final: 0.6830 (p90) REVERT: F 183 THR cc_start: 0.7958 (p) cc_final: 0.7392 (t) REVERT: F 184 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7742 (mmmt) REVERT: F 189 THR cc_start: 0.8204 (p) cc_final: 0.7661 (t) REVERT: F 196 MET cc_start: 0.7145 (mtp) cc_final: 0.6813 (mtp) REVERT: F 237 ILE cc_start: 0.9106 (mm) cc_final: 0.8530 (mt) REVERT: F 246 LEU cc_start: 0.8042 (mt) cc_final: 0.7779 (mt) REVERT: F 256 TYR cc_start: 0.7577 (t80) cc_final: 0.6632 (t80) REVERT: F 291 ARG cc_start: 0.8088 (mtt90) cc_final: 0.7026 (mtt90) REVERT: F 295 ASN cc_start: 0.8137 (m-40) cc_final: 0.7830 (m-40) REVERT: F 296 GLU cc_start: 0.7465 (pt0) cc_final: 0.7151 (pt0) REVERT: F 326 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7725 (mm-30) REVERT: F 333 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8271 (ttpp) REVERT: F 338 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7007 (mm-30) REVERT: F 370 ASP cc_start: 0.7280 (m-30) cc_final: 0.7010 (m-30) REVERT: F 404 ILE cc_start: 0.8621 (mt) cc_final: 0.8074 (mt) REVERT: F 405 LYS cc_start: 0.7385 (tptp) cc_final: 0.6113 (mmmt) REVERT: F 407 ARG cc_start: 0.8143 (ttp80) cc_final: 0.7467 (tmm-80) REVERT: G 8 ASP cc_start: 0.8616 (m-30) cc_final: 0.8216 (m-30) REVERT: G 19 LEU cc_start: 0.8219 (mt) cc_final: 0.7887 (tt) REVERT: G 77 TYR cc_start: 0.8521 (t80) cc_final: 0.7947 (t80) REVERT: G 78 LEU cc_start: 0.9486 (mt) cc_final: 0.9248 (mt) REVERT: G 89 TYR cc_start: 0.8093 (t80) cc_final: 0.7687 (t80) REVERT: G 91 PHE cc_start: 0.8614 (t80) cc_final: 0.8135 (t80) REVERT: G 93 ILE cc_start: 0.9015 (tt) cc_final: 0.8415 (pt) REVERT: G 97 LYS cc_start: 0.8486 (mmtp) cc_final: 0.7942 (mmtp) REVERT: G 100 SER cc_start: 0.8605 (p) cc_final: 0.8075 (p) REVERT: G 186 ASN cc_start: 0.8079 (p0) cc_final: 0.5490 (p0) REVERT: G 238 ASP cc_start: 0.8469 (m-30) cc_final: 0.8069 (m-30) REVERT: G 240 LEU cc_start: 0.9083 (mt) cc_final: 0.8871 (mt) REVERT: G 276 ASP cc_start: 0.8584 (p0) cc_final: 0.7951 (p0) REVERT: G 283 LYS cc_start: 0.9220 (pttm) cc_final: 0.8922 (pttp) REVERT: G 285 VAL cc_start: 0.9180 (p) cc_final: 0.8353 (p) REVERT: G 296 LYS cc_start: 0.8889 (mppt) cc_final: 0.8650 (mmmt) REVERT: G 307 MET cc_start: 0.8961 (mmt) cc_final: 0.8458 (mmt) REVERT: G 328 GLN cc_start: 0.6909 (tp40) cc_final: 0.6587 (tp40) outliers start: 3 outliers final: 0 residues processed: 1153 average time/residue: 0.1674 time to fit residues: 288.2744 Evaluate side-chains 1072 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1071 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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: 0.6980 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 285 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 158 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 193 ASN C 114 GLN C 398 GLN D 114 GLN D 403 GLN D 422 GLN E 219 HIS F 13 GLN F 48 HIS F 114 GLN ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.104582 restraints weight = 48761.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108225 restraints weight = 25370.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110582 restraints weight = 15488.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112244 restraints weight = 10664.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113257 restraints weight = 8051.670| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24515 Z= 0.149 Angle : 0.634 9.219 33269 Z= 0.334 Chirality : 0.044 0.284 3697 Planarity : 0.004 0.076 4105 Dihedral : 10.307 171.683 3441 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % 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: 1.18 (0.14), residues: 1443 sheet: -1.25 (0.27), residues: 387 loop : -1.33 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 143 TYR 0.037 0.002 TYR B 165 PHE 0.022 0.002 PHE E 16 TRP 0.043 0.002 TRP F 154 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24510) covalent geometry : angle 0.62973 / 0.33 (33263) hydrogen bonds : bond 0.03599 / 2.42 ( 1174) hydrogen bonds : angle 4.99184 / 3.57 ( 3363) metal coordination : bond 0.00973 / 0.49 ( 4) metal coordination : angle 5.45418 / 2.83 ( 6) Misc. bond : bond 0.00027 / 0.01 ( 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 1163 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1162 time to evaluate : 0.746 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: 0.8030 (tpp) cc_final: 0.7767 (tpp) REVERT: A 3 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 11 PHE cc_start: 0.7751 (m-10) cc_final: 0.7476 (m-10) REVERT: A 19 VAL cc_start: 0.8226 (m) cc_final: 0.7931 (p) REVERT: A 26 GLU cc_start: 0.7821 (pm20) cc_final: 0.7238 (pm20) REVERT: A 29 GLU cc_start: 0.7653 (tt0) cc_final: 0.7450 (tt0) REVERT: A 35 ASN cc_start: 0.8510 (m-40) cc_final: 0.8144 (m110) REVERT: A 39 LEU cc_start: 0.9114 (mt) cc_final: 0.8884 (mt) REVERT: A 42 SER cc_start: 0.8539 (m) cc_final: 0.8313 (p) REVERT: A 60 LEU cc_start: 0.9123 (tp) cc_final: 0.8917 (tp) REVERT: A 73 VAL cc_start: 0.8912 (t) cc_final: 0.8210 (p) REVERT: A 93 GLU cc_start: 0.8089 (tp30) cc_final: 0.7561 (tp30) REVERT: A 104 PHE cc_start: 0.7915 (t80) cc_final: 0.7513 (t80) REVERT: A 123 LYS cc_start: 0.8338 (mmtp) cc_final: 0.8022 (mmtp) REVERT: A 146 PHE cc_start: 0.8289 (m-10) cc_final: 0.7861 (m-10) REVERT: A 163 LEU cc_start: 0.8754 (tp) cc_final: 0.8543 (tt) REVERT: A 171 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7722 (mmtm) REVERT: A 174 PHE cc_start: 0.8661 (m-80) cc_final: 0.8411 (m-80) REVERT: A 184 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8173 (mmtp) REVERT: A 188 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 214 TYR cc_start: 0.8490 (m-80) cc_final: 0.7766 (m-80) REVERT: A 215 LEU cc_start: 0.8431 (tp) cc_final: 0.8188 (tp) REVERT: A 235 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8134 (ttpt) REVERT: A 241 MET cc_start: 0.8135 (mmm) cc_final: 0.7568 (mmm) REVERT: A 248 ASP cc_start: 0.7700 (m-30) cc_final: 0.7351 (m-30) REVERT: A 265 LYS cc_start: 0.8916 (ttpp) cc_final: 0.8558 (ttpp) REVERT: A 268 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 278 LYS cc_start: 0.8414 (tptm) cc_final: 0.7908 (mtpp) REVERT: A 279 GLN cc_start: 0.8903 (tt0) cc_final: 0.8468 (tt0) REVERT: A 316 CYS cc_start: 0.8088 (m) cc_final: 0.7603 (m) REVERT: A 345 GLU cc_start: 0.7067 (pp20) cc_final: 0.6836 (pp20) REVERT: A 384 MET cc_start: 0.8362 (ttt) cc_final: 0.8017 (ttm) REVERT: A 426 GLN cc_start: 0.8214 (mt0) cc_final: 0.7879 (mt0) REVERT: B 15 TYR cc_start: 0.8311 (t80) cc_final: 0.7773 (t80) REVERT: B 23 MET cc_start: 0.8118 (mmm) cc_final: 0.7693 (mmm) REVERT: B 26 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7132 (mt-10) REVERT: B 54 ASN cc_start: 0.8636 (m-40) cc_final: 0.8370 (m-40) REVERT: B 79 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8348 (ttmm) REVERT: B 86 ASP cc_start: 0.7533 (t70) cc_final: 0.7299 (t0) REVERT: B 87 HIS cc_start: 0.7939 (t-90) cc_final: 0.7601 (t-90) REVERT: B 103 MET cc_start: 0.7800 (mmm) cc_final: 0.7488 (mmm) REVERT: B 109 LYS cc_start: 0.9219 (tptt) cc_final: 0.8941 (ttmm) REVERT: B 139 ARG cc_start: 0.7856 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: B 145 SER cc_start: 0.8564 (p) cc_final: 0.7710 (p) REVERT: B 147 ASP cc_start: 0.7039 (m-30) cc_final: 0.6672 (m-30) REVERT: B 159 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7631 (mm-30) REVERT: B 161 ARG cc_start: 0.8238 (ttp-110) cc_final: 0.7968 (ttp-110) REVERT: B 166 MET cc_start: 0.7301 (ppp) cc_final: 0.7060 (ppp) REVERT: B 167 ASN cc_start: 0.8518 (m-40) cc_final: 0.8235 (m-40) REVERT: B 191 THR cc_start: 0.8414 (p) cc_final: 0.8167 (p) REVERT: B 213 ASP cc_start: 0.7799 (m-30) cc_final: 0.7565 (m-30) REVERT: B 226 MET cc_start: 0.8259 (mmm) cc_final: 0.7631 (mmp) REVERT: B 231 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 243 ASP cc_start: 0.7177 (t0) cc_final: 0.6839 (t0) REVERT: B 245 SER cc_start: 0.8393 (t) cc_final: 0.7126 (p) REVERT: B 248 ASP cc_start: 0.7448 (m-30) cc_final: 0.7121 (m-30) REVERT: B 258 GLU cc_start: 0.8347 (pt0) cc_final: 0.8046 (pt0) REVERT: B 260 LYS cc_start: 0.8758 (tttp) cc_final: 0.8449 (tttp) REVERT: B 263 MET cc_start: 0.7925 (mmm) cc_final: 0.7680 (mmm) REVERT: B 274 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7370 (mtm180) REVERT: B 278 LYS cc_start: 0.8501 (tptp) cc_final: 0.8262 (tptp) REVERT: B 279 GLN cc_start: 0.8554 (tt0) cc_final: 0.7952 (tt0) REVERT: B 318 SER cc_start: 0.8104 (m) cc_final: 0.7383 (t) REVERT: B 368 MET cc_start: 0.8301 (tpp) cc_final: 0.8064 (ttt) REVERT: B 392 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7013 (tm-30) REVERT: B 403 GLN cc_start: 0.7225 (tt0) cc_final: 0.6454 (pt0) REVERT: B 413 LYS cc_start: 0.8452 (tppt) cc_final: 0.7861 (tppt) REVERT: C 13 GLN cc_start: 0.7906 (tp40) cc_final: 0.7326 (tp40) REVERT: C 26 GLU cc_start: 0.8063 (pt0) cc_final: 0.7714 (pt0) REVERT: C 39 LEU cc_start: 0.8605 (mt) cc_final: 0.8318 (mt) REVERT: C 85 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7688 (mm-30) REVERT: C 113 ILE cc_start: 0.8932 (mt) cc_final: 0.8581 (mm) REVERT: C 140 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7801 (tm-30) REVERT: C 166 MET cc_start: 0.7278 (tpt) cc_final: 0.6660 (tpt) REVERT: C 178 ILE cc_start: 0.8011 (tp) cc_final: 0.7659 (mm) REVERT: C 226 MET cc_start: 0.8500 (mmm) cc_final: 0.8255 (mmp) REVERT: C 241 MET cc_start: 0.8158 (mmm) cc_final: 0.7572 (mmm) REVERT: C 243 ASP cc_start: 0.7740 (t0) cc_final: 0.7454 (t0) REVERT: C 247 ASP cc_start: 0.7962 (m-30) cc_final: 0.7644 (m-30) REVERT: C 263 MET cc_start: 0.7453 (mmm) cc_final: 0.7183 (mmm) REVERT: C 279 GLN cc_start: 0.8163 (tt0) cc_final: 0.7819 (tt0) REVERT: C 292 SER cc_start: 0.9065 (m) cc_final: 0.8685 (t) REVERT: C 295 ASN cc_start: 0.8100 (t0) cc_final: 0.7883 (t0) REVERT: C 315 ILE cc_start: 0.8403 (pt) cc_final: 0.8134 (pt) REVERT: C 318 SER cc_start: 0.7928 (t) cc_final: 0.7558 (p) REVERT: C 342 LEU cc_start: 0.8825 (tp) cc_final: 0.8587 (tp) REVERT: C 345 GLU cc_start: 0.8216 (tt0) cc_final: 0.7830 (tt0) REVERT: C 356 VAL cc_start: 0.8333 (m) cc_final: 0.8034 (p) REVERT: C 423 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8490 (mmmm) REVERT: D 2 VAL cc_start: 0.9014 (p) cc_final: 0.8734 (m) REVERT: D 41 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8196 (ttpp) REVERT: D 47 TYR cc_start: 0.9018 (m-80) cc_final: 0.8107 (m-80) REVERT: D 62 ASN cc_start: 0.8301 (t0) cc_final: 0.8080 (t0) REVERT: D 67 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 74 LYS cc_start: 0.8980 (tttp) cc_final: 0.8701 (mmmm) REVERT: D 89 TRP cc_start: 0.8018 (t60) cc_final: 0.7465 (t60) REVERT: D 93 GLU cc_start: 0.7758 (mm-30) cc_final: 0.6850 (mm-30) REVERT: D 96 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8075 (ttpp) REVERT: D 103 MET cc_start: 0.7648 (mmm) cc_final: 0.7017 (mmm) REVERT: D 109 LYS cc_start: 0.8242 (tttp) cc_final: 0.7864 (ttmm) REVERT: D 114 GLN cc_start: 0.7564 (mt0) cc_final: 0.7361 (mt0) REVERT: D 118 GLU cc_start: 0.7300 (tp30) cc_final: 0.6894 (tp30) REVERT: D 140 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7855 (mm110) REVERT: D 143 SER cc_start: 0.9049 (m) cc_final: 0.8270 (t) REVERT: D 154 TRP cc_start: 0.8751 (t60) cc_final: 0.8475 (t60) REVERT: D 155 MET cc_start: 0.7872 (tpt) cc_final: 0.7267 (tpt) REVERT: D 189 THR cc_start: 0.8656 (p) cc_final: 0.6893 (p) REVERT: D 196 MET cc_start: 0.7516 (mtp) cc_final: 0.7268 (mtp) REVERT: D 226 MET cc_start: 0.7089 (mmm) cc_final: 0.6683 (mmm) REVERT: D 264 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8186 (mm-30) REVERT: D 280 TYR cc_start: 0.8451 (m-80) cc_final: 0.8043 (m-80) REVERT: D 301 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8440 (mmtt) REVERT: D 307 ILE cc_start: 0.8212 (mm) cc_final: 0.7987 (mm) REVERT: D 324 TYR cc_start: 0.7701 (m-80) cc_final: 0.7355 (m-80) REVERT: D 326 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7100 (mm-30) REVERT: D 329 TYR cc_start: 0.5960 (t80) cc_final: 0.5179 (t80) REVERT: D 333 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7580 (ttmt) REVERT: D 338 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6873 (mt-10) REVERT: D 347 GLU cc_start: 0.7788 (tp30) cc_final: 0.6978 (tp30) REVERT: D 349 VAL cc_start: 0.9130 (t) cc_final: 0.8928 (p) REVERT: D 392 GLU cc_start: 0.7754 (tp30) cc_final: 0.7253 (tp30) REVERT: E 1 MET cc_start: 0.7755 (ptm) cc_final: 0.7093 (ptm) REVERT: E 12 ASP cc_start: 0.8284 (t0) cc_final: 0.8043 (t70) REVERT: E 34 LYS cc_start: 0.8805 (tttp) cc_final: 0.8244 (tttp) REVERT: E 35 ASN cc_start: 0.8405 (m-40) cc_final: 0.7760 (m-40) REVERT: E 38 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8451 (mtpt) REVERT: E 39 LEU cc_start: 0.8729 (mt) cc_final: 0.8423 (mt) REVERT: E 41 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8588 (ttpt) REVERT: E 47 TYR cc_start: 0.6318 (t80) cc_final: 0.6029 (t80) REVERT: E 53 ILE cc_start: 0.8997 (mm) cc_final: 0.8727 (tp) REVERT: E 79 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7915 (mtmt) REVERT: E 86 ASP cc_start: 0.8427 (t0) cc_final: 0.8178 (t70) REVERT: E 93 GLU cc_start: 0.7945 (tp30) cc_final: 0.7348 (tp30) REVERT: E 95 GLU cc_start: 0.8506 (tt0) cc_final: 0.7960 (tt0) REVERT: E 96 LYS cc_start: 0.8491 (tttp) cc_final: 0.8160 (tttp) REVERT: E 104 PHE cc_start: 0.8636 (t80) cc_final: 0.8121 (t80) REVERT: E 146 PHE cc_start: 0.7517 (m-10) cc_final: 0.7135 (m-10) REVERT: E 181 LYS cc_start: 0.8472 (tmmt) cc_final: 0.7961 (tmmt) REVERT: E 215 LEU cc_start: 0.9088 (tp) cc_final: 0.8826 (tp) REVERT: E 237 ILE cc_start: 0.8872 (mt) cc_final: 0.8637 (mt) REVERT: E 241 MET cc_start: 0.7845 (mmm) cc_final: 0.7334 (mmm) REVERT: E 247 ASP cc_start: 0.8077 (p0) cc_final: 0.7776 (p0) REVERT: E 263 MET cc_start: 0.8623 (mmp) cc_final: 0.8347 (tpp) REVERT: E 269 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8434 (ttmm) REVERT: E 271 THR cc_start: 0.9221 (p) cc_final: 0.8826 (t) REVERT: E 300 LYS cc_start: 0.8065 (tttp) cc_final: 0.7742 (tttp) REVERT: E 301 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7660 (ptpt) REVERT: E 333 LYS cc_start: 0.7882 (tttp) cc_final: 0.7455 (tttp) REVERT: E 411 LYS cc_start: 0.8510 (tttt) cc_final: 0.8241 (mtpp) REVERT: F 13 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7870 (tm-30) REVERT: F 22 TYR cc_start: 0.8425 (m-80) cc_final: 0.8177 (m-10) REVERT: F 29 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7560 (mm-30) REVERT: F 34 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8136 (ttmm) REVERT: F 38 