Starting phenix.real_space_refine on Mon May 4 10:15:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ya5_72721/05_2026/9ya5_72721.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 3 5.21 5 S 130 5.16 5 C 12323 2.51 5 N 3379 2.21 5 O 3873 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19724 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3369 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain: "E" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "I" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3369 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain: "K" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2904 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 12, 'TRANS': 357} Chain breaks: 1 Chain: "N" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2899 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 12, 'TRANS': 356} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.25 Number of scatterers: 19724 At special positions: 0 Unit cell: (104.613, 110.767, 198.677, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 130 16.00 P 16 15.00 Mg 3 11.99 O 3873 8.00 N 3379 7.00 C 12323 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 873.5 milliseconds 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4606 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 49.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.115A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.704A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.373A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.509A pdb=" N THR A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.695A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.148A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.141A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 4.017A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.842A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.788A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.096A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.023A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.833A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N CYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.557A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.794A pdb=" N VAL B 326 " --> pdb=" O SER B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.182A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 426 removed outlier: 3.851A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 36 through 43 removed outlier: 4.297A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.639A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.240A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.561A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 195 " --> pdb=" O THR E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.613A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.153A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.860A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 removed outlier: 3.534A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.223A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.787A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 4.236A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.049A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 78 removed outlier: 4.045A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.621A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 112 through 127 removed outlier: 3.824A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS I 127 " --> pdb=" O GLU I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.621A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.779A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 4.196A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 276 through 281 removed outlier: 4.315A pdb=" N GLN I 280 " --> pdb=" O ARG I 276 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR I 281 " --> pdb=" O GLY I 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 276 through 281' Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.563A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.570A pdb=" N MET I 299 " --> pdb=" O SER I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 removed outlier: 3.644A pdb=" N VAL I 326 " --> pdb=" O SER I 322 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.156A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.246A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.829A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 88 removed outlier: 4.140A pdb=" N GLU K 79 " --> pdb=" O ARG K 75 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU K 80 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 removed outlier: 3.545A pdb=" N GLN K 121 " --> pdb=" O GLY K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 163 Processing helix chain 'K' and resid 188 through 203 removed outlier: 3.693A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 291 Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.692A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 353 removed outlier: 3.507A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 379 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 87 removed outlier: 3.603A pdb=" N GLU N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 108 Processing helix chain 'N' and resid 117 through 134 removed outlier: 3.736A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 203 removed outlier: 3.526A pdb=" N ILE N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 289 Processing helix chain 'N' and resid 305 through 308 removed outlier: 3.770A pdb=" N ASP N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 350 removed outlier: 4.050A pdb=" N GLY N 350 " --> pdb=" O ARG N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 379 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.973A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.736A pdb=" N ALA A 374 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.334A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.775A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AA6, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.704A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA8, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.761A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.842A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL I 5 " --> pdb=" O GLN I 134 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N THR I 136 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE I 7 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N SER I 138 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ALA I 9 " --> pdb=" O SER I 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS I 137 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE I 202 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS I 201 " --> pdb=" O PRO I 268 " (cutoff:3.500A) removed outlier: 10.606A pdb=" N PHE I 270 " --> pdb=" O CYS I 201 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.529A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.529A pdb=" N VAL K 8 " --> pdb=" O TYR K 54 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR K 56 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL K 10 " --> pdb=" O TYR K 56 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N CYS K 92 " --> pdb=" O ALA K 326 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL K 328 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE K 94 " --> pdb=" O VAL K 328 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA K 330 " --> pdb=" O PHE K 94 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYR K 96 " --> pdb=" O ALA K 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AB5, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.543A pdb=" N ARG K 167 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AB7, first strand: chain 'N' and resid 54 through 56 removed outlier: 8.536A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET N 327 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG N 324 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 54 through 56 removed outlier: 8.536A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET N 327 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG N 324 " --> pdb=" O ASN N 90 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'N' and resid 168 through 170 Processing sheet with id=AC2, first strand: chain 'N' and resid 205 through 206 985 hydrogen bonds defined for protein. 