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8716 (mmtp) REVERT: F 43 HIS cc_start: 0.8495 (t-90) cc_final: 0.7849 (t-90) REVERT: F 60 LEU cc_start: 0.8753 (tp) cc_final: 0.8532 (tp) REVERT: F 61 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7337 (mm-30) REVERT: F 82 ASP cc_start: 0.7581 (t0) cc_final: 0.7286 (t0) REVERT: F 95 GLU cc_start: 0.8097 (tt0) cc_final: 0.7647 (tt0) REVERT: F 96 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8303 (ttpp) REVERT: F 109 LYS cc_start: 0.8720 (tttm) cc_final: 0.8462 (tttt) REVERT: F 116 ASN cc_start: 0.8631 (t0) cc_final: 0.8178 (t0) REVERT: F 119 LEU cc_start: 0.8588 (mt) cc_final: 0.8147 (mt) REVERT: F 157 ASP cc_start: 0.7628 (m-30) cc_final: 0.6907 (m-30) REVERT: F 158 TYR cc_start: 0.7588 (p90) cc_final: 0.7166 (p90) REVERT: F 183 THR cc_start: 0.7927 (p) cc_final: 0.7382 (t) REVERT: F 184 LYS cc_start: 0.8047 (mmtp) cc_final: 0.7705 (mmmt) REVERT: F 189 THR cc_start: 0.8101 (p) cc_final: 0.7553 (t) REVERT: F 237 ILE cc_start: 0.9116 (mm) cc_final: 0.8329 (mt) REVERT: F 256 TYR cc_start: 0.7580 (t80) cc_final: 0.6981 (t80) REVERT: F 260 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8063 (ttmm) REVERT: F 265 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8297 (mmtm) REVERT: F 296 GLU cc_start: 0.7501 (pt0) cc_final: 0.7281 (pt0) REVERT: F 326 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7715 (mm-30) REVERT: F 333 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8319 (ttpp) REVERT: F 338 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7159 (mm-30) REVERT: F 340 ARG cc_start: 0.9086 (ttt-90) cc_final: 0.8781 (ttt-90) REVERT: F 370 ASP cc_start: 0.7283 (m-30) cc_final: 0.7054 (m-30) REVERT: F 404 ILE cc_start: 0.8507 (mt) cc_final: 0.8001 (mt) REVERT: F 405 LYS cc_start: 0.7000 (tptp) cc_final: 0.6300 (tptp) REVERT: F 407 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7934 (ttp80) REVERT: F 411 LYS cc_start: 0.6806 (mtmm) cc_final: 0.6498 (mtpp) REVERT: F 430 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6894 (mm-30) REVERT: G 7 ILE cc_start: 0.9175 (pt) cc_final: 0.8900 (tp) REVERT: G 8 ASP cc_start: 0.8756 (m-30) cc_final: 0.8399 (m-30) REVERT: G 19 LEU cc_start: 0.8226 (mt) cc_final: 0.7982 (tt) REVERT: G 63 ILE cc_start: 0.8619 (mp) cc_final: 0.8385 (mm) REVERT: G 67 ASN cc_start: 0.8221 (t0) cc_final: 0.8002 (t0) REVERT: G 77 TYR cc_start: 0.8356 (t80) cc_final: 0.7860 (t80) REVERT: G 78 LEU cc_start: 0.9433 (mt) cc_final: 0.9162 (mt) REVERT: G 82 GLU cc_start: 0.8380 (tp30) cc_final: 0.8145 (tp30) REVERT: G 89 TYR cc_start: 0.8157 (t80) cc_final: 0.7666 (t80) REVERT: G 93 ILE cc_start: 0.8936 (tt) cc_final: 0.7949 (pt) REVERT: G 95 LYS cc_start: 0.9058 (mtpp) cc_final: 0.8308 (mtpp) REVERT: G 96 GLU cc_start: 0.7942 (pp20) cc_final: 0.7252 (pp20) REVERT: G 97 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8268 (mmtp) REVERT: G 238 ASP cc_start: 0.8535 (m-30) cc_final: 0.8200 (m-30) REVERT: G 240 LEU cc_start: 0.9054 (mt) cc_final: 0.8751 (mt) REVERT: G 276 ASP cc_start: 0.8635 (p0) cc_final: 0.8129 (p0) REVERT: G 278 ILE cc_start: 0.9115 (mp) cc_final: 0.8888 (mp) REVERT: G 279 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8886 (mttm) REVERT: G 283 LYS cc_start: 0.9193 (pttm) cc_final: 0.8907 (pttp) REVERT: G 285 VAL cc_start: 0.8927 (p) cc_final: 0.8438 (p) REVERT: G 307 MET cc_start: 0.8935 (mmt) cc_final: 0.8529 (mmm) REVERT: G 328 GLN cc_start: 0.7611 (tp40) cc_final: 0.7230 (tp40) REVERT: G 333 LYS cc_start: 0.9179 (mptt) cc_final: 0.8579 (mmtt) REVERT: G 334 MET cc_start: 0.8016 (tpp) cc_final: 0.7732 (tpp) outliers start: 1 outliers final: 0 residues processed: 1162 average time/residue: 0.1612 time to fit residues: 281.9883 Evaluate side-chains 1085 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1085 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.0270 chunk 203 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 282 optimal weight: 30.0000 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 193 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN D 240 ASN D 422 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 288 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** 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** G 324 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.104312 restraints weight = 48478.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.107917 restraints weight = 25348.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110285 restraints weight = 15542.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111876 restraints weight = 10721.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113009 restraints weight = 8168.000| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 24515 Z= 0.147 Angle : 0.639 11.391 33269 Z= 0.334 Chirality : 0.044 0.273 3697 Planarity : 0.005 0.068 4105 Dihedral : 10.267 170.836 3441 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 1.08 (0.14), residues: 1447 sheet: -1.23 (0.27), residues: 387 loop : -1.38 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 274 TYR 0.040 0.002 TYR G 54 PHE 0.019 0.002 PHE A 303 TRP 0.032 0.002 TRP E 414 HIS 0.010 0.001 HIS G 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24510) covalent geometry : angle 0.63496 / 0.33 (33263) hydrogen bonds : bond 0.03533 / 2.38 ( 1174) hydrogen bonds : angle 4.95221 / 3.53 ( 3363) metal coordination : bond 0.00990 / 0.50 ( 4) metal coordination : angle 5.20593 / 2.71 ( 6) Misc. bond : bond 0.00032 / 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 1145 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1145 time to evaluate : 0.782 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: 0.8057 (tpp) cc_final: 0.7802 (tpp) REVERT: A 3 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 11 PHE cc_start: 0.7700 (m-10) cc_final: 0.7478 (m-10) REVERT: A 19 VAL cc_start: 0.8213 (m) cc_final: 0.7918 (p) REVERT: A 26 GLU cc_start: 0.7851 (pm20) cc_final: 0.7272 (pm20) REVERT: A 35 ASN cc_start: 0.8513 (m-40) cc_final: 0.8145 (m110) REVERT: A 39 LEU cc_start: 0.9077 (mt) cc_final: 0.8847 (mt) REVERT: A 73 VAL cc_start: 0.8905 (t) cc_final: 0.8239 (p) REVERT: A 85 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 93 GLU cc_start: 0.8016 (tp30) cc_final: 0.7478 (tp30) REVERT: A 104 PHE cc_start: 0.7905 (t80) cc_final: 0.7450 (t80) REVERT: A 131 VAL cc_start: 0.8762 (m) cc_final: 0.8519 (p) REVERT: A 139 ARG cc_start: 0.7610 (ttm-80) cc_final: 0.7296 (ttm-80) REVERT: A 146 PHE cc_start: 0.8309 (m-10) cc_final: 0.7920 (m-10) REVERT: A 153 ASP cc_start: 0.8441 (t0) cc_final: 0.8095 (t0) REVERT: A 171 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7716 (mmtm) REVERT: A 184 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8276 (mmtp) REVERT: A 188 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7453 (mt-10) REVERT: A 214 TYR cc_start: 0.8500 (m-80) cc_final: 0.8009 (m-10) REVERT: A 235 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8125 (ttpt) REVERT: A 238 ASP cc_start: 0.8593 (m-30) cc_final: 0.8391 (m-30) REVERT: A 241 MET cc_start: 0.8067 (mmm) cc_final: 0.7507 (mmm) REVERT: A 248 ASP cc_start: 0.7703 (m-30) cc_final: 0.7332 (m-30) REVERT: A 263 MET cc_start: 0.7652 (mmp) cc_final: 0.7389 (mmp) REVERT: A 265 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8581 (ttpp) REVERT: A 268 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7779 (mt-10) REVERT: A 278 LYS cc_start: 0.8245 (tptm) cc_final: 0.7909 (mtpp) REVERT: A 279 GLN cc_start: 0.8868 (tt0) cc_final: 0.8425 (tt0) REVERT: A 282 THR cc_start: 0.8563 (m) cc_final: 0.8169 (t) REVERT: A 313 LEU cc_start: 0.6807 (tt) cc_final: 0.6602 (tt) REVERT: A 316 CYS cc_start: 0.8014 (m) cc_final: 0.7549 (m) REVERT: A 345 GLU cc_start: 0.7127 (pp20) cc_final: 0.6875 (pp20) REVERT: A 384 MET cc_start: 0.8391 (ttt) cc_final: 0.8036 (ttm) REVERT: A 426 GLN cc_start: 0.8154 (mt0) cc_final: 0.7787 (mt0) REVERT: B 15 TYR cc_start: 0.8309 (t80) cc_final: 0.7734 (t80) REVERT: B 23 MET cc_start: 0.8069 (mmm) cc_final: 0.7647 (mmm) REVERT: B 26 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7030 (mt-10) REVERT: B 43 HIS cc_start: 0.8717 (t-90) cc_final: 0.8311 (t-170) REVERT: B 54 ASN cc_start: 0.8651 (m-40) cc_final: 0.8391 (m-40) REVERT: B 79 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8293 (ttmm) REVERT: B 87 HIS cc_start: 0.7956 (t-90) cc_final: 0.7690 (t-90) REVERT: B 95 GLU cc_start: 0.8330 (tt0) cc_final: 0.7699 (tt0) REVERT: B 103 MET cc_start: 0.7812 (mmm) cc_final: 0.7531 (mmm) REVERT: B 109 LYS cc_start: 0.9254 (tptt) cc_final: 0.8774 (ttmm) REVERT: B 145 SER cc_start: 0.8584 (p) cc_final: 0.7656 (p) REVERT: B 147 ASP cc_start: 0.7033 (m-30) cc_final: 0.6683 (m-30) REVERT: B 155 MET cc_start: 0.7748 (tpp) cc_final: 0.7096 (tpp) REVERT: B 161 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7936 (ttp-110) REVERT: B 166 MET cc_start: 0.7356 (ppp) cc_final: 0.7091 (ppp) REVERT: B 191 THR cc_start: 0.8426 (p) cc_final: 0.8167 (p) REVERT: B 213 ASP cc_start: 0.7806 (m-30) cc_final: 0.7536 (m-30) REVERT: B 226 MET cc_start: 0.8275 (mmm) cc_final: 0.7652 (mmp) REVERT: B 231 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 243 ASP cc_start: 0.7190 (t0) cc_final: 0.6886 (t0) REVERT: B 245 SER cc_start: 0.8330 (t) cc_final: 0.7075 (p) REVERT: B 248 ASP cc_start: 0.7451 (m-30) cc_final: 0.6908 (m-30) REVERT: B 258 GLU cc_start: 0.8383 (pt0) cc_final: 0.8105 (pt0) REVERT: B 265 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8616 (ttpp) REVERT: B 278 LYS cc_start: 0.8465 (tptp) cc_final: 0.8250 (tptp) REVERT: B 279 GLN cc_start: 0.8559 (tt0) cc_final: 0.7871 (tt0) REVERT: B 298 LYS cc_start: 0.8697 (pttp) cc_final: 0.8448 (pttp) REVERT: B 318 SER cc_start: 0.8074 (m) cc_final: 0.7366 (t) REVERT: B 392 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7060 (tm-30) REVERT: B 403 GLN cc_start: 0.7187 (tt0) cc_final: 0.6506 (pt0) REVERT: B 413 LYS cc_start: 0.8460 (tppt) cc_final: 0.7282 (tppt) REVERT: B 414 TRP cc_start: 0.7018 (m-90) cc_final: 0.6594 (m-90) REVERT: B 427 LYS cc_start: 0.8210 (tttm) cc_final: 0.7716 (tttm) REVERT: C 13 GLN cc_start: 0.7913 (tp40) cc_final: 0.7283 (tp40) REVERT: C 26 GLU cc_start: 0.8072 (pt0) cc_final: 0.7737 (pt0) REVERT: C 41 LYS cc_start: 0.8772 (tttt) cc_final: 0.8319 (tttt) REVERT: C 56 LEU cc_start: 0.8833 (mm) cc_final: 0.8631 (mm) REVERT: C 79 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7674 (mtmm) REVERT: C 85 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7710 (mm-30) REVERT: C 113 ILE cc_start: 0.8931 (mt) cc_final: 0.8541 (mm) REVERT: C 140 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 166 MET cc_start: 0.7281 (tpt) cc_final: 0.6747 (tpt) REVERT: C 178 ILE cc_start: 0.7805 (tp) cc_final: 0.7350 (mm) REVERT: C 226 MET cc_start: 0.8434 (mmm) cc_final: 0.8183 (mmp) REVERT: C 240 ASN cc_start: 0.8244 (t0) cc_final: 0.7937 (t0) REVERT: C 241 MET cc_start: 0.8159 (mmm) cc_final: 0.7539 (mmm) REVERT: C 243 ASP cc_start: 0.7748 (t0) cc_final: 0.7482 (t0) REVERT: C 263 MET cc_start: 0.7478 (mmm) cc_final: 0.7133 (mmm) REVERT: C 279 GLN cc_start: 0.8163 (tt0) cc_final: 0.7773 (tt0) REVERT: C 292 SER cc_start: 0.9060 (m) cc_final: 0.8694 (t) REVERT: C 295 ASN cc_start: 0.8136 (t0) cc_final: 0.7759 (t0) REVERT: C 315 ILE cc_start: 0.8368 (pt) cc_final: 0.8154 (pt) REVERT: C 318 SER cc_start: 0.7882 (t) cc_final: 0.7515 (p) REVERT: C 342 LEU cc_start: 0.8767 (tp) cc_final: 0.8533 (tp) REVERT: C 345 GLU cc_start: 0.8261 (tt0) cc_final: 0.7852 (tt0) REVERT: C 356 VAL cc_start: 0.8329 (m) cc_final: 0.8062 (p) REVERT: D 41 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8129 (ttmm) REVERT: D 46 GLU cc_start: 0.8167 (tt0) cc_final: 0.7633 (tt0) REVERT: D 47 TYR cc_start: 0.8999 (m-80) cc_final: 0.7926 (m-80) REVERT: D 62 ASN cc_start: 0.8329 (t0) cc_final: 0.8085 (t0) REVERT: D 67 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7701 (tm-30) REVERT: D 74 LYS cc_start: 0.9004 (tttp) cc_final: 0.8736 (mmmm) REVERT: D 89 TRP cc_start: 0.8030 (t60) cc_final: 0.7597 (t60) REVERT: D 93 GLU cc_start: 0.7707 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 96 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8038 (ttpp) REVERT: D 109 LYS cc_start: 0.8250 (tttp) cc_final: 0.7890 (ttmm) REVERT: D 114 GLN cc_start: 0.7483 (mt0) cc_final: 0.7263 (mt0) REVERT: D 118 GLU cc_start: 0.7198 (tp30) cc_final: 0.6894 (tp30) REVERT: D 143 SER cc_start: 0.9069 (m) cc_final: 0.8345 (t) REVERT: D 154 TRP cc_start: 0.8693 (t60) cc_final: 0.8458 (t60) REVERT: D 155 MET cc_start: 0.7892 (tpt) cc_final: 0.7280 (tpt) REVERT: D 189 THR cc_start: 0.8624 (p) cc_final: 0.6887 (p) REVERT: D 196 MET cc_start: 0.7573 (mtp) cc_final: 0.7340 (mtp) REVERT: D 226 MET cc_start: 0.7091 (mmm) cc_final: 0.6721 (mmm) REVERT: D 263 MET cc_start: 0.7922 (mmm) cc_final: 0.7711 (mmm) REVERT: D 280 TYR cc_start: 0.8492 (m-80) cc_final: 0.8083 (m-80) REVERT: D 300 LYS cc_start: 0.8440 (mttm) cc_final: 0.7859 (mttm) REVERT: D 301 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8469 (mmtt) REVERT: D 324 TYR cc_start: 0.7686 (m-80) cc_final: 0.7354 (m-80) REVERT: D 326 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7124 (mm-30) REVERT: D 347 GLU cc_start: 0.7880 (tp30) cc_final: 0.7187 (tp30) REVERT: D 368 MET cc_start: 0.7696 (ttp) cc_final: 0.7414 (ttm) REVERT: D 392 GLU cc_start: 0.7743 (tp30) cc_final: 0.7395 (tp30) REVERT: E 1 MET cc_start: 0.7718 (ptm) cc_final: 0.7292 (ptm) REVERT: E 12 ASP cc_start: 0.8265 (t0) cc_final: 0.8060 (t70) REVERT: E 23 MET cc_start: 0.8380 (mmt) cc_final: 0.8062 (mmt) REVERT: E 34 LYS cc_start: 0.8812 (tttp) cc_final: 0.8211 (tttp) REVERT: E 35 ASN cc_start: 0.8401 (m-40) cc_final: 0.7819 (m-40) REVERT: E 38 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8355 (mtpt) REVERT: E 47 TYR cc_start: 0.6344 (t80) cc_final: 0.6057 (t80) REVERT: E 79 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7873 (mtmt) REVERT: E 86 ASP cc_start: 0.8481 (t0) cc_final: 0.8228 (t0) REVERT: E 93 GLU cc_start: 0.7964 (tp30) cc_final: 0.7333 (tp30) REVERT: E 95 GLU cc_start: 0.8656 (tt0) cc_final: 0.8031 (tt0) REVERT: E 96 LYS cc_start: 0.8498 (tttp) cc_final: 0.8217 (tttp) REVERT: E 104 PHE cc_start: 0.8514 (t80) cc_final: 0.8076 (t80) REVERT: E 118 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7946 (mt-10) REVERT: E 146 PHE cc_start: 0.7547 (m-10) cc_final: 0.7186 (m-10) REVERT: E 181 LYS cc_start: 0.8540 (tmmt) cc_final: 0.8165 (tmmt) REVERT: E 193 ASN cc_start: 0.8368 (m-40) cc_final: 0.7937 (m110) REVERT: E 215 LEU cc_start: 0.9095 (tp) cc_final: 0.8822 (tp) REVERT: E 228 MET cc_start: 0.7436 (ptt) cc_final: 0.7136 (ptt) REVERT: E 236 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7565 (ttm110) REVERT: E 241 MET cc_start: 0.7810 (mmm) cc_final: 0.7366 (mmm) REVERT: E 269 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8468 (ttmm) REVERT: E 271 THR cc_start: 0.9224 (p) cc_final: 0.8794 (t) REVERT: E 298 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8431 (mtpp) REVERT: E 300 LYS cc_start: 0.8112 (tttp) cc_final: 0.7829 (tttp) REVERT: E 301 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7684 (ptpt) REVERT: E 329 TYR cc_start: 0.6838 (t80) cc_final: 0.6631 (t80) REVERT: E 333 LYS cc_start: 0.7865 (tttp) cc_final: 0.7340 (tttp) REVERT: E 402 LYS cc_start: 0.7449 (ttmm) cc_final: 0.7116 (ttpp) REVERT: F 13 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7917 (tp40) REVERT: F 18 LYS cc_start: 0.8692 (tppt) cc_final: 0.8286 (tppt) REVERT: F 22 TYR cc_start: 0.8379 (m-80) cc_final: 0.8152 (m-10) REVERT: F 29 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7576 (mm-30) REVERT: F 34 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8080 (ttmm) REVERT: F 38 LYS cc_start: 0.9101 (mmtp) cc_final: 0.8811 (mmtp) REVERT: F 43 HIS cc_start: 0.8488 (t-90) cc_final: 0.7884 (t-90) REVERT: F 61 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7286 (mm-30) REVERT: F 62 ASN cc_start: 0.8476 (m-40) cc_final: 0.8055 (t0) REVERT: F 82 ASP cc_start: 0.7600 (t0) cc_final: 0.7279 (t0) REVERT: F 93 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7627 (mt-10) REVERT: F 95 GLU cc_start: 0.8101 (tt0) cc_final: 0.7641 (tt0) REVERT: F 96 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8273 (ttpp) REVERT: F 109 LYS cc_start: 0.8678 (tttm) cc_final: 0.8434 (tttm) REVERT: F 116 ASN cc_start: 0.8658 (t0) cc_final: 0.8214 (t0) REVERT: F 119 LEU cc_start: 0.8595 (mt) cc_final: 0.8201 (mt) REVERT: F 123 LYS cc_start: 0.8616 (tppt) cc_final: 0.8376 (tppt) REVERT: F 136 ASP cc_start: 0.7732 (t0) cc_final: 0.6309 (t0) REVERT: F 155 MET cc_start: 0.6631 (tpp) cc_final: 0.5893 (tpp) REVERT: F 157 ASP cc_start: 0.7877 (m-30) cc_final: 0.7428 (m-30) REVERT: F 183 THR cc_start: 0.7936 (p) cc_final: 0.7406 (t) REVERT: F 184 LYS cc_start: 0.8092 (mmtp) cc_final: 0.7730 (mmmt) REVERT: F 189 THR cc_start: 0.8076 (p) cc_final: 0.7622 (t) REVERT: F 191 THR cc_start: 0.8691 (p) cc_final: 0.7386 (m) REVERT: F 237 ILE cc_start: 0.9152 (mm) cc_final: 0.8353 (mt) REVERT: F 256 TYR cc_start: 0.7598 (t80) cc_final: 0.7180 (t80) REVERT: F 260 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7943 (ttmm) REVERT: F 265 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8406 (mmtm) REVERT: F 280 TYR cc_start: 0.8137 (m-80) cc_final: 0.7816 (m-80) REVERT: F 291 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7315 (mtt90) REVERT: F 296 GLU cc_start: 0.7608 (pt0) cc_final: 0.7250 (pt0) REVERT: F 326 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7698 (mm-30) REVERT: F 333 LYS cc_start: 0.8589 (ttpp) cc_final: 0.8372 (ttpp) REVERT: F 338 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6990 (mm-30) REVERT: F 340 ARG cc_start: 0.9058 (ttt-90) cc_final: 0.8724 (tpt-90) REVERT: F 404 ILE cc_start: 0.8399 (mt) cc_final: 0.7959 (mt) REVERT: F 405 LYS cc_start: 0.7069 (tptp) cc_final: 0.6449 (tptp) REVERT: F 407 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7993 (ttp80) REVERT: F 411 LYS cc_start: 0.6909 (mtmm) cc_final: 0.6647 (mtpp) REVERT: G 7 ILE cc_start: 0.9154 (pt) cc_final: 0.8908 (tp) REVERT: G 8 ASP cc_start: 0.8756 (m-30) cc_final: 0.8433 (m-30) REVERT: G 19 LEU cc_start: 0.8229 (mt) cc_final: 0.8018 (tt) REVERT: G 55 TYR cc_start: 0.7955 (m-80) cc_final: 0.7539 (m-80) REVERT: G 77 TYR cc_start: 0.8354 (t80) cc_final: 0.7901 (t80) REVERT: G 78 LEU cc_start: 0.9454 (mt) cc_final: 0.9199 (mt) REVERT: G 89 TYR cc_start: 0.8160 (t80) cc_final: 0.7699 (t80) REVERT: G 92 GLU cc_start: 0.8652 (tp30) cc_final: 0.8298 (tp30) REVERT: G 93 ILE cc_start: 0.8874 (tt) cc_final: 0.7943 (pt) REVERT: G 95 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8321 (mtpp) REVERT: G 96 GLU cc_start: 0.7768 (pp20) cc_final: 0.7332 (pp20) REVERT: G 100 SER cc_start: 0.8780 (p) cc_final: 0.8080 (p) REVERT: G 147 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8135 (mmmt) REVERT: G 151 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8560 (pttp) REVERT: G 238 ASP cc_start: 0.8490 (m-30) cc_final: 0.8127 (m-30) REVERT: G 240 LEU cc_start: 0.9070 (mt) cc_final: 0.8759 (mt) REVERT: G 268 LEU cc_start: 0.7875 (mt) cc_final: 0.6451 (mt) REVERT: G 276 ASP cc_start: 0.8661 (p0) cc_final: 0.8310 (p0) REVERT: G 279 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8927 (mttm) REVERT: G 295 ASP cc_start: 0.8576 (p0) cc_final: 0.7967 (p0) REVERT: G 296 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8616 (mmmt) REVERT: G 305 ASN cc_start: 0.8146 (t0) cc_final: 0.7945 (t0) REVERT: G 307 MET cc_start: 0.8897 (mmt) cc_final: 0.8553 (mmm) REVERT: G 323 LYS cc_start: 0.9328 (pttm) cc_final: 0.9089 (ptpp) REVERT: G 328 GLN cc_start: 0.7667 (tp40) cc_final: 0.7208 (tp40) REVERT: G 333 LYS cc_start: 0.9208 (mptt) cc_final: 0.8734 (tppt) outliers start: 0 outliers final: 0 residues processed: 1145 average time/residue: 0.1746 time to fit residues: 299.3221 Evaluate side-chains 1070 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1070 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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: 9.9990 chunk 249 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 260 optimal weight: 0.0030 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 220 ASN A 240 ASN B 99 GLN B 193 ASN B 295 ASN C 114 GLN ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN E 403 GLN F 48 HIS ** F 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.129273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107637 restraints weight = 48416.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111431 restraints weight = 25050.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113998 restraints weight = 15282.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.115575 restraints weight = 10441.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.116783 restraints weight = 7951.561| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 24515 Z= 0.157 Angle : 0.649 9.165 33269 Z= 0.340 Chirality : 0.044 0.237 3697 Planarity : 0.004 0.069 4105 Dihedral : 10.279 170.574 3441 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.04 % Allowed : 2.13 % Favored : 97.83 % 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: 1.00 (0.14), residues: 1451 sheet: -1.31 (0.27), residues: 397 loop : -1.34 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 236 TYR 0.036 0.002 TYR B 165 PHE 0.022 0.002 PHE E 16 TRP 0.031 0.002 TRP E 414 HIS 0.008 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (24510) covalent geometry : angle 0.64610 / 0.34 (33263) hydrogen bonds : bond 0.03473 / 2.37 ( 1174) hydrogen bonds : angle 4.90384 / 3.49 ( 3363) metal coordination : bond 0.00986 / 0.49 ( 4) metal coordination : angle 4.68991 / 2.44 ( 6) Misc. bond : bond 0.00032 / 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 1150 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1149 time to evaluate : 0.618 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: A 1 MET cc_start: 0.7919 (tpp) cc_final: 0.7712 (tpp) REVERT: A 3 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 11 PHE cc_start: 0.7703 (m-10) cc_final: 0.7431 (m-10) REVERT: A 19 VAL cc_start: 0.8201 (m) cc_final: 0.7893 (p) REVERT: A 26 GLU cc_start: 0.7875 (pm20) cc_final: 0.7284 (pm20) REVERT: A 29 GLU cc_start: 0.7637 (tt0) cc_final: 0.7282 (tt0) REVERT: A 35 ASN cc_start: 0.8550 (m-40) cc_final: 0.8209 (m110) REVERT: A 61 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6618 (tm-30) REVERT: A 73 VAL cc_start: 0.8937 (t) cc_final: 0.8458 (p) REVERT: A 82 ASP cc_start: 0.7517 (t0) cc_final: 0.7286 (t0) REVERT: A 83 SER cc_start: 0.8476 (m) cc_final: 0.8231 (m) REVERT: A 85 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7100 (mm-30) REVERT: A 93 GLU cc_start: 0.8094 (tp30) cc_final: 0.7514 (tp30) REVERT: A 104 PHE cc_start: 0.7918 (t80) cc_final: 0.7508 (t80) REVERT: A 112 GLU cc_start: 0.8132 (tt0) cc_final: 0.7921 (tt0) REVERT: A 113 ILE cc_start: 0.8975 (mt) cc_final: 0.8739 (mt) REVERT: A 123 LYS cc_start: 0.8423 (mttp) cc_final: 0.8176 (mttp) REVERT: A 128 MET cc_start: 0.8386 (tpt) cc_final: 0.8136 (tpt) REVERT: A 131 VAL cc_start: 0.8824 (m) cc_final: 0.8467 (p) REVERT: A 146 PHE cc_start: 0.8350 (m-10) cc_final: 0.7910 (m-10) REVERT: A 150 VAL cc_start: 0.8745 (p) cc_final: 0.8281 (m) REVERT: A 153 ASP cc_start: 0.8555 (t0) cc_final: 0.8180 (t0) REVERT: A 171 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7678 (mmtm) REVERT: A 184 LYS cc_start: 0.8616 (mmtp) cc_final: 0.8360 (mmtp) REVERT: A 188 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 203 LYS cc_start: 0.7935 (pttm) cc_final: 0.7156 (pttm) REVERT: A 214 TYR cc_start: 0.8483 (m-80) cc_final: 0.8060 (m-10) REVERT: A 228 MET cc_start: 0.7650 (mtp) cc_final: 0.7312 (mtp) REVERT: A 235 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8149 (ttpt) REVERT: A 238 ASP cc_start: 0.8614 (m-30) cc_final: 0.8403 (m-30) REVERT: A 241 MET cc_start: 0.8111 (mmm) cc_final: 0.7554 (mmm) REVERT: A 248 ASP cc_start: 0.7692 (m-30) cc_final: 0.7359 (m-30) REVERT: A 263 MET cc_start: 0.7749 (mmp) cc_final: 0.7486 (mmp) REVERT: A 265 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8580 (ttpp) REVERT: A 268 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 278 LYS cc_start: 0.8262 (tptm) cc_final: 0.7858 (mtpp) REVERT: A 279 GLN cc_start: 0.8860 (tt0) cc_final: 0.8360 (tt0) REVERT: A 313 LEU cc_start: 0.6751 (tt) cc_final: 0.6535 (tt) REVERT: A 316 CYS cc_start: 0.8066 (m) cc_final: 0.7631 (m) REVERT: A 345 GLU cc_start: 0.7164 (pp20) cc_final: 0.6878 (pp20) REVERT: A 384 MET cc_start: 0.8459 (ttt) cc_final: 0.8017 (ttm) REVERT: A 426 GLN cc_start: 0.8165 (mt0) cc_final: 0.7781 (mt0) REVERT: B 4 ILE cc_start: 0.8457 (tp) cc_final: 0.8234 (tp) REVERT: B 15 TYR cc_start: 0.8473 (t80) cc_final: 0.7975 (t80) REVERT: B 26 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6972 (mp0) REVERT: B 47 TYR cc_start: 0.8569 (m-80) cc_final: 0.7858 (m-80) REVERT: B 54 ASN cc_start: 0.8624 (m-40) cc_final: 0.8383 (m-40) REVERT: B 87 HIS cc_start: 0.7957 (t-90) cc_final: 0.7722 (t-90) REVERT: B 95 GLU cc_start: 0.8341 (tt0) cc_final: 0.7682 (tt0) REVERT: B 103 MET cc_start: 0.7882 (mmm) cc_final: 0.7624 (mmm) REVERT: B 109 LYS cc_start: 0.9283 (tptt) cc_final: 0.8656 (tptt) REVERT: B 145 SER cc_start: 0.8603 (p) cc_final: 0.7694 (p) REVERT: B 147 ASP cc_start: 0.6987 (m-30) cc_final: 0.6610 (m-30) REVERT: B 155 MET cc_start: 0.7747 (tpp) cc_final: 0.7208 (tpp) REVERT: B 171 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7705 (mmmm) REVERT: B 175 LYS cc_start: 0.8128 (tppt) cc_final: 0.7904 (tppt) REVERT: B 191 THR cc_start: 0.8391 (p) cc_final: 0.8167 (p) REVERT: B 213 ASP cc_start: 0.7825 (m-30) cc_final: 0.7085 (m-30) REVERT: B 226 MET cc_start: 0.8207 (mmm) cc_final: 0.7465 (mmp) REVERT: B 231 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7758 (mm-30) REVERT: B 243 ASP cc_start: 0.7233 (t0) cc_final: 0.6911 (t0) REVERT: B 245 SER cc_start: 0.8285 (t) cc_final: 0.7105 (p) REVERT: B 248 ASP cc_start: 0.7442 (m-30) cc_final: 0.7155 (m-30) REVERT: B 258 GLU cc_start: 0.8415 (pt0) cc_final: 0.8102 (pt0) REVERT: B 263 MET cc_start: 0.8103 (mmm) cc_final: 0.7891 (mmt) REVERT: B 265 LYS cc_start: 0.8967 (ttpp) cc_final: 0.8750 (ttpp) REVERT: B 269 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7703 (mtmm) REVERT: B 278 LYS cc_start: 0.8452 (tptp) cc_final: 0.8213 (tptp) REVERT: B 279 GLN cc_start: 0.8485 (tt0) cc_final: 0.7810 (tt0) REVERT: B 318 SER cc_start: 0.8080 (m) cc_final: 0.7354 (t) REVERT: B 392 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7089 (tm-30) REVERT: B 403 GLN cc_start: 0.7005 (tt0) cc_final: 0.6417 (pt0) REVERT: B 413 LYS cc_start: 0.8525 (tppt) cc_final: 0.7460 (tppt) REVERT: B 414 TRP cc_start: 0.7051 (m-90) cc_final: 0.6621 (m-90) REVERT: C 13 GLN cc_start: 0.7960 (tp40) cc_final: 0.7348 (tp40) REVERT: C 26 GLU cc_start: 0.8175 (pt0) cc_final: 0.7833 (pt0) REVERT: C 41 LYS cc_start: 0.8779 (tttt) cc_final: 0.8330 (tttt) REVERT: C 85 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7720 (mm-30) REVERT: C 103 MET cc_start: 0.8160 (mmt) cc_final: 0.7910 (mmt) REVERT: C 113 ILE cc_start: 0.8971 (mt) cc_final: 0.8601 (mm) REVERT: C 140 GLN cc_start: 0.8131 (tm-30) cc_final: 0.7872 (tm-30) REVERT: C 161 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7901 (ttp80) REVERT: C 166 MET cc_start: 0.7398 (tpt) cc_final: 0.6944 (tpt) REVERT: C 203 LYS cc_start: 0.8107 (mtmm) cc_final: 0.7767 (mtmm) REVERT: C 213 ASP cc_start: 0.8266 (m-30) cc_final: 0.7767 (m-30) REVERT: C 226 MET cc_start: 0.8449 (mmm) cc_final: 0.8096 (mmm) REVERT: C 235 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8651 (ttpp) REVERT: C 241 MET cc_start: 0.8157 (mmm) cc_final: 0.7489 (mmm) REVERT: C 243 ASP cc_start: 0.7775 (t0) cc_final: 0.7538 (t0) REVERT: C 263 MET cc_start: 0.7516 (mmm) cc_final: 0.7207 (mmm) REVERT: C 279 GLN cc_start: 0.8173 (tt0) cc_final: 0.7749 (tt0) REVERT: C 280 TYR cc_start: 0.8705 (m-80) cc_final: 0.7859 (m-80) REVERT: C 292 SER cc_start: 0.9082 (m) cc_final: 0.8696 (t) REVERT: C 295 ASN cc_start: 0.8182 (t0) cc_final: 0.7794 (t0) REVERT: C 318 SER cc_start: 0.7835 (t) cc_final: 0.7478 (p) REVERT: C 342 LEU cc_start: 0.8745 (tp) cc_final: 0.8526 (tp) REVERT: C 345 GLU cc_start: 0.8344 (tt0) cc_final: 0.7993 (tt0) REVERT: C 356 VAL cc_start: 0.8314 (m) cc_final: 0.8013 (p) REVERT: C 367 ASN cc_start: 0.7895 (m110) cc_final: 0.7659 (m110) REVERT: C 393 LEU cc_start: 0.8982 (mt) cc_final: 0.8776 (mt) REVERT: D 2 VAL cc_start: 0.9041 (p) cc_final: 0.8831 (m) REVERT: D 41 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8218 (ttpp) REVERT: D 47 TYR cc_start: 0.9009 (m-80) cc_final: 0.8104 (m-80) REVERT: D 62 ASN cc_start: 0.8328 (t0) cc_final: 0.8111 (t0) REVERT: D 74 LYS cc_start: 0.9009 (tttp) cc_final: 0.8722 (mmmm) REVERT: D 109 LYS cc_start: 0.8248 (tttp) cc_final: 0.7889 (ttmm) REVERT: D 114 GLN cc_start: 0.7473 (mt0) cc_final: 0.7260 (mt0) REVERT: D 118 GLU cc_start: 0.7219 (tp30) cc_final: 0.6875 (tp30) REVERT: D 136 ASP cc_start: 0.7917 (t70) cc_final: 0.7618 (t0) REVERT: D 140 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8010 (mm-40) REVERT: D 143 SER cc_start: 0.9061 (m) cc_final: 0.8401 (t) REVERT: D 158 TYR cc_start: 0.7520 (p90) cc_final: 0.6653 (p90) REVERT: D 189 THR cc_start: 0.8628 (p) cc_final: 0.6681 (p) REVERT: D 196 MET cc_start: 0.7599 (mtp) cc_final: 0.7343 (mtp) REVERT: D 226 MET cc_start: 0.7132 (mmm) cc_final: 0.6326 (mmm) REVERT: D 238 ASP cc_start: 0.8971 (m-30) cc_final: 0.8348 (m-30) REVERT: D 264 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8304 (mm-30) REVERT: D 300 LYS cc_start: 0.8519 (mttm) cc_final: 0.7989 (mttm) REVERT: D 301 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8552 (mmtt) REVERT: D 324 TYR cc_start: 0.7709 (m-80) cc_final: 0.7295 (m-80) REVERT: D 326 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7159 (mm-30) REVERT: D 333 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7618 (ttmt) REVERT: D 338 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6896 (mt-10) REVERT: D 347 GLU cc_start: 0.7919 (tp30) cc_final: 0.7342 (tp30) REVERT: D 350 LEU cc_start: 0.9065 (tp) cc_final: 0.8716 (tt) REVERT: D 368 MET cc_start: 0.7774 (ttp) cc_final: 0.7543 (ttm) REVERT: D 391 GLU cc_start: 0.7919 (tt0) cc_final: 0.7679 (tt0) REVERT: E 1 MET cc_start: 0.7797 (ptm) cc_final: 0.7329 (ptm) REVERT: E 23 MET cc_start: 0.8426 (mmt) cc_final: 0.8154 (mmt) REVERT: E 34 LYS cc_start: 0.8875 (tttp) cc_final: 0.8337 (tttp) REVERT: E 38 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8377 (mtpt) REVERT: E 39 LEU cc_start: 0.8751 (mt) cc_final: 0.8455 (mt) REVERT: E 47 TYR cc_start: 0.6365 (t80) cc_final: 0.6052 (t80) REVERT: E 53 ILE cc_start: 0.9013 (mm) cc_final: 0.8742 (tp) REVERT: E 79 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7861 (mtmt) REVERT: E 86 ASP cc_start: 0.8487 (t0) cc_final: 0.8174 (t0) REVERT: E 93 GLU cc_start: 0.8007 (tp30) cc_final: 0.7400 (tp30) REVERT: E 95 GLU cc_start: 0.8688 (tt0) cc_final: 0.7991 (tt0) REVERT: E 103 MET cc_start: 0.7788 (mmp) cc_final: 0.7453 (mmt) REVERT: E 118 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7975 (mt-10) REVERT: E 146 PHE cc_start: 0.7590 (m-10) cc_final: 0.7151 (m-10) REVERT: E 177 ARG cc_start: 0.7748 (mtt90) cc_final: 0.7412 (mtt90) REVERT: E 181 LYS cc_start: 0.8464 (tmmt) cc_final: 0.8157 (tmmt) REVERT: E 195 LEU cc_start: 0.8048 (tp) cc_final: 0.7726 (tt) REVERT: E 215 LEU cc_start: 0.9072 (tp) cc_final: 0.8848 (tp) REVERT: E 236 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7607 (ttm110) REVERT: E 241 MET cc_start: 0.7716 (mmm) cc_final: 0.7280 (mmm) REVERT: E 245 SER cc_start: 0.8781 (t) cc_final: 0.8257 (p) REVERT: E 260 LYS cc_start: 0.8794 (tptm) cc_final: 0.8425 (tptm) REVERT: E 265 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8706 (mtmt) REVERT: E 269 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8437 (ttmm) REVERT: E 271 THR cc_start: 0.9200 (p) cc_final: 0.8787 (t) REVERT: E 301 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7700 (ptpt) REVERT: E 329 TYR cc_start: 0.6878 (t80) cc_final: 0.6672 (t80) REVERT: E 333 LYS cc_start: 0.7827 (tttp) cc_final: 0.7283 (tttp) REVERT: E 423 LYS cc_start: 0.8933 (mttm) cc_final: 0.8656 (mtpp) REVERT: F 5 ILE cc_start: 0.8913 (mt) cc_final: 0.8477 (mt) REVERT: F 13 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7941 (tp40) REVERT: F 15 TYR cc_start: 0.8607 (t80) cc_final: 0.7243 (t80) REVERT: F 18 LYS cc_start: 0.8740 (tppt) cc_final: 0.8390 (tppt) REVERT: F 22 TYR cc_start: 0.8469 (m-80) cc_final: 0.8168 (m-10) REVERT: F 29 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 34 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8005 (ttmm) REVERT: F 43 HIS cc_start: 0.8458 (t-90) cc_final: 0.7785 (t-90) REVERT: F 60 LEU cc_start: 0.8802 (tp) cc_final: 0.8544 (tp) REVERT: F 61 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7367 (mm-30) REVERT: F 82 ASP cc_start: 0.7658 (t0) cc_final: 0.7336 (t0) REVERT: F 93 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7723 (mt-10) REVERT: F 95 GLU cc_start: 0.8122 (tt0) cc_final: 0.7651 (tt0) REVERT: F 96 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8296 (ttpp) REVERT: F 116 ASN cc_start: 0.8725 (t0) cc_final: 0.7331 (t0) REVERT: F 119 LEU cc_start: 0.8645 (mt) cc_final: 0.8188 (mt) REVERT: F 125 ASN cc_start: 0.8815 (p0) cc_final: 0.8402 (p0) REVERT: F 149 TYR cc_start: 0.6260 (t80) cc_final: 0.6026 (t80) REVERT: F 152 HIS cc_start: 0.7960 (t70) cc_final: 0.7494 (t70) REVERT: F 155 MET cc_start: 0.6677 (tpp) cc_final: 0.5925 (tpp) REVERT: F 157 ASP cc_start: 0.7653 (m-30) cc_final: 0.7052 (m-30) REVERT: F 158 TYR cc_start: 0.7800 (p90) cc_final: 0.7247 (p90) REVERT: F 183 THR cc_start: 0.8015 (p) cc_final: 0.7519 (t) REVERT: F 184 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7734 (mmmt) REVERT: F 189 THR cc_start: 0.7998 (p) cc_final: 0.7541 (t) REVERT: F 191 THR cc_start: 0.8713 (p) cc_final: 0.7389 (m) REVERT: F 226 MET cc_start: 0.7407 (mmm) cc_final: 0.7029 (mmm) REVERT: F 236 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8483 (ttm170) REVERT: F 246 LEU cc_start: 0.7555 (mt) cc_final: 0.7308 (mt) REVERT: F 256 TYR cc_start: 0.7631 (t80) cc_final: 0.7000 (t80) REVERT: F 260 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8054 (ttmm) REVERT: F 265 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8384 (mmtm) REVERT: F 326 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7703 (mm-30) REVERT: F 338 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7164 (mm-30) REVERT: F 340 ARG cc_start: 0.9069 (ttt-90) cc_final: 0.8744 (tpt-90) REVERT: F 404 ILE cc_start: 0.8433 (mt) cc_final: 0.7958 (mt) REVERT: F 405 LYS cc_start: 0.6894 (tptp) cc_final: 0.6338 (tptp) REVERT: F 407 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7945 (ttp80) REVERT: F 411 LYS cc_start: 0.6971 (mtmm) cc_final: 0.6722 (mtpp) REVERT: F 422 GLN cc_start: 0.7234 (mt0) cc_final: 0.6938 (mt0) REVERT: G 8 ASP cc_start: 0.8791 (m-30) cc_final: 0.8543 (m-30) REVERT: G 19 LEU cc_start: 0.8263 (mt) cc_final: 0.8024 (tt) REVERT: G 77 TYR cc_start: 0.8449 (t80) cc_final: 0.7999 (t80) REVERT: G 78 LEU cc_start: 0.9441 (mt) cc_final: 0.9169 (mt) REVERT: G 82 GLU cc_start: 0.8443 (tp30) cc_final: 0.8050 (tp30) REVERT: G 89 TYR cc_start: 0.8202 (t80) cc_final: 0.7816 (t80) REVERT: G 91 PHE cc_start: 0.8643 (t80) cc_final: 0.8440 (t80) REVERT: G 95 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8392 (mtpp) REVERT: G 100 SER cc_start: 0.8822 (p) cc_final: 0.8295 (p) REVERT: G 151 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8519 (pttm) REVERT: G 238 ASP cc_start: 0.8551 (m-30) cc_final: 0.8244 (m-30) REVERT: G 276 ASP cc_start: 0.8372 (p0) cc_final: 0.7942 (p0) REVERT: G 279 LYS cc_start: 0.9255 (mtmm) cc_final: 0.9028 (mttt) REVERT: G 291 VAL cc_start: 0.7945 (t) cc_final: 0.7483 (t) REVERT: G 306 ASP cc_start: 0.8250 (t0) cc_final: 0.8039 (t0) REVERT: G 307 MET cc_start: 0.8852 (mmt) cc_final: 0.8478 (mmm) REVERT: G 328 GLN cc_start: 0.7855 (tp40) cc_final: 0.7354 (tp40) REVERT: G 330 LEU cc_start: 0.9153 (mt) cc_final: 0.8667 (mt) REVERT: G 331 MET cc_start: 0.8368 (mmp) cc_final: 0.7655 (mmm) REVERT: G 333 LYS cc_start: 0.9262 (mptt) cc_final: 0.8733 (tppt) outliers start: 1 outliers final: 0 residues processed: 1150 average time/residue: 0.1781 time to fit residues: 307.4567 Evaluate side-chains 1054 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1054 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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: 10.0000 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 0.0060 chunk 280 optimal weight: 0.0870 chunk 1 optimal weight: 4.9990 overall best weight: 2.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 193 ASN A 220 ASN A 240 ASN A 302 ASN B 99 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 167 ASN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN F 425 ASN ** F 426 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105720 restraints weight = 48594.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.109460 restraints weight = 25146.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111970 restraints weight = 15282.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113512 restraints weight = 10444.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114750 restraints weight = 7972.165| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24515 Z= 0.186 Angle : 0.666 10.603 33269 Z= 0.348 Chirality : 0.046 0.241 3697 Planarity : 0.004 0.060 4105 Dihedral : 10.310 170.759 3441 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.04 % Allowed : 1.26 % Favored : 98.70 % 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: -0.31 (0.16), residues: 2917 helix: 0.97 (0.14), residues: 1448 sheet: -1.33 (0.27), residues: 375 loop : -1.33 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 236 TYR 0.043 0.002 TYR G 54 PHE 0.026 0.002 PHE E 28 TRP 0.031 0.002 TRP E 414 HIS 0.011 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (24510) covalent geometry : angle 0.66291 / 0.35 (33263) hydrogen bonds : bond 0.03466 / 2.36 ( 1174) hydrogen bonds : angle 4.92135 / 3.51 ( 3363) metal coordination : bond 0.01160 / 0.58 ( 4) metal coordination : angle 4.51730 / 2.33 ( 6) Misc. bond : bond 0.00025 / 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 1127 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1126 time to evaluate : 0.925 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: A 1 MET cc_start: 0.8263 (tpp) cc_final: 0.7934 (tpp) REVERT: A 3 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 11 PHE cc_start: 0.7797 (m-10) cc_final: 0.7442 (m-10) REVERT: A 19 VAL cc_start: 0.8224 (m) cc_final: 0.7954 (p) REVERT: A 26 GLU cc_start: 0.7859 (pm20) cc_final: 0.7305 (pm20) REVERT: A 29 GLU cc_start: 0.7592 (tt0) cc_final: 0.7312 (tt0) REVERT: A 35 ASN cc_start: 0.8508 (m-40) cc_final: 0.8185 (m110) REVERT: A 61 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6451 (tm-30) REVERT: A 73 VAL cc_start: 0.8949 (t) cc_final: 0.8438 (p) REVERT: A 79 LYS cc_start: 0.8766 (ttmt) cc_final: 0.8209 (ttmt) REVERT: A 82 ASP cc_start: 0.7550 (t0) cc_final: 0.7261 (t0) REVERT: A 83 SER cc_start: 0.8367 (m) cc_final: 0.8101 (m) REVERT: A 104 PHE cc_start: 0.8019 (t80) cc_final: 0.7500 (t80) REVERT: A 113 ILE cc_start: 0.9029 (mt) cc_final: 0.8780 (mt) REVERT: A 118 GLU cc_start: 0.7361 (pt0) cc_final: 0.7150 (pt0) REVERT: A 128 MET cc_start: 0.8343 (tpt) cc_final: 0.8119 (tpt) REVERT: A 146 PHE cc_start: 0.8402 (m-10) cc_final: 0.7955 (m-10) REVERT: A 150 VAL cc_start: 0.8797 (p) cc_final: 0.8319 (m) REVERT: A 153 ASP cc_start: 0.8526 (t0) cc_final: 0.8139 (t0) REVERT: A 171 LYS cc_start: 0.8195 (mmtp) cc_final: 0.7674 (mmtm) REVERT: A 184 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8312 (mmtp) REVERT: A 188 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 203 LYS cc_start: 0.7991 (pttm) cc_final: 0.7149 (pttm) REVERT: A 207 LEU cc_start: 0.8343 (mt) cc_final: 0.8130 (mp) REVERT: A 214 TYR cc_start: 0.8574 (m-80) cc_final: 0.8147 (m-10) REVERT: A 235 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8179 (ttpt) REVERT: A 241 MET cc_start: 0.8062 (mmm) cc_final: 0.7520 (mmm) REVERT: A 248 ASP cc_start: 0.7417 (m-30) cc_final: 0.7022 (m-30) REVERT: A 263 MET cc_start: 0.7779 (mmp) cc_final: 0.7516 (mmp) REVERT: A 265 LYS cc_start: 0.8922 (ttpp) cc_final: 0.8579 (ttpp) REVERT: A 268 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 313 LEU cc_start: 0.6826 (tt) cc_final: 0.6612 (tt) REVERT: A 316 CYS cc_start: 0.8109 (m) cc_final: 0.7689 (m) REVERT: A 345 GLU cc_start: 0.7098 (pp20) cc_final: 0.6822 (pp20) REVERT: A 384 MET cc_start: 0.8373 (ttt) cc_final: 0.7970 (ttm) REVERT: A 416 LYS cc_start: 0.8839 (mppt) cc_final: 0.8359 (mppt) REVERT: A 426 GLN cc_start: 0.8099 (mt0) cc_final: 0.7699 (mt0) REVERT: B 3 GLU cc_start: 0.7611 (tt0) cc_final: 0.7115 (tt0) REVERT: B 4 ILE cc_start: 0.8616 (tp) cc_final: 0.8369 (tp) REVERT: B 15 TYR cc_start: 0.8496 (t80) cc_final: 0.8150 (t80) REVERT: B 26 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6975 (mt-10) REVERT: B 41 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8516 (ttmt) REVERT: B 43 HIS cc_start: 0.8739 (t-90) cc_final: 0.8140 (t-170) REVERT: B 47 TYR cc_start: 0.8613 (m-80) cc_final: 0.8064 (m-80) REVERT: B 54 ASN cc_start: 0.8665 (m-40) cc_final: 0.8385 (m-40) REVERT: B 79 LYS cc_start: 0.8823 (ttmm) cc_final: 0.7898 (ttmm) REVERT: B 87 HIS cc_start: 0.8047 (t-90) cc_final: 0.7795 (t-90) REVERT: B 95 GLU cc_start: 0.8315 (tt0) cc_final: 0.7761 (tt0) REVERT: B 96 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8480 (mtpp) REVERT: B 103 MET cc_start: 0.7766 (mmm) cc_final: 0.7490 (mmm) REVERT: B 109 LYS cc_start: 0.9199 (tptt) cc_final: 0.8576 (tptt) REVERT: B 145 SER cc_start: 0.8590 (p) cc_final: 0.8049 (t) REVERT: B 155 MET cc_start: 0.7785 (tpp) cc_final: 0.7180 (tpp) REVERT: B 171 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7715 (mmmm) REVERT: B 213 ASP cc_start: 0.7831 (m-30) cc_final: 0.7095 (m-30) REVERT: B 226 MET cc_start: 0.8264 (mmm) cc_final: 0.7522 (mmp) REVERT: B 231 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7860 (mm-30) REVERT: B 243 ASP cc_start: 0.7179 (t0) cc_final: 0.6860 (t0) REVERT: B 245 SER cc_start: 0.8408 (t) cc_final: 0.7180 (p) REVERT: B 248 ASP cc_start: 0.7496 (m-30) cc_final: 0.7182 (m-30) REVERT: B 258 GLU cc_start: 0.8335 (pt0) cc_final: 0.8066 (pt0) REVERT: B 263 MET cc_start: 0.8218 (mmm) cc_final: 0.7911 (mmt) REVERT: B 265 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8703 (ttpp) REVERT: B 269 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7764 (mtmm) REVERT: B 278 LYS cc_start: 0.8520 (tptp) cc_final: 0.8294 (tptp) REVERT: B 279 GLN cc_start: 0.8508 (tt0) cc_final: 0.7857 (tt0) REVERT: B 318 SER cc_start: 0.8098 (m) cc_final: 0.7363 (t) REVERT: B 392 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7108 (tm-30) REVERT: B 403 GLN cc_start: 0.7078 (tt0) cc_final: 0.6525 (pt0) REVERT: B 413 LYS cc_start: 0.8497 (tppt) cc_final: 0.7509 (tppt) REVERT: B 414 TRP cc_start: 0.7113 (m-90) cc_final: 0.6688 (m-90) REVERT: B 419 MET cc_start: 0.4751 (tpp) cc_final: 0.4173 (ttm) REVERT: C 3 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8043 (mm-30) REVERT: C 13 GLN cc_start: 0.7996 (tp40) cc_final: 0.7335 (tp40) REVERT: C 26 GLU cc_start: 0.8031 (pt0) cc_final: 0.7717 (pt0) REVERT: C 41 LYS cc_start: 0.8779 (tttt) cc_final: 0.8324 (tttt) REVERT: C 85 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7715 (mm-30) REVERT: C 113 ILE cc_start: 0.9043 (mt) cc_final: 0.8703 (mm) REVERT: C 140 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7889 (tm-30) REVERT: C 161 ARG cc_start: 0.8360 (ttp80) cc_final: 0.8150 (ttp80) REVERT: C 166 MET cc_start: 0.7302 (tpt) cc_final: 0.7038 (tpt) REVERT: C 178 ILE cc_start: 0.8044 (tp) cc_final: 0.7546 (mm) REVERT: C 203 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7508 (mtmm) REVERT: C 213 ASP cc_start: 0.8269 (m-30) cc_final: 0.7779 (m-30) REVERT: C 226 MET cc_start: 0.8406 (mmm) cc_final: 0.7921 (mmp) REVERT: C 235 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8671 (ttpp) REVERT: C 241 MET cc_start: 0.8142 (mmm) cc_final: 0.7579 (mmm) REVERT: C 243 ASP cc_start: 0.7778 (t0) cc_final: 0.7530 (t0) REVERT: C 263 MET cc_start: 0.7403 (mmm) cc_final: 0.7170 (mmm) REVERT: C 288 ASN cc_start: 0.8613 (m110) cc_final: 0.8331 (m110) REVERT: C 292 SER cc_start: 0.9065 (m) cc_final: 0.8663 (t) REVERT: C 295 ASN cc_start: 0.8162 (t0) cc_final: 0.7946 (t0) REVERT: C 318 SER cc_start: 0.7834 (t) cc_final: 0.7492 (p) REVERT: C 333 LYS cc_start: 0.7943 (ttpt) cc_final: 0.7516 (ttpt) REVERT: C 342 LEU cc_start: 0.8793 (tp) cc_final: 0.8593 (tp) REVERT: C 356 VAL cc_start: 0.8383 (m) cc_final: 0.8091 (p) REVERT: D 26 GLU cc_start: 0.8041 (pm20) cc_final: 0.7828 (pm20) REVERT: D 41 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8259 (ttpp) REVERT: D 47 TYR cc_start: 0.8938 (m-80) cc_final: 0.8067 (m-80) REVERT: D 74 LYS cc_start: 0.8992 (tttp) cc_final: 0.8697 (mmmm) REVERT: D 90 LEU cc_start: 0.8527 (mm) cc_final: 0.8213 (mm) REVERT: D 103 MET cc_start: 0.7258 (mmp) cc_final: 0.6655 (mmp) REVERT: D 118 GLU cc_start: 0.7147 (tp30) cc_final: 0.6824 (tp30) REVERT: D 126 LYS cc_start: 0.8663 (tptt) cc_final: 0.8403 (tptt) REVERT: D 136 ASP cc_start: 0.7867 (t70) cc_final: 0.7604 (t0) REVERT: D 140 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7909 (mm-40) REVERT: D 143 SER cc_start: 0.9052 (m) cc_final: 0.8388 (t) REVERT: D 147 ASP cc_start: 0.7363 (p0) cc_final: 0.7069 (p0) REVERT: D 155 MET cc_start: 0.7740 (tpt) cc_final: 0.7026 (tpt) REVERT: D 189 THR cc_start: 0.8552 (p) cc_final: 0.7225 (t) REVERT: D 196 MET cc_start: 0.7481 (mtp) cc_final: 0.7278 (mtp) REVERT: D 223 TYR cc_start: 0.8096 (t80) cc_final: 0.7435 (t80) REVERT: D 226 MET cc_start: 0.7239 (mmm) cc_final: 0.6327 (mmm) REVERT: D 238 ASP cc_start: 0.8543 (m-30) cc_final: 0.8086 (m-30) REVERT: D 241 MET cc_start: 0.8347 (mtp) cc_final: 0.8039 (mtp) REVERT: D 280 TYR cc_start: 0.8505 (m-80) cc_final: 0.8031 (m-80) REVERT: D 300 LYS cc_start: 0.8417 (mttm) cc_final: 0.7893 (mttm) REVERT: D 324 TYR cc_start: 0.7678 (m-80) cc_final: 0.7302 (m-80) REVERT: D 326 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7140 (mm-30) REVERT: D 329 TYR cc_start: 0.5986 (t80) cc_final: 0.5460 (t80) REVERT: D 333 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7741 (ttmt) REVERT: D 338 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 347 GLU cc_start: 0.7799 (tp30) cc_final: 0.7175 (tp30) REVERT: D 413 LYS cc_start: 0.8624 (mptt) cc_final: 0.8080 (mptt) REVERT: E 1 MET cc_start: 0.7790 (ptm) cc_final: 0.7308 (ptm) REVERT: E 23 MET cc_start: 0.8409 (mmt) cc_final: 0.8120 (mmt) REVERT: E 34 LYS cc_start: 0.8797 (tttp) cc_final: 0.8206 (tttp) REVERT: E 35 ASN cc_start: 0.8402 (m-40) cc_final: 0.7988 (m-40) REVERT: E 38 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8409 (mtpt) REVERT: E 41 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8706 (ttpt) REVERT: E 47 TYR cc_start: 0.6289 (t80) cc_final: 0.6040 (t80) REVERT: E 79 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7931 (mtmt) REVERT: E 86 ASP cc_start: 0.8534 (t0) cc_final: 0.8243 (t0) REVERT: E 93 GLU cc_start: 0.7929 (tp30) cc_final: 0.7356 (tp30) REVERT: E 95 GLU cc_start: 0.8626 (tt0) cc_final: 0.7999 (tt0) REVERT: E 103 MET cc_start: 0.7730 (mmp) cc_final: 0.7333 (mmp) REVERT: E 146 PHE cc_start: 0.7481 (m-10) cc_final: 0.6990 (m-10) REVERT: E 181 LYS cc_start: 0.8519 (tmmt) cc_final: 0.8253 (tmmt) REVERT: E 195 LEU cc_start: 0.8016 (tp) cc_final: 0.7666 (tt) REVERT: E 236 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7609 (ttm110) REVERT: E 241 MET cc_start: 0.7603 (mmm) cc_final: 0.7200 (mmm) REVERT: E 248 ASP cc_start: 0.7650 (m-30) cc_final: 0.7306 (m-30) REVERT: E 260 LYS cc_start: 0.8784 (tptm) cc_final: 0.8489 (tptm) REVERT: E 269 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8470 (ttmm) REVERT: E 271 THR cc_start: 0.9231 (p) cc_final: 0.8818 (t) REVERT: E 293 LEU cc_start: 0.8922 (tp) cc_final: 0.8718 (tp) REVERT: E 296 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 301 LYS cc_start: 0.8124 (ptpt) cc_final: 0.7666 (ptpt) REVERT: E 333 LYS cc_start: 0.7864 (tttp) cc_final: 0.7484 (tttp) REVERT: E 416 LYS cc_start: 0.8238 (mttp) cc_final: 0.7975 (mttp) REVERT: E 423 LYS cc_start: 0.8896 (mttm) cc_final: 0.8659 (mtpp) REVERT: F 5 ILE cc_start: 0.8918 (mt) cc_final: 0.8650 (mt) REVERT: F 13 GLN cc_start: 0.8123 (tp-100) cc_final: 0.7915 (tp40) REVERT: F 15 TYR cc_start: 0.8544 (t80) cc_final: 0.7322 (t80) REVERT: F 18 LYS cc_start: 0.8694 (tppt) cc_final: 0.8358 (tppt) REVERT: F 22 TYR cc_start: 0.8434 (m-80) cc_final: 0.8210 (m-10) REVERT: F 29 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7569 (mm-30) REVERT: F 34 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8076 (ttmm) REVERT: F 43 HIS cc_start: 0.8514 (t-90) cc_final: 0.7906 (t-90) REVERT: F 60 LEU cc_start: 0.8833 (tp) cc_final: 0.8571 (tp) REVERT: F 61 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7362 (mm-30) REVERT: F 62 ASN cc_start: 0.8349 (m-40) cc_final: 0.7979 (t0) REVERT: F 82 ASP cc_start: 0.7631 (t0) cc_final: 0.7328 (t0) REVERT: F 93 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7847 (mm-30) REVERT: F 95 GLU cc_start: 0.8075 (tt0) cc_final: 0.7686 (tt0) REVERT: F 96 LYS cc_start: 0.8828 (ttpp) cc_final: 0.8361 (ttpp) REVERT: F 114 GLN cc_start: 0.8614 (mt0) cc_final: 0.8291 (mt0) REVERT: F 116 ASN cc_start: 0.8499 (t0) cc_final: 0.7988 (t0) REVERT: F 119 LEU cc_start: 0.8572 (mt) cc_final: 0.8140 (mt) REVERT: F 123 LYS cc_start: 0.8564 (tppt) cc_final: 0.8278 (tppt) REVERT: F 136 ASP cc_start: 0.7466 (t0) cc_final: 0.6844 (t0) REVERT: F 149 TYR cc_start: 0.6247 (t80) cc_final: 0.6020 (t80) REVERT: F 152 HIS cc_start: 0.7894 (t70) cc_final: 0.7508 (t70) REVERT: F 155 MET cc_start: 0.6715 (tpp) cc_final: 0.5918 (tpp) REVERT: F 157 ASP cc_start: 0.7705 (m-30) cc_final: 0.7056 (m-30) REVERT: F 158 TYR cc_start: 0.7771 (p90) cc_final: 0.7249 (p90) REVERT: F 183 THR cc_start: 0.8108 (p) cc_final: 0.7610 (t) REVERT: F 184 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7861 (mmmt) REVERT: F 189 THR cc_start: 0.8109 (p) cc_final: 0.7643 (t) REVERT: F 191 THR cc_start: 0.8696 (p) cc_final: 0.7399 (m) REVERT: F 246 LEU cc_start: 0.7593 (mt) cc_final: 0.7371 (mt) REVERT: F 256 TYR cc_start: 0.7686 (t80) cc_final: 0.7113 (t80) REVERT: F 260 LYS cc_start: 0.8235 (ttmm) cc_final: 0.7942 (ttmm) REVERT: F 265 LYS cc_start: 0.8817 (mmtm) cc_final: 0.8390 (mmtm) REVERT: F 326 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7463 (mm-30) REVERT: F 333 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8422 (ttpp) REVERT: F 338 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7256 (mm-30) REVERT: F 340 ARG cc_start: 0.9063 (ttt-90) cc_final: 0.8686 (tpt-90) REVERT: F 359 GLN cc_start: 0.8279 (mt0) cc_final: 0.8049 (mp10) REVERT: F 404 ILE cc_start: 0.8442 (mt) cc_final: 0.7893 (mt) REVERT: F 405 LYS cc_start: 0.7155 (tptp) cc_final: 0.6541 (tptp) REVERT: F 411 LYS cc_start: 0.7012 (mtmm) cc_final: 0.6790 (mtpp) REVERT: F 416 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7781 (mtpp) REVERT: F 422 GLN cc_start: 0.7272 (mt0) cc_final: 0.7041 (mt0) REVERT: G 8 ASP cc_start: 0.8792 (m-30) cc_final: 0.8502 (m-30) REVERT: G 78 LEU cc_start: 0.9405 (mt) cc_final: 0.9162 (mt) REVERT: G 81 PHE cc_start: 0.8352 (m-80) cc_final: 0.7222 (m-10) REVERT: G 82 GLU cc_start: 0.8289 (tp30) cc_final: 0.7909 (tp30) REVERT: G 89 TYR cc_start: 0.8100 (t80) cc_final: 0.7786 (t80) REVERT: G 92 GLU cc_start: 0.8571 (tp30) cc_final: 0.6641 (tp30) REVERT: G 95 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8180 (mtpp) REVERT: G 238 ASP cc_start: 0.8420 (m-30) cc_final: 0.8083 (m-30) REVERT: G 240 LEU cc_start: 0.9077 (mt) cc_final: 0.8868 (mt) REVERT: G 266 TRP cc_start: 0.7220 (m-90) cc_final: 0.6988 (m-90) REVERT: G 276 ASP cc_start: 0.8205 (p0) cc_final: 0.7760 (p0) REVERT: G 279 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8816 (mttt) REVERT: G 283 LYS cc_start: 0.8922 (pttm) cc_final: 0.8679 (pttt) REVERT: G 307 MET cc_start: 0.8774 (mmt) cc_final: 0.8417 (mmm) REVERT: G 328 GLN cc_start: 0.7951 (tp40) cc_final: 0.7460 (tp40) REVERT: G 333 LYS cc_start: 0.9260 (mptt) cc_final: 0.8867 (mmtt) REVERT: G 334 MET cc_start: 0.7994 (mtm) cc_final: 0.7658 (mtm) outliers start: 1 outliers final: 1 residues processed: 1126 average time/residue: 0.1770 time to fit residues: 298.6150 Evaluate side-chains 1062 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1061 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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: 3.9990 chunk 70 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 chunk 122 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 116 ASN A 219 HIS A 220 ASN A 240 ASN A 295 ASN B 99 GLN B 114 GLN B 193 ASN D 62 ASN D 114 GLN ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107861 restraints weight = 48231.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111604 restraints weight = 24793.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114177 restraints weight = 15065.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.115914 restraints weight = 10258.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116923 restraints weight = 7643.891| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24515 Z= 0.140 Angle : 0.654 11.883 33269 Z= 0.342 Chirality : 0.045 0.270 3697 Planarity : 0.005 0.078 4105 Dihedral : 10.271 168.822 3441 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.04 % Allowed : 0.83 % Favored : 99.13 % 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: -0.35 (0.16), residues: 2917 helix: 0.97 (0.14), residues: 1447 sheet: -1.45 (0.26), residues: 401 loop : -1.34 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 280 TYR 0.036 0.002 TYR B 165 PHE 0.024 0.002 PHE A 16 TRP 0.034 0.002 TRP G 266 HIS 0.008 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (24510) covalent geometry : angle 0.65187 / 0.34 (33263) hydrogen bonds : bond 0.03358 / 2.31 ( 1174) hydrogen bonds : angle 4.89740 / 3.50 ( 3363) metal coordination : bond 0.00847 / 0.43 ( 4) metal coordination : angle 4.25278 / 2.22 ( 6) Misc. bond : bond 0.00034 / 0.02 ( 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 1130 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1129 time to evaluate : 0.818 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: 0.8069 (tpp) cc_final: 0.7558 (tpp) REVERT: A 3 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 4 ILE cc_start: 0.8934 (tt) cc_final: 0.8603 (tp) REVERT: A 11 PHE cc_start: 0.7744 (m-10) cc_final: 0.7459 (m-10) REVERT: A 19 VAL cc_start: 0.8200 (m) cc_final: 0.7922 (p) REVERT: A 26 GLU cc_start: 0.7784 (pm20) cc_final: 0.7339 (pm20) REVERT: A 27 TYR cc_start: 0.7620 (m-10) cc_final: 0.7146 (m-10) REVERT: A 29 GLU cc_start: 0.7591 (tt0) cc_final: 0.7304 (tt0) REVERT: A 35 ASN cc_start: 0.8487 (m-40) cc_final: 0.8129 (m110) REVERT: A 61 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6490 (tm-30) REVERT: A 73 VAL cc_start: 0.8967 (t) cc_final: 0.8488 (p) REVERT: A 79 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8167 (ttmt) REVERT: A 83 SER cc_start: 0.8316 (m) cc_final: 0.8114 (m) REVERT: A 93 GLU cc_start: 0.8118 (tp30) cc_final: 0.7716 (tp30) REVERT: A 104 PHE cc_start: 0.7980 (t80) cc_final: 0.7655 (t80) REVERT: A 113 ILE cc_start: 0.9108 (mt) cc_final: 0.8727 (mt) REVERT: A 123 LYS cc_start: 0.8308 (mttp) cc_final: 0.8062 (mttp) REVERT: A 146 PHE cc_start: 0.8392 (m-10) cc_final: 0.7856 (m-10) REVERT: A 150 VAL cc_start: 0.8720 (p) cc_final: 0.7925 (m) REVERT: A 153 ASP cc_start: 0.8525 (t0) cc_final: 0.8165 (t0) REVERT: A 171 LYS cc_start: 0.8164 (mmtp) cc_final: 0.7652 (mmtm) REVERT: A 188 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 203 LYS cc_start: 0.7982 (pttm) cc_final: 0.7246 (pttm) REVERT: A 207 LEU cc_start: 0.8293 (mt) cc_final: 0.8072 (mp) REVERT: A 214 TYR cc_start: 0.8530 (m-80) cc_final: 0.8119 (m-10) REVERT: A 235 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8153 (ttpt) REVERT: A 238 ASP cc_start: 0.8648 (m-30) cc_final: 0.8398 (m-30) REVERT: A 241 MET cc_start: 0.8007 (mmm) cc_final: 0.7480 (mmm) REVERT: A 248 ASP cc_start: 0.7194 (m-30) cc_final: 0.6744 (m-30) REVERT: A 263 MET cc_start: 0.7819 (mmp) cc_final: 0.7546 (mmp) REVERT: A 265 LYS cc_start: 0.8921 (ttpp) cc_final: 0.8531 (ttpp) REVERT: A 268 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 278 LYS cc_start: 0.8284 (tptm) cc_final: 0.7836 (mtpp) REVERT: A 316 CYS cc_start: 0.8249 (m) cc_final: 0.7719 (m) REVERT: A 345 GLU cc_start: 0.7023 (pp20) cc_final: 0.6798 (pp20) REVERT: A 384 MET cc_start: 0.8437 (ttt) cc_final: 0.7826 (ttm) REVERT: A 411 LYS cc_start: 0.7572 (tttt) cc_final: 0.7244 (tttt) REVERT: A 415 ASN cc_start: 0.8003 (t0) cc_final: 0.7518 (t0) REVERT: A 416 LYS cc_start: 0.8953 (mppt) cc_final: 0.8398 (mppt) REVERT: A 426 GLN cc_start: 0.8148 (mt0) cc_final: 0.7762 (mt0) REVERT: B 15 TYR cc_start: 0.8465 (t80) cc_final: 0.8155 (t80) REVERT: B 23 MET cc_start: 0.8378 (mmm) cc_final: 0.7783 (mmm) REVERT: B 26 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6967 (mp0) REVERT: B 41 LYS cc_start: 0.8822 (ttmt) cc_final: 0.8463 (ttmt) REVERT: B 43 HIS cc_start: 0.8756 (t-90) cc_final: 0.8165 (t-170) REVERT: B 47 TYR cc_start: 0.8586 (m-80) cc_final: 0.8086 (m-80) REVERT: B 54 ASN cc_start: 0.8529 (m-40) cc_final: 0.8288 (m-40) REVERT: B 87 HIS cc_start: 0.7966 (t-90) cc_final: 0.7762 (t-90) REVERT: B 95 GLU cc_start: 0.8350 (tt0) cc_final: 0.7951 (tt0) REVERT: B 103 MET cc_start: 0.7821 (mmm) cc_final: 0.7457 (mmm) REVERT: B 109 LYS cc_start: 0.9195 (tptt) cc_final: 0.8589 (tptt) REVERT: B 145 SER cc_start: 0.8641 (p) cc_final: 0.7954 (t) REVERT: B 155 MET cc_start: 0.7741 (tpp) cc_final: 0.7269 (tpp) REVERT: B 171 LYS cc_start: 0.8226 (mmmm) cc_final: 0.7726 (mmmm) REVERT: B 191 THR cc_start: 0.8427 (p) cc_final: 0.8210 (p) REVERT: B 194 VAL cc_start: 0.8228 (t) cc_final: 0.7265 (t) REVERT: B 213 ASP cc_start: 0.7821 (m-30) cc_final: 0.7593 (m-30) REVERT: B 226 MET cc_start: 0.8163 (mmm) cc_final: 0.7499 (mmp) REVERT: B 231 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7766 (mm-30) REVERT: B 243 ASP cc_start: 0.7174 (t0) cc_final: 0.6856 (t0) REVERT: B 245 SER cc_start: 0.8340 (t) cc_final: 0.7129 (p) REVERT: B 248 ASP cc_start: 0.7447 (m-30) cc_final: 0.7157 (m-30) REVERT: B 258 GLU cc_start: 0.8355 (pt0) cc_final: 0.8041 (pt0) REVERT: B 260 LYS cc_start: 0.8945 (tppp) cc_final: 0.8745 (tptm) REVERT: B 265 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8715 (ttpp) REVERT: B 269 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7729 (mtmm) REVERT: B 278 LYS cc_start: 0.8500 (tptp) cc_final: 0.8273 (tptp) REVERT: B 279 GLN cc_start: 0.8462 (tt0) cc_final: 0.7873 (tt0) REVERT: B 300 LYS cc_start: 0.8468 (mtpt) cc_final: 0.7750 (mtpt) REVERT: B 318 SER cc_start: 0.8004 (m) cc_final: 0.7261 (t) REVERT: B 345 GLU cc_start: 0.8129 (tt0) cc_final: 0.7926 (tt0) REVERT: B 384 MET cc_start: 0.8435 (mmm) cc_final: 0.7914 (mmt) REVERT: B 392 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7091 (tm-30) REVERT: B 403 GLN cc_start: 0.6921 (tt0) cc_final: 0.6481 (pt0) REVERT: B 413 LYS cc_start: 0.8531 (tppt) cc_final: 0.7998 (tppt) REVERT: C 3 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8062 (mm-30) REVERT: C 13 GLN cc_start: 0.7873 (tp40) cc_final: 0.7158 (tp40) REVERT: C 26 GLU cc_start: 0.8078 (pt0) cc_final: 0.7737 (pt0) REVERT: C 41 LYS cc_start: 0.8761 (tttt) cc_final: 0.8291 (tttt) REVERT: C 56 LEU cc_start: 0.9097 (mm) cc_final: 0.8832 (mm) REVERT: C 85 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7676 (mm-30) REVERT: C 113 ILE cc_start: 0.9024 (mt) cc_final: 0.8638 (mm) REVERT: C 140 GLN cc_start: 0.8062 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 154 TRP cc_start: 0.8692 (t60) cc_final: 0.8178 (t60) REVERT: C 166 MET cc_start: 0.7305 (tpt) cc_final: 0.6850 (tpt) REVERT: C 178 ILE cc_start: 0.8004 (tp) cc_final: 0.7555 (mm) REVERT: C 203 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7491 (mtmm) REVERT: C 213 ASP cc_start: 0.8257 (m-30) cc_final: 0.7790 (m-30) REVERT: C 226 MET cc_start: 0.8377 (mmm) cc_final: 0.7956 (mmp) REVERT: C 235 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8595 (ttpp) REVERT: C 238 ASP cc_start: 0.8165 (m-30) cc_final: 0.7625 (m-30) REVERT: C 240 ASN cc_start: 0.8120 (t0) cc_final: 0.7882 (t0) REVERT: C 241 MET cc_start: 0.8074 (mmm) cc_final: 0.7565 (mmm) REVERT: C 263 MET cc_start: 0.7398 (mmm) cc_final: 0.7092 (mmm) REVERT: C 279 GLN cc_start: 0.8173 (tt0) cc_final: 0.7741 (tt0) REVERT: C 288 ASN cc_start: 0.8566 (m110) cc_final: 0.8337 (m110) REVERT: C 292 SER cc_start: 0.9057 (m) cc_final: 0.8658 (t) REVERT: C 315 ILE cc_start: 0.8475 (pt) cc_final: 0.8152 (pt) REVERT: C 318 SER cc_start: 0.7765 (t) cc_final: 0.7336 (p) REVERT: C 333 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7534 (ttpt) REVERT: C 356 VAL cc_start: 0.8378 (m) cc_final: 0.8041 (p) REVERT: C 393 LEU cc_start: 0.8911 (mt) cc_final: 0.8703 (mt) REVERT: D 41 LYS cc_start: 0.8660 (ttpp) cc_final: 0.8187 (ttpp) REVERT: D 46 GLU cc_start: 0.8130 (tt0) cc_final: 0.7656 (tt0) REVERT: D 47 TYR cc_start: 0.8934 (m-80) cc_final: 0.7771 (m-80) REVERT: D 74 LYS cc_start: 0.8965 (tttp) cc_final: 0.8686 (mmmm) REVERT: D 90 LEU cc_start: 0.8457 (mm) cc_final: 0.8074 (mm) REVERT: D 96 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8303 (ttmt) REVERT: D 103 MET cc_start: 0.7198 (mmp) cc_final: 0.6765 (mmp) REVERT: D 109 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7817 (ttmm) REVERT: D 118 GLU cc_start: 0.7087 (tp30) cc_final: 0.6787 (tp30) REVERT: D 136 ASP cc_start: 0.8011 (t70) cc_final: 0.7799 (t70) REVERT: D 140 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7949 (mm110) REVERT: D 143 SER cc_start: 0.9034 (m) cc_final: 0.8323 (t) REVERT: D 155 MET cc_start: 0.7738 (tpt) cc_final: 0.7283 (tpt) REVERT: D 189 THR cc_start: 0.8594 (p) cc_final: 0.7158 (t) REVERT: D 196 MET cc_start: 0.7467 (mtp) cc_final: 0.7146 (mtp) REVERT: D 222 LEU cc_start: 0.8779 (tp) cc_final: 0.8519 (tt) REVERT: D 223 TYR cc_start: 0.8119 (t80) cc_final: 0.6997 (t80) REVERT: D 226 MET cc_start: 0.7169 (mmm) cc_final: 0.6302 (mmm) REVERT: D 280 TYR cc_start: 0.8475 (m-80) cc_final: 0.7955 (m-80) REVERT: D 300 LYS cc_start: 0.8431 (mttm) cc_final: 0.7866 (mttm) REVERT: D 324 TYR cc_start: 0.7680 (m-80) cc_final: 0.7266 (m-80) REVERT: D 326 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7115 (mm-30) REVERT: D 329 TYR cc_start: 0.5814 (t80) cc_final: 0.5153 (t80) REVERT: D 333 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7547 (ttmt) REVERT: D 338 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6997 (mt-10) REVERT: D 347 GLU cc_start: 0.7892 (tp30) cc_final: 0.7220 (tp30) REVERT: D 392 GLU cc_start: 0.7515 (tp30) cc_final: 0.7105 (tp30) REVERT: D 397 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 413 LYS cc_start: 0.8549 (mptt) cc_final: 0.8029 (mptt) REVERT: E 23 MET cc_start: 0.8444 (mmt) cc_final: 0.8116 (mmt) REVERT: E 29 GLU cc_start: 0.6905 (mm-30) cc_final: 0.6606 (mm-30) REVERT: E 34 LYS cc_start: 0.8764 (tttp) cc_final: 0.8168 (tttp) REVERT: E 35 ASN cc_start: 0.8402 (m-40) cc_final: 0.7853 (m-40) REVERT: E 38 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8332 (mtpt) REVERT: E 39 LEU cc_start: 0.8703 (mt) cc_final: 0.8407 (mt) REVERT: E 47 TYR cc_start: 0.6272 (t80) cc_final: 0.6005 (t80) REVERT: E 79 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7890 (mtmt) REVERT: E 86 ASP cc_start: 0.8522 (t0) cc_final: 0.8246 (t0) REVERT: E 95 GLU cc_start: 0.8617 (tt0) cc_final: 0.7894 (tt0) REVERT: E 119 LEU cc_start: 0.8940 (mt) cc_final: 0.8477 (mt) REVERT: E 146 PHE cc_start: 0.7372 (m-10) cc_final: 0.6920 (m-10) REVERT: E 181 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8113 (tmmt) REVERT: E 195 LEU cc_start: 0.8037 (tp) cc_final: 0.7658 (tt) REVERT: E 228 MET cc_start: 0.7563 (ptt) cc_final: 0.7232 (ptt) REVERT: E 236 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7699 (ttm110) REVERT: E 238 ASP cc_start: 0.8672 (m-30) cc_final: 0.8457 (m-30) REVERT: E 241 MET cc_start: 0.7555 (mmm) cc_final: 0.7109 (mmm) REVERT: E 260 LYS cc_start: 0.8740 (tptm) cc_final: 0.8437 (tptm) REVERT: E 269 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8445 (ttmm) REVERT: E 271 THR cc_start: 0.9200 (p) cc_final: 0.8797 (t) REVERT: E 300 LYS cc_start: 0.8108 (tttm) cc_final: 0.7840 (tttm) REVERT: E 301 LYS cc_start: 0.8135 (ptpt) cc_final: 0.7742 (ptpt) REVERT: F 5 ILE cc_start: 0.8921 (mt) cc_final: 0.8589 (mt) REVERT: F 13 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7880 (tp40) REVERT: F 15 TYR cc_start: 0.8552 (t80) cc_final: 0.7225 (t80) REVERT: F 18 LYS cc_start: 0.8679 (tppt) cc_final: 0.8471 (tppt) REVERT: F 22 TYR cc_start: 0.8405 (m-80) cc_final: 0.8135 (m-10) REVERT: F 29 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7568 (mm-30) REVERT: F 34 LYS cc_start: 0.8974 (ttmt) cc_final: 0.8097 (ttmm) REVERT: F 38 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8722 (mmtp) REVERT: F 43 HIS cc_start: 0.8382 (t-90) cc_final: 0.7773 (t-90) REVERT: F 60 LEU cc_start: 0.8808 (tp) cc_final: 0.8562 (tp) REVERT: F 61 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7357 (mm-30) REVERT: F 79 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8784 (mtmt) REVERT: F 82 ASP cc_start: 0.7513 (t0) cc_final: 0.7240 (t0) REVERT: F 93 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7644 (mt-10) REVERT: F 95 GLU cc_start: 0.8034 (tt0) cc_final: 0.7619 (tt0) REVERT: F 96 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8275 (ttpp) REVERT: F 116 ASN cc_start: 0.8496 (t0) cc_final: 0.7986 (t0) REVERT: F 119 LEU cc_start: 0.8575 (mt) cc_final: 0.8166 (mt) REVERT: F 123 LYS cc_start: 0.8571 (tppt) cc_final: 0.8288 (tppt) REVERT: F 152 HIS cc_start: 0.7888 (t70) cc_final: 0.7499 (t70) REVERT: F 155 MET cc_start: 0.6674 (tpp) cc_final: 0.5865 (tpp) REVERT: F 157 ASP cc_start: 0.7649 (m-30) cc_final: 0.7067 (m-30) REVERT: F 158 TYR cc_start: 0.7704 (p90) cc_final: 0.7227 (p90) REVERT: F 183 THR cc_start: 0.8102 (p) cc_final: 0.7557 (t) REVERT: F 184 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7866 (mmmt) REVERT: F 189 THR cc_start: 0.7945 (p) cc_final: 0.7352 (t) REVERT: F 226 MET cc_start: 0.7236 (mmm) cc_final: 0.6839 (mmm) REVERT: F 236 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8262 (ttm110) REVERT: F 246 LEU cc_start: 0.7428 (mt) cc_final: 0.7199 (mt) REVERT: F 256 TYR cc_start: 0.7660 (t80) cc_final: 0.6946 (t80) REVERT: F 258 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7916 (mt-10) REVERT: F 260 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7956 (ttmm) REVERT: F 265 LYS cc_start: 0.8762 (mmtm) cc_final: 0.8350 (mmtm) REVERT: F 291 ARG cc_start: 0.8097 (mtt90) cc_final: 0.7705 (mtt-85) REVERT: F 326 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7421 (mm-30) REVERT: F 333 LYS cc_start: 0.8630 (ttpp) cc_final: 0.8379 (ttpp) REVERT: F 338 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7159 (mm-30) REVERT: F 340 ARG cc_start: 0.9030 (ttt-90) cc_final: 0.8683 (tpt-90) REVERT: F 404 ILE cc_start: 0.8291 (mt) cc_final: 0.7851 (mt) REVERT: F 405 LYS cc_start: 0.7146 (tptp) cc_final: 0.6660 (tppp) REVERT: F 411 LYS cc_start: 0.7072 (mtmm) cc_final: 0.6842 (mtpp) REVERT: F 419 MET cc_start: 0.3915 (tpp) cc_final: 0.2962 (tpt) REVERT: F 422 GLN cc_start: 0.7172 (mt0) cc_final: 0.6948 (mt0) REVERT: F 423 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8684 (mtpt) REVERT: G 8 ASP cc_start: 0.8808 (m-30) cc_final: 0.8537 (m-30) REVERT: G 78 LEU cc_start: 0.9404 (mt) cc_final: 0.9168 (mt) REVERT: G 82 GLU cc_start: 0.8342 (tp30) cc_final: 0.7865 (tp30) REVERT: G 89 TYR cc_start: 0.8147 (t80) cc_final: 0.7821 (t80) REVERT: G 95 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8281 (mtpp) REVERT: G 99 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7953 (tmtt) REVERT: G 100 SER cc_start: 0.8556 (p) cc_final: 0.7133 (p) REVERT: G 151 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8502 (pttm) REVERT: G 238 ASP cc_start: 0.8394 (m-30) cc_final: 0.7912 (m-30) REVERT: G 240 LEU cc_start: 0.9072 (mt) cc_final: 0.8864 (mt) REVERT: G 271 GLU cc_start: 0.8670 (tp30) cc_final: 0.8459 (tp30) REVERT: G 279 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8801 (mttm) REVERT: G 296 LYS cc_start: 0.9055 (mmtm) cc_final: 0.8717 (mmmt) REVERT: G 307 MET cc_start: 0.8744 (mmt) cc_final: 0.8416 (mmm) REVERT: G 323 LYS cc_start: 0.9303 (pttm) cc_final: 0.8929 (pttp) REVERT: G 328 GLN cc_start: 0.8147 (tp40) cc_final: 0.7628 (tp40) REVERT: G 330 LEU cc_start: 0.9000 (mm) cc_final: 0.8465 (mm) REVERT: G 333 LYS cc_start: 0.9260 (mptt) cc_final: 0.9039 (mttt) outliers start: 1 outliers final: 0 residues processed: 1130 average time/residue: 0.1688 time to fit residues: 286.1387 Evaluate side-chains 1063 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1063 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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: 0.1980 chunk 257 optimal weight: 0.9990 chunk 239 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 ASN A 240 ASN D 62 ASN D 100 GLN D 114 GLN ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 398 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 100 GLN F 167 ASN ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.130489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109107 restraints weight = 48276.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.112934 restraints weight = 24767.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115510 restraints weight = 14994.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117182 restraints weight = 10179.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118369 restraints weight = 7655.081| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24515 Z= 0.142 Angle : 0.669 12.108 33269 Z= 0.347 Chirality : 0.045 0.254 3697 Planarity : 0.005 0.056 4105 Dihedral : 10.219 166.406 3441 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.04 % Allowed : 0.55 % Favored : 99.41 % 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: 1450 sheet: -1.33 (0.27), residues: 382 loop : -1.34 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 224 TYR 0.032 0.002 TYR G 54 PHE 0.019 0.002 PHE D 11 TRP 0.040 0.002 TRP D 428 HIS 0.006 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (24510) covalent geometry : angle 0.66639 / 0.35 (33263) hydrogen bonds : bond 0.03331 / 2.26 ( 1174) hydrogen bonds : angle 4.86595 / 3.47 ( 3363) metal coordination : bond 0.00802 / 0.40 ( 4) metal coordination : angle 4.24343 / 2.22 ( 6) Misc. bond : bond 0.00036 / 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 1141 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1140 time to evaluate : 0.674 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: 0.7959 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 11 PHE cc_start: 0.7657 (m-10) cc_final: 0.7210 (m-10) REVERT: A 19 VAL cc_start: 0.8216 (m) cc_final: 0.7907 (p) REVERT: A 26 GLU cc_start: 0.7813 (pm20) cc_final: 0.7358 (pm20) REVERT: A 29 GLU cc_start: 0.7594 (tt0) cc_final: 0.7328 (tt0) REVERT: A 35 ASN cc_start: 0.8500 (m-40) cc_final: 0.8141 (m110) REVERT: A 39 LEU cc_start: 0.8976 (mt) cc_final: 0.8774 (mt) REVERT: A 47 TYR cc_start: 0.6664 (m-80) cc_final: 0.6222 (m-80) REVERT: A 61 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6535 (tm-30) REVERT: A 73 VAL cc_start: 0.9001 (t) cc_final: 0.8536 (p) REVERT: A 104 PHE cc_start: 0.7904 (t80) cc_final: 0.7513 (t80) REVERT: A 123 LYS cc_start: 0.8351 (mttp) cc_final: 0.8094 (mttp) REVERT: A 146 PHE cc_start: 0.8353 (m-10) cc_final: 0.7909 (m-10) REVERT: A 150 VAL cc_start: 0.8316 (p) cc_final: 0.7739 (m) REVERT: A 171 LYS cc_start: 0.8206 (mmtp) cc_final: 0.7735 (mmtm) REVERT: A 203 LYS cc_start: 0.8004 (pttm) cc_final: 0.7239 (pttm) REVERT: A 214 TYR cc_start: 0.8499 (m-80) cc_final: 0.8121 (m-10) REVERT: A 235 LYS cc_start: 0.8682 (ttpt) cc_final: 0.8148 (ttpt) REVERT: A 238 ASP cc_start: 0.8733 (m-30) cc_final: 0.8506 (m-30) REVERT: A 241 MET cc_start: 0.8017 (mmm) cc_final: 0.7443 (mmm) REVERT: A 248 ASP cc_start: 0.7067 (m-30) cc_final: 0.6674 (m-30) REVERT: A 265 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8579 (ttpp) REVERT: A 268 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 269 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7439 (mtmm) REVERT: A 278 LYS cc_start: 0.8138 (tptm) cc_final: 0.7788 (mtpp) REVERT: A 313 LEU cc_start: 0.6717 (tt) cc_final: 0.6492 (tt) REVERT: A 316 CYS cc_start: 0.8202 (m) cc_final: 0.7685 (m) REVERT: A 342 LEU cc_start: 0.8600 (tp) cc_final: 0.7957 (tp) REVERT: A 382 ASP cc_start: 0.8150 (m-30) cc_final: 0.7860 (m-30) REVERT: A 384 MET cc_start: 0.8459 (ttt) cc_final: 0.7923 (ttm) REVERT: A 415 ASN cc_start: 0.8017 (t0) cc_final: 0.7496 (t0) REVERT: A 416 LYS cc_start: 0.8935 (mppt) cc_final: 0.8378 (mppt) REVERT: A 426 GLN cc_start: 0.8154 (mt0) cc_final: 0.7626 (mt0) REVERT: B 3 GLU cc_start: 0.7402 (tt0) cc_final: 0.6821 (tt0) REVERT: B 4 ILE cc_start: 0.8466 (tp) cc_final: 0.8175 (tp) REVERT: B 15 TYR cc_start: 0.8505 (t80) cc_final: 0.8122 (t80) REVERT: B 23 MET cc_start: 0.8424 (mmm) cc_final: 0.7789 (mmm) REVERT: B 26 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7025 (mp0) REVERT: B 41 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8426 (ttmt) REVERT: B 43 HIS cc_start: 0.8730 (t-90) cc_final: 0.8108 (t-170) REVERT: B 47 TYR cc_start: 0.8569 (m-80) cc_final: 0.8063 (m-80) REVERT: B 54 ASN cc_start: 0.8485 (m-40) cc_final: 0.8248 (m-40) REVERT: B 95 GLU cc_start: 0.8344 (tt0) cc_final: 0.7913 (tt0) REVERT: B 103 MET cc_start: 0.7893 (mmm) cc_final: 0.7546 (mmm) REVERT: B 109 LYS cc_start: 0.9234 (tptt) cc_final: 0.8625 (tptt) REVERT: B 114 GLN cc_start: 0.8934 (tt0) cc_final: 0.8566 (tt0) REVERT: B 145 SER cc_start: 0.8554 (p) cc_final: 0.7880 (t) REVERT: B 155 MET cc_start: 0.7788 (tpp) cc_final: 0.7333 (tpp) REVERT: B 175 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7701 (mmtt) REVERT: B 194 VAL cc_start: 0.8266 (t) cc_final: 0.7867 (t) REVERT: B 213 ASP cc_start: 0.7856 (m-30) cc_final: 0.7296 (m-30) REVERT: B 226 MET cc_start: 0.8144 (mmm) cc_final: 0.7548 (mmp) REVERT: B 231 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7795 (mm-30) REVERT: B 243 ASP cc_start: 0.7154 (t0) cc_final: 0.6865 (t0) REVERT: B 245 SER cc_start: 0.8320 (t) cc_final: 0.7131 (p) REVERT: B 248 ASP cc_start: 0.7446 (m-30) cc_final: 0.7184 (m-30) REVERT: B 258 GLU cc_start: 0.8369 (pt0) cc_final: 0.8061 (pt0) REVERT: B 265 LYS cc_start: 0.8985 (ttpp) cc_final: 0.8741 (ttpp) REVERT: B 269 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7701 (mtmm) REVERT: B 278 LYS cc_start: 0.8415 (tptp) cc_final: 0.8143 (tptp) REVERT: B 279 GLN cc_start: 0.8445 (tt0) cc_final: 0.7813 (tt0) REVERT: B 300 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7727 (mtpt) REVERT: B 318 SER cc_start: 0.7944 (m) cc_final: 0.7217 (t) REVERT: B 345 GLU cc_start: 0.8132 (tt0) cc_final: 0.7925 (tt0) REVERT: B 384 MET cc_start: 0.8426 (mmm) cc_final: 0.8201 (mmm) REVERT: B 392 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7133 (tm-30) REVERT: B 403 GLN cc_start: 0.6994 (tt0) cc_final: 0.6470 (pt0) REVERT: B 413 LYS cc_start: 0.8687 (tppt) cc_final: 0.8040 (tppt) REVERT: B 414 TRP cc_start: 0.7917 (m100) cc_final: 0.7546 (m100) REVERT: B 419 MET cc_start: 0.4537 (tpp) cc_final: 0.3898 (ttm) REVERT: B 427 LYS cc_start: 0.8078 (tttm) cc_final: 0.7577 (ttmm) REVERT: C 3 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 13 GLN cc_start: 0.7931 (tp40) cc_final: 0.7635 (tp40) REVERT: C 26 GLU cc_start: 0.8150 (pt0) cc_final: 0.7800 (pt0) REVERT: C 41 LYS cc_start: 0.8710 (tttt) cc_final: 0.8248 (tttt) REVERT: C 56 LEU cc_start: 0.9076 (mm) cc_final: 0.8847 (mm) REVERT: C 60 LEU cc_start: 0.8673 (mm) cc_final: 0.8300 (tp) REVERT: C 85 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 154 TRP cc_start: 0.8633 (t60) cc_final: 0.8243 (t60) REVERT: C 166 MET cc_start: 0.7350 (tpt) cc_final: 0.6864 (tpt) REVERT: C 178 ILE cc_start: 0.7913 (tp) cc_final: 0.7538 (mm) REVERT: C 203 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7474 (mtmm) REVERT: C 213 ASP cc_start: 0.8252 (m-30) cc_final: 0.7801 (m-30) REVERT: C 226 MET cc_start: 0.8345 (mmm) cc_final: 0.7920 (mmp) REVERT: C 235 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8590 (ttpp) REVERT: C 238 ASP cc_start: 0.8096 (m-30) cc_final: 0.7597 (m-30) REVERT: C 240 ASN cc_start: 0.8112 (t0) cc_final: 0.7895 (t0) REVERT: C 241 MET cc_start: 0.8089 (mmm) cc_final: 0.7662 (mmm) REVERT: C 288 ASN cc_start: 0.8649 (m110) cc_final: 0.8406 (m110) REVERT: C 292 SER cc_start: 0.9066 (m) cc_final: 0.8683 (t) REVERT: C 312 TYR cc_start: 0.5894 (t80) cc_final: 0.5537 (t80) REVERT: C 315 ILE cc_start: 0.8439 (pt) cc_final: 0.8157 (pt) REVERT: C 318 SER cc_start: 0.7733 (t) cc_final: 0.7257 (p) REVERT: C 333 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7479 (ttpt) REVERT: C 356 VAL cc_start: 0.8408 (m) cc_final: 0.8060 (p) REVERT: C 367 ASN cc_start: 0.7853 (m110) cc_final: 0.7638 (m110) REVERT: C 426 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7220 (mm-40) REVERT: D 2 VAL cc_start: 0.9158 (m) cc_final: 0.8682 (p) REVERT: D 15 TYR cc_start: 0.8144 (t80) cc_final: 0.7447 (t80) REVERT: D 26 GLU cc_start: 0.8024 (pm20) cc_final: 0.7798 (pm20) REVERT: D 41 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8225 (ttpp) REVERT: D 46 GLU cc_start: 0.8178 (tt0) cc_final: 0.7678 (tt0) REVERT: D 47 TYR cc_start: 0.8958 (m-80) cc_final: 0.7838 (m-80) REVERT: D 74 LYS cc_start: 0.8979 (tttp) cc_final: 0.8720 (mmmm) REVERT: D 90 LEU cc_start: 0.8401 (mm) cc_final: 0.8017 (mm) REVERT: D 96 LYS cc_start: 0.8650 (ttmt) cc_final: 0.8429 (ttmt) REVERT: D 109 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7831 (ttmm) REVERT: D 114 GLN cc_start: 0.7334 (mt0) cc_final: 0.7128 (mt0) REVERT: D 143 SER cc_start: 0.9007 (m) cc_final: 0.8329 (t) REVERT: D 154 TRP cc_start: 0.8739 (t60) cc_final: 0.7928 (t60) REVERT: D 155 MET cc_start: 0.7774 (tpt) cc_final: 0.7376 (tpt) REVERT: D 189 THR cc_start: 0.8613 (p) cc_final: 0.7226 (t) REVERT: D 196 MET cc_start: 0.7566 (mtp) cc_final: 0.7239 (mtp) REVERT: D 222 LEU cc_start: 0.8770 (tp) cc_final: 0.8470 (tt) REVERT: D 226 MET cc_start: 0.7132 (mmm) cc_final: 0.6262 (mmm) REVERT: D 276 ILE cc_start: 0.8149 (mt) cc_final: 0.7938 (mt) REVERT: D 280 TYR cc_start: 0.8474 (m-80) cc_final: 0.7928 (m-80) REVERT: D 300 LYS cc_start: 0.8475 (mttm) cc_final: 0.7988 (mttm) REVERT: D 303 PHE cc_start: 0.8305 (t80) cc_final: 0.8072 (t80) REVERT: D 324 TYR cc_start: 0.7707 (m-80) cc_final: 0.7346 (m-80) REVERT: D 329 TYR cc_start: 0.5728 (t80) cc_final: 0.5112 (t80) REVERT: D 333 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7496 (ttmt) REVERT: D 338 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6995 (mt-10) REVERT: D 347 GLU cc_start: 0.7950 (tp30) cc_final: 0.7309 (tp30) REVERT: D 368 MET cc_start: 0.7736 (ttp) cc_final: 0.7499 (ttm) REVERT: D 392 GLU cc_start: 0.7632 (tp30) cc_final: 0.7182 (tp30) REVERT: D 413 LYS cc_start: 0.8609 (mptt) cc_final: 0.8035 (mptt) REVERT: E 1 MET cc_start: 0.7797 (ppp) cc_final: 0.6061 (ppp) REVERT: E 23 MET cc_start: 0.8484 (mmt) cc_final: 0.8239 (mmt) REVERT: E 34 LYS cc_start: 0.8832 (tttp) cc_final: 0.8257 (tttp) REVERT: E 35 ASN cc_start: 0.8438 (m-40) cc_final: 0.7940 (m-40) REVERT: E 38 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8370 (mtpt) REVERT: E 39 LEU cc_start: 0.8710 (mt) cc_final: 0.8422 (mt) REVERT: E 47 TYR cc_start: 0.6333 (t80) cc_final: 0.6066 (t80) REVERT: E 86 ASP cc_start: 0.8497 (t0) cc_final: 0.8221 (t0) REVERT: E 90 LEU cc_start: 0.8610 (tp) cc_final: 0.8381 (tp) REVERT: E 95 GLU cc_start: 0.8620 (tt0) cc_final: 0.7880 (tt0) REVERT: E 139 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7549 (ttp80) REVERT: E 146 PHE cc_start: 0.7429 (m-10) cc_final: 0.6875 (m-10) REVERT: E 181 LYS cc_start: 0.8536 (tmmt) cc_final: 0.8161 (tmmt) REVERT: E 195 LEU cc_start: 0.8052 (tp) cc_final: 0.7707 (tt) REVERT: E 228 MET cc_start: 0.7560 (ptt) cc_final: 0.7250 (ptt) REVERT: E 236 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7701 (ttm110) REVERT: E 253 HIS cc_start: 0.7707 (m90) cc_final: 0.7232 (m90) REVERT: E 271 THR cc_start: 0.9171 (p) cc_final: 0.8732 (t) REVERT: E 296 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7098 (mt-10) REVERT: E 301 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7692 (ptpt) REVERT: E 333 LYS cc_start: 0.7872 (tttp) cc_final: 0.7411 (tttp) REVERT: E 397 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7915 (mt-10) REVERT: F 5 ILE cc_start: 0.8900 (mt) cc_final: 0.8559 (mt) REVERT: F 13 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7939 (tp40) REVERT: F 15 TYR cc_start: 0.8563 (t80) cc_final: 0.7256 (t80) REVERT: F 18 LYS cc_start: 0.8726 (tppt) cc_final: 0.8519 (tppt) REVERT: F 22 TYR cc_start: 0.8438 (m-80) cc_final: 0.8132 (m-10) REVERT: F 29 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7574 (mm-30) REVERT: F 34 LYS cc_start: 0.8932 (ttmt) cc_final: 0.8045 (ttmm) REVERT: F 38 LYS cc_start: 0.9118 (mmtp) cc_final: 0.8754 (mmtp) REVERT: F 43 HIS cc_start: 0.8335 (t-90) cc_final: 0.7724 (t-90) REVERT: F 60 LEU cc_start: 0.8806 (tp) cc_final: 0.8563 (tp) REVERT: F 61 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7425 (mm-30) REVERT: F 79 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8765 (mtmt) REVERT: F 82 ASP cc_start: 0.7496 (t0) cc_final: 0.7196 (t0) REVERT: F 93 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7871 (mm-30) REVERT: F 95 GLU cc_start: 0.8049 (tt0) cc_final: 0.7638 (tt0) REVERT: F 96 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8335 (ttpp) REVERT: F 116 ASN cc_start: 0.8572 (t0) cc_final: 0.7838 (t0) REVERT: F 119 LEU cc_start: 0.8607 (mt) cc_final: 0.8178 (mt) REVERT: F 128 MET cc_start: 0.7615 (ptp) cc_final: 0.7351 (ptt) REVERT: F 155 MET cc_start: 0.6647 (tpp) cc_final: 0.5851 (tpp) REVERT: F 157 ASP cc_start: 0.7849 (m-30) cc_final: 0.7479 (m-30) REVERT: F 158 TYR cc_start: 0.7750 (p90) cc_final: 0.7200 (p90) REVERT: F 183 THR cc_start: 0.8039 (p) cc_final: 0.7509 (t) REVERT: F 184 LYS cc_start: 0.8181 (mmtp) cc_final: 0.7873 (mmmt) REVERT: F 189 THR cc_start: 0.7888 (p) cc_final: 0.7293 (t) REVERT: F 246 LEU cc_start: 0.7352 (mt) cc_final: 0.7149 (mt) REVERT: F 256 TYR cc_start: 0.7653 (t80) cc_final: 0.7131 (t80) REVERT: F 260 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8018 (ttmm) REVERT: F 265 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8334 (mmtm) REVERT: F 291 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7205 (mtt-85) REVERT: F 326 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7397 (mm-30) REVERT: F 333 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8417 (ttpp) REVERT: F 338 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7116 (mm-30) REVERT: F 340 ARG cc_start: 0.8990 (ttt-90) cc_final: 0.8699 (tpt-90) REVERT: F 404 ILE cc_start: 0.8327 (mt) cc_final: 0.7822 (mt) REVERT: F 405 LYS cc_start: 0.7067 (tptp) cc_final: 0.6186 (tppp) REVERT: F 416 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7794 (mtpp) REVERT: F 422 GLN cc_start: 0.7164 (mt0) cc_final: 0.6763 (mt0) REVERT: F 423 LYS cc_start: 0.8848 (mmmt) cc_final: 0.8634 (mmtp) REVERT: G 78 LEU cc_start: 0.9438 (mt) cc_final: 0.9180 (mt) REVERT: G 82 GLU cc_start: 0.8462 (tp30) cc_final: 0.8025 (tp30) REVERT: G 85 LEU cc_start: 0.9324 (mm) cc_final: 0.8720 (mm) REVERT: G 92 GLU cc_start: 0.8542 (tp30) cc_final: 0.6717 (tp30) REVERT: G 95 LYS cc_start: 0.9034 (mtpp) cc_final: 0.8385 (mtpp) REVERT: G 100 SER cc_start: 0.8409 (p) cc_final: 0.7916 (p) REVERT: G 151 LYS cc_start: 0.8826 (ptpp) cc_final: 0.8511 (pttm) REVERT: G 238 ASP cc_start: 0.8448 (m-30) cc_final: 0.7948 (m-30) REVERT: G 279 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8911 (mttm) REVERT: G 307 MET cc_start: 0.8831 (mmt) cc_final: 0.8470 (mmm) REVERT: G 323 LYS cc_start: 0.9321 (pttm) cc_final: 0.8997 (pttp) REVERT: G 330 LEU cc_start: 0.9037 (mm) cc_final: 0.8335 (mm) REVERT: G 333 LYS cc_start: 0.9266 (mptt) cc_final: 0.9011 (mttm) REVERT: G 334 MET cc_start: 0.8656 (ptp) cc_final: 0.8174 (ptp) outliers start: 1 outliers final: 0 residues processed: 1141 average time/residue: 0.1700 time to fit residues: 290.4253 Evaluate side-chains 1059 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1059 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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: 4.9990 chunk 111 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 240 ASN A 302 ASN B 403 GLN D 62 ASN D 100 GLN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 426 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.121047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100095 restraints weight = 49785.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.103555 restraints weight = 26159.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105886 restraints weight = 16201.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107435 restraints weight = 11240.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108417 restraints weight = 8595.663| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24515 Z= 0.286 Angle : 0.754 12.037 33269 Z= 0.398 Chirality : 0.049 0.265 3697 Planarity : 0.005 0.071 4105 Dihedral : 10.435 169.688 3441 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % 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: -0.51 (0.16), residues: 2917 helix: 0.79 (0.14), residues: 1450 sheet: -1.42 (0.27), residues: 368 loop : -1.40 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 236 TYR 0.043 0.002 TYR C 312 PHE 0.025 0.003 PHE D 417 TRP 0.053 0.003 TRP G 159 HIS 0.009 0.001 HIS B 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.29 (24510) covalent geometry : angle 0.75191 / 0.40 (33263) hydrogen bonds : bond 0.03657 / 2.55 ( 1174) hydrogen bonds : angle 5.06289 / 3.60 ( 3363) metal coordination : bond 0.01665 / 0.84 ( 4) metal coordination : angle 4.70094 / 2.30 ( 6) Misc. bond : bond 0.00031 / 0.02 ( 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 1131 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1130 time to evaluate : 0.616 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: A 3 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7445 (mm-30) REVERT: A 11 PHE cc_start: 0.7907 (m-10) cc_final: 0.7431 (m-10) REVERT: A 19 VAL cc_start: 0.8207 (m) cc_final: 0.7943 (p) REVERT: A 26 GLU cc_start: 0.7852 (pm20) cc_final: 0.7389 (pm20) REVERT: A 47 TYR cc_start: 0.6669 (m-80) cc_final: 0.6299 (m-80) REVERT: A 61 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6554 (tm-30) REVERT: A 73 VAL cc_start: 0.8998 (t) cc_final: 0.8519 (p) REVERT: A 79 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8064 (ttmt) REVERT: A 82 ASP cc_start: 0.7565 (t0) cc_final: 0.7285 (t0) REVERT: A 83 SER cc_start: 0.8508 (m) cc_final: 0.8265 (m) REVERT: A 85 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7366 (mm-30) REVERT: A 104 PHE cc_start: 0.7967 (t80) cc_final: 0.7636 (t80) REVERT: A 123 LYS cc_start: 0.8348 (mttp) cc_final: 0.8137 (mttp) REVERT: A 139 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.6843 (ttm-80) REVERT: A 146 PHE cc_start: 0.8590 (m-10) cc_final: 0.8189 (m-80) REVERT: A 150 VAL cc_start: 0.8597 (p) cc_final: 0.7808 (m) REVERT: A 153 ASP cc_start: 0.8703 (t0) cc_final: 0.8339 (t0) REVERT: A 188 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 189 THR cc_start: 0.8350 (p) cc_final: 0.8144 (m) REVERT: A 214 TYR cc_start: 0.8617 (m-80) cc_final: 0.8215 (m-10) REVERT: A 235 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8203 (ttpt) REVERT: A 238 ASP cc_start: 0.8724 (m-30) cc_final: 0.8495 (m-30) REVERT: A 241 MET cc_start: 0.8038 (mmm) cc_final: 0.7483 (mmm) REVERT: A 248 ASP cc_start: 0.7210 (m-30) cc_final: 0.6871 (m-30) REVERT: A 265 LYS cc_start: 0.8903 (ttpp) cc_final: 0.8567 (ttpp) REVERT: A 268 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 278 LYS cc_start: 0.8360 (tptm) cc_final: 0.7737 (mtpp) REVERT: A 279 GLN cc_start: 0.8592 (tt0) cc_final: 0.8365 (tt0) REVERT: A 293 LEU cc_start: 0.8850 (tp) cc_final: 0.8649 (tt) REVERT: A 316 CYS cc_start: 0.8158 (m) cc_final: 0.7627 (m) REVERT: A 384 MET cc_start: 0.8503 (ttt) cc_final: 0.7940 (ttm) REVERT: A 398 GLN cc_start: 0.6873 (mt0) cc_final: 0.6625 (mt0) REVERT: A 415 ASN cc_start: 0.8081 (t0) cc_final: 0.7543 (t0) REVERT: A 416 LYS cc_start: 0.8906 (mppt) cc_final: 0.8363 (mppt) REVERT: A 426 GLN cc_start: 0.8261 (mt0) cc_final: 0.7702 (mt0) REVERT: B 4 ILE cc_start: 0.8678 (tp) cc_final: 0.8361 (tp) REVERT: B 23 MET cc_start: 0.8530 (mmm) cc_final: 0.7932 (mmm) REVERT: B 41 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8489 (ttmt) REVERT: B 47 TYR cc_start: 0.8521 (m-80) cc_final: 0.7766 (m-80) REVERT: B 95 GLU cc_start: 0.8331 (tt0) cc_final: 0.8014 (tt0) REVERT: B 103 MET cc_start: 0.7833 (mmm) cc_final: 0.7551 (mmm) REVERT: B 109 LYS cc_start: 0.9255 (tptt) cc_final: 0.8599 (tptt) REVERT: B 114 GLN cc_start: 0.8920 (tt0) cc_final: 0.8672 (tt0) REVERT: B 155 MET cc_start: 0.7950 (tpp) cc_final: 0.7488 (tpp) REVERT: B 175 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7744 (mmtt) REVERT: B 184 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8165 (mmmt) REVERT: B 213 ASP cc_start: 0.7829 (m-30) cc_final: 0.7308 (m-30) REVERT: B 226 MET cc_start: 0.8233 (mmm) cc_final: 0.7514 (mmp) REVERT: B 231 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7880 (mm-30) REVERT: B 243 ASP cc_start: 0.7130 (t0) cc_final: 0.6836 (t0) REVERT: B 245 SER cc_start: 0.8426 (t) cc_final: 0.7613 (t) REVERT: B 258 GLU cc_start: 0.8382 (pt0) cc_final: 0.8121 (pt0) REVERT: B 265 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8621 (ttpp) REVERT: B 278 LYS cc_start: 0.8486 (tptp) cc_final: 0.8240 (tptp) REVERT: B 279 GLN cc_start: 0.8501 (tt0) cc_final: 0.7922 (tt0) REVERT: B 298 LYS cc_start: 0.8689 (pttp) cc_final: 0.8459 (pttp) REVERT: B 300 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7804 (mtpt) REVERT: B 318 SER cc_start: 0.8061 (m) cc_final: 0.7405 (t) REVERT: B 392 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 403 GLN cc_start: 0.7429 (tt0) cc_final: 0.6625 (pt0) REVERT: B 413 LYS cc_start: 0.8730 (tppt) cc_final: 0.8177 (tppt) REVERT: B 414 TRP cc_start: 0.7973 (m100) cc_final: 0.7541 (m100) REVERT: B 419 MET cc_start: 0.4600 (tpp) cc_final: 0.4242 (ttm) REVERT: B 427 LYS cc_start: 0.8124 (tttm) cc_final: 0.7670 (ttmm) REVERT: C 3 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 13 GLN cc_start: 0.8027 (tp40) cc_final: 0.7705 (tp40) REVERT: C 26 GLU cc_start: 0.8073 (pt0) cc_final: 0.7759 (pt0) REVERT: C 41 LYS cc_start: 0.8728 (tttt) cc_final: 0.8297 (tttt) REVERT: C 60 LEU cc_start: 0.8722 (mm) cc_final: 0.8347 (tp) REVERT: C 85 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7772 (mm-30) REVERT: C 109 LYS cc_start: 0.8921 (tppt) cc_final: 0.8545 (mmmm) REVERT: C 113 ILE cc_start: 0.9068 (mt) cc_final: 0.8820 (mm) REVERT: C 166 MET cc_start: 0.7351 (tpt) cc_final: 0.6757 (tpt) REVERT: C 178 ILE cc_start: 0.8169 (tp) cc_final: 0.7764 (mm) REVERT: C 184 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8437 (mtmm) REVERT: C 203 LYS cc_start: 0.8289 (mtmm) cc_final: 0.7694 (mtmm) REVERT: C 213 ASP cc_start: 0.8303 (m-30) cc_final: 0.7865 (m-30) REVERT: C 226 MET cc_start: 0.8411 (mmm) cc_final: 0.7828 (mmm) REVERT: C 241 MET cc_start: 0.8147 (mmm) cc_final: 0.7601 (mmm) REVERT: C 279 GLN cc_start: 0.8257 (tt0) cc_final: 0.7837 (tt0) REVERT: C 288 ASN cc_start: 0.8636 (m110) cc_final: 0.8342 (m110) REVERT: C 292 SER cc_start: 0.9081 (m) cc_final: 0.8690 (t) REVERT: C 315 ILE cc_start: 0.8555 (pt) cc_final: 0.8313 (pt) REVERT: C 318 SER cc_start: 0.7866 (t) cc_final: 0.7446 (p) REVERT: C 333 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7549 (ttpt) REVERT: C 335 ILE cc_start: 0.8506 (tp) cc_final: 0.8129 (tp) REVERT: C 355 GLN cc_start: 0.6940 (mp10) cc_final: 0.6721 (mp10) REVERT: C 426 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7533 (mm-40) REVERT: D 2 VAL cc_start: 0.9165 (m) cc_final: 0.8701 (p) REVERT: D 15 TYR cc_start: 0.8190 (t80) cc_final: 0.7581 (t80) REVERT: D 26 GLU cc_start: 0.8183 (pm20) cc_final: 0.7921 (pm20) REVERT: D 41 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8238 (ttmm) REVERT: D 74 LYS cc_start: 0.9021 (tttp) cc_final: 0.8749 (mmmm) REVERT: D 90 LEU cc_start: 0.8499 (mm) cc_final: 0.8156 (mm) REVERT: D 118 GLU cc_start: 0.7141 (tp30) cc_final: 0.6765 (tp30) REVERT: D 126 LYS cc_start: 0.8686 (tptt) cc_final: 0.8413 (tptt) REVERT: D 143 SER cc_start: 0.9040 (m) cc_final: 0.8308 (t) REVERT: D 147 ASP cc_start: 0.7439 (p0) cc_final: 0.7132 (p0) REVERT: D 154 TRP cc_start: 0.8861 (t60) cc_final: 0.8483 (t60) REVERT: D 155 MET cc_start: 0.7750 (tpt) cc_final: 0.6697 (tpt) REVERT: D 189 THR cc_start: 0.8681 (p) cc_final: 0.7376 (t) REVERT: D 196 MET cc_start: 0.7285 (mtp) cc_final: 0.6891 (mtp) REVERT: D 223 TYR cc_start: 0.8395 (t80) cc_final: 0.6913 (t80) REVERT: D 226 MET cc_start: 0.7314 (mmm) cc_final: 0.6308 (mmm) REVERT: D 228 MET cc_start: 0.7287 (mtm) cc_final: 0.6974 (ptm) REVERT: D 233 CYS cc_start: 0.7775 (m) cc_final: 0.7083 (m) REVERT: D 241 MET cc_start: 0.8124 (mtp) cc_final: 0.7611 (mtm) REVERT: D 263 MET cc_start: 0.7791 (mmm) cc_final: 0.7566 (mmm) REVERT: D 280 TYR cc_start: 0.8493 (m-80) cc_final: 0.7975 (m-80) REVERT: D 324 TYR cc_start: 0.7850 (m-80) cc_final: 0.7478 (m-80) REVERT: D 326 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7459 (mm-30) REVERT: D 338 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7052 (mt-10) REVERT: D 347 GLU cc_start: 0.7847 (tp30) cc_final: 0.7235 (tp30) REVERT: D 397 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7680 (mt-10) REVERT: E 23 MET cc_start: 0.8501 (mmt) cc_final: 0.8178 (mmt) REVERT: E 34 LYS cc_start: 0.8869 (tttp) cc_final: 0.8354 (tttp) REVERT: E 38 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8452 (mtpt) REVERT: E 39 LEU cc_start: 0.8835 (mt) cc_final: 0.8572 (mt) REVERT: E 41 LYS cc_start: 0.8974 (ttpt) cc_final: 0.8572 (ttpt) REVERT: E 47 TYR cc_start: 0.6516 (t80) cc_final: 0.6207 (t80) REVERT: E 103 MET cc_start: 0.7919 (mmm) cc_final: 0.7540 (mmt) REVERT: E 118 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7881 (mt-10) REVERT: E 168 LYS cc_start: 0.7600 (mmpt) cc_final: 0.7222 (mmpt) REVERT: E 177 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7190 (mtt90) REVERT: E 181 LYS cc_start: 0.8583 (tmmt) cc_final: 0.8260 (tmmt) REVERT: E 195 LEU cc_start: 0.8105 (tp) cc_final: 0.7832 (tt) REVERT: E 226 MET cc_start: 0.5643 (mmm) cc_final: 0.5367 (mmm) REVERT: E 238 ASP cc_start: 0.8822 (m-30) cc_final: 0.8599 (m-30) REVERT: E 248 ASP cc_start: 0.7336 (m-30) cc_final: 0.6975 (m-30) REVERT: E 253 HIS cc_start: 0.7677 (m90) cc_final: 0.7293 (m90) REVERT: E 256 TYR cc_start: 0.8544 (t80) cc_final: 0.8164 (t80) REVERT: E 260 LYS cc_start: 0.8770 (tptm) cc_final: 0.8460 (tptm) REVERT: E 269 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8567 (ttmm) REVERT: E 271 THR cc_start: 0.9186 (p) cc_final: 0.8772 (t) REVERT: E 298 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8462 (mtpp) REVERT: E 301 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7730 (ptpt) REVERT: E 329 TYR cc_start: 0.6725 (t80) cc_final: 0.6506 (t80) REVERT: E 333 LYS cc_start: 0.7958 (tttp) cc_final: 0.7518 (tttp) REVERT: E 423 LYS cc_start: 0.8957 (mttm) cc_final: 0.8755 (mttm) REVERT: F 7 SER cc_start: 0.8889 (m) cc_final: 0.8385 (p) REVERT: F 13 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7908 (tp40) REVERT: F 22 TYR cc_start: 0.8434 (m-80) cc_final: 0.8184 (m-10) REVERT: F 29 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7631 (mm-30) REVERT: F 34 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8109 (ttmm) REVERT: F 38 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8913 (mmtp) REVERT: F 41 LYS cc_start: 0.8812 (tttp) cc_final: 0.8042 (tttp) REVERT: F 60 LEU cc_start: 0.8862 (tp) cc_final: 0.8625 (tp) REVERT: F 61 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7550 (mm-30) REVERT: F 67 GLU cc_start: 0.8023 (tp30) cc_final: 0.7741 (tp30) REVERT: F 79 LYS cc_start: 0.9182 (mtmt) cc_final: 0.8971 (mtmt) REVERT: F 82 ASP cc_start: 0.7516 (t0) cc_final: 0.7166 (t0) REVERT: F 93 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7854 (mm-30) REVERT: F 95 GLU cc_start: 0.8052 (tt0) cc_final: 0.7689 (tt0) REVERT: F 96 LYS cc_start: 0.8811 (ttpp) cc_final: 0.8433 (ttpp) REVERT: F 109 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8079 (ttpt) REVERT: F 116 ASN cc_start: 0.8728 (t0) cc_final: 0.8040 (t0) REVERT: F 119 LEU cc_start: 0.8684 (mt) cc_final: 0.8245 (mt) REVERT: F 123 LYS cc_start: 0.8619 (tppt) cc_final: 0.8323 (tppt) REVERT: F 128 MET cc_start: 0.7616 (ptp) cc_final: 0.7389 (ptt) REVERT: F 149 TYR cc_start: 0.6225 (t80) cc_final: 0.5904 (t80) REVERT: F 155 MET cc_start: 0.6752 (tpp) cc_final: 0.6106 (tpp) REVERT: F 157 ASP cc_start: 0.7692 (m-30) cc_final: 0.7267 (m-30) REVERT: F 158 TYR cc_start: 0.7857 (p90) cc_final: 0.7283 (p90) REVERT: F 183 THR cc_start: 0.8109 (p) cc_final: 0.7601 (t) REVERT: F 184 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7997 (mmmt) REVERT: F 189 THR cc_start: 0.8223 (p) cc_final: 0.7584 (t) REVERT: F 238 ASP cc_start: 0.7843 (m-30) cc_final: 0.7364 (m-30) REVERT: F 246 LEU cc_start: 0.7573 (mt) cc_final: 0.7355 (mt) REVERT: F 260 LYS cc_start: 0.8259 (ttmm) cc_final: 0.8028 (ttmm) REVERT: F 265 LYS cc_start: 0.8892 (mmtm) cc_final: 0.8454 (mmtm) REVERT: F 326 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 333 LYS cc_start: 0.8633 (ttpp) cc_final: 0.8410 (ttpp) REVERT: F 338 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7220 (mm-30) REVERT: F 340 ARG cc_start: 0.9022 (ttt-90) cc_final: 0.8589 (tpt-90) REVERT: F 404 ILE cc_start: 0.8329 (mt) cc_final: 0.8029 (mt) REVERT: F 405 LYS cc_start: 0.6858 (tptp) cc_final: 0.6492 (tppt) REVERT: G 7 ILE cc_start: 0.8862 (tp) cc_final: 0.8261 (tp) REVERT: G 78 LEU cc_start: 0.9430 (mt) cc_final: 0.9146 (mt) REVERT: G 85 LEU cc_start: 0.9281 (mm) cc_final: 0.8680 (mm) REVERT: G 92 GLU cc_start: 0.8654 (tp30) cc_final: 0.7258 (tp30) REVERT: G 95 LYS cc_start: 0.9010 (mtpp) cc_final: 0.8377 (mtpp) REVERT: G 96 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7849 (mm-30) REVERT: G 100 SER cc_start: 0.8720 (p) cc_final: 0.8331 (p) REVERT: G 147 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8048 (mmmt) REVERT: G 238 ASP cc_start: 0.8549 (m-30) cc_final: 0.8127 (m-30) REVERT: G 279 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8852 (mttm) REVERT: G 291 VAL cc_start: 0.7719 (t) cc_final: 0.7455 (t) REVERT: G 293 PHE cc_start: 0.7862 (m-80) cc_final: 0.7326 (m-10) REVERT: G 307 MET cc_start: 0.8874 (mmt) cc_final: 0.8452 (mmm) REVERT: G 330 LEU cc_start: 0.8941 (mm) cc_final: 0.8303 (mm) REVERT: G 333 LYS cc_start: 0.9271 (mptt) cc_final: 0.8849 (mmtt) REVERT: G 334 MET cc_start: 0.8675 (ptp) cc_final: 0.8085 (ptp) outliers start: 1 outliers final: 1 residues processed: 1130 average time/residue: 0.1603 time to fit residues: 272.7984 Evaluate side-chains 1040 residues out of total 2539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1039 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 0.1980 chunk 122 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 169 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 286 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 HIS A 240 ASN A 295 ASN B 403 GLN D 62 ASN D 100 GLN D 114 GLN E 200 ASN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 167 ASN ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 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 ** 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 = 0.3718 r_free = 0.3718 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107821 restraints weight = 48271.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111590 restraints weight = 24950.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114171 restraints weight = 15205.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115868 restraints weight = 10386.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.116861 restraints weight = 7784.939| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 24515 Z= 0.153 Angle : 0.717 12.460 33269 Z= 0.374 Chirality : 0.046 0.288 3697 Planarity : 0.005 0.068 4105 Dihedral : 10.317 164.579 3441 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % 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: -0.41 (0.16), residues: 2917 helix: 0.90 (0.14), residues: 1447 sheet: -1.39 (0.27), residues: 369 loop : -1.40 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 139 TYR 0.037 0.002 TYR G 54 PHE 0.025 0.002 PHE E 146 TRP 0.041 0.002 TRP G 294 HIS 0.010 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24510) covalent geometry : angle 0.71490 / 0.37 (33263) hydrogen bonds : bond 0.03580 / 2.41 ( 1174) hydrogen bonds : angle 4.93578 / 3.51 ( 3363) metal coordination : bond 0.00831 / 0.42 ( 4) metal coordination : angle 4.46567 / 2.34 ( 6) Misc. bond : bond 0.00033 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.28 seconds wall clock time: 94 minutes 28.15 seconds (5668.15 seconds total)