2838 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.42 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3572 1.32 - 1.45: 5225 1.45 - 1.57: 11096 1.57 - 1.70: 32 1.70 - 1.82: 212 Bond restraints: 20137 Sorted by residual: bond pdb=" N VAL N 205 " pdb=" CA VAL N 205 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.14e-02 7.69e+03 1.20e+01 bond pdb=" N ASN N 211 " pdb=" CA ASN N 211 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.23e-02 6.61e+03 8.36e+00 bond pdb=" CA LYS A 112 " pdb=" C LYS A 112 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.34e-02 5.57e+03 5.80e+00 bond pdb=" N ARG N 216 " pdb=" CA ARG N 216 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.22e-02 6.72e+03 5.78e+00 bond pdb=" N SER N 214 " pdb=" CA SER N 214 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.21e-02 6.83e+03 5.48e+00 ... (remaining 20132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 26906 2.79 - 5.58: 388 5.58 - 8.38: 32 8.38 - 11.17: 6 11.17 - 13.96: 1 Bond angle restraints: 27333 Sorted by residual: angle pdb=" CB MET N 138 " pdb=" CG MET N 138 " pdb=" SD MET N 138 " ideal model delta sigma weight residual 112.70 126.66 -13.96 3.00e+00 1.11e-01 2.17e+01 angle pdb=" CA GLU K 371 " pdb=" CB GLU K 371 " pdb=" CG GLU K 371 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.96e+01 angle pdb=" CB LYS N 48 " pdb=" CG LYS N 48 " pdb=" CD LYS N 48 " ideal model delta sigma weight residual 111.30 120.61 -9.31 2.30e+00 1.89e-01 1.64e+01 angle pdb=" N ILE A 110 " pdb=" CA ILE A 110 " pdb=" C ILE A 110 " ideal model delta sigma weight residual 110.72 114.70 -3.98 1.01e+00 9.80e-01 1.55e+01 angle pdb=" CA LYS N 48 " pdb=" CB LYS N 48 " pdb=" CG LYS N 48 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 27328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 11892 35.93 - 71.87: 352 71.87 - 107.80: 29 107.80 - 143.73: 3 143.73 - 179.67: 3 Dihedral angle restraints: 12279 sinusoidal: 5108 harmonic: 7171 Sorted by residual: dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual -99.13 80.54 -179.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PB GTP E 501 " pdb=" PA GTP E 501 " ideal model delta sinusoidal sigma weight residual 291.08 135.66 155.42 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" CD ARG N 216 " pdb=" NE ARG N 216 " pdb=" CZ ARG N 216 " pdb=" NH1 ARG N 216 " ideal model delta sinusoidal sigma weight residual 0.00 -58.13 58.13 1 1.00e+01 1.00e-02 4.53e+01 ... (remaining 12276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2738 0.081 - 0.161: 261 0.161 - 0.242: 7 0.242 - 0.322: 0 0.322 - 0.403: 1 Chirality restraints: 3007 Sorted by residual: chirality pdb=" CB ILE N 282 " pdb=" CA ILE N 282 " pdb=" CG1 ILE N 282 " pdb=" CG2 ILE N 282 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" C10 TA1 B 502 " pdb=" C02 TA1 B 502 " pdb=" C11 TA1 B 502 " pdb=" C18 TA1 B 502 " both_signs ideal model delta sigma weight residual False 2.54 2.33 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C10 TA1 I 502 " pdb=" C02 TA1 I 502 " pdb=" C11 TA1 I 502 " pdb=" C18 TA1 I 502 " both_signs ideal model delta sigma weight residual False 2.54 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 3004 not shown) Planarity restraints: 3543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 216 " -0.947 9.50e-02 1.11e+02 4.25e-01 1.09e+02 pdb=" NE ARG N 216 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG N 216 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG N 216 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG N 216 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 31 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.79e+00 pdb=" N PRO B 32 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER K 182 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.34e+00 pdb=" C SER K 182 " 0.047 2.00e-02 2.50e+03 pdb=" O SER K 182 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS K 183 " -0.016 2.00e-02 2.50e+03 ... (remaining 3540 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 13 2.54 - 3.13: 15114 3.13 - 3.72: 30282 3.72 - 4.31: 41883 4.31 - 4.90: 72316 Nonbonded interactions: 159608 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.948 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.960 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 2.005 2.170 nonbonded pdb=" OG SER K 104 " pdb="MG MG K 501 " model vdw 2.021 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 2.032 2.170 ... (remaining 159603 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 'E' } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = (chain 'K' and resid 5 through 379) selection = (chain 'N' and resid 5 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.710 Find NCS groups from input model: 0.370 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.005 0.047 20139 Z= 0.213 Angle : 0.779 13.960 27333 Z= 0.402 Chirality : 0.047 0.403 3007 Planarity : 0.009 0.425 3543 Dihedral : 16.840 179.669 7673 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 1.74 % Allowed : 20.40 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.17), residues: 2459 helix: 1.22 (0.16), residues: 1019 sheet: -0.75 (0.23), residues: 457 loop : -1.02 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 320 TYR 0.037 0.001 TYR A 24 PHE 0.040 0.002 PHE B 212 TRP 0.013 0.002 TRP A 21 HIS 0.004 0.001 HIS I 227 Details of bonding type rmsd covalent geometry : bond 0.00467 (20137) covalent geometry : angle 0.77857 (27333) hydrogen bonds : bond 0.16529 ( 927) hydrogen bonds : angle 5.98726 ( 2838) Misc. bond : bond 0.00149 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8715 (mt0) cc_final: 0.8447 (mt0) REVERT: A 39 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7242 (p0) REVERT: A 113 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: A 120 ASP cc_start: 0.8937 (t70) cc_final: 0.8675 (m-30) REVERT: A 253 THR cc_start: 0.8952 (m) cc_final: 0.8658 (p) REVERT: A 290 GLU cc_start: 0.9003 (pt0) cc_final: 0.8593 (pm20) REVERT: A 432 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.5529 (t80) REVERT: B 86 ARG cc_start: 0.5677 (tpt170) cc_final: 0.5083 (tpt170) REVERT: B 125 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 245 GLN cc_start: 0.8708 (mm110) cc_final: 0.8465 (mm-40) REVERT: B 288 GLU cc_start: 0.7763 (tp30) cc_final: 0.7468 (tp30) REVERT: B 297 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7476 (tttt) REVERT: B 347 ASN cc_start: 0.8121 (t0) cc_final: 0.7723 (t0) REVERT: B 383 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8603 (mt-10) REVERT: E 1 MET cc_start: 0.7438 (ppp) cc_final: 0.7234 (ppp) REVERT: E 423 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 432 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.6963 (t80) REVERT: I 124 SER cc_start: 0.8628 (t) cc_final: 0.8292 (p) REVERT: I 125 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7658 (pp20) REVERT: I 172 SER cc_start: 0.8797 (m) cc_final: 0.7978 (t) REVERT: I 205 GLU cc_start: 0.8813 (tp30) cc_final: 0.8283 (tp30) REVERT: I 211 CYS cc_start: 0.9337 (m) cc_final: 0.8929 (m) REVERT: I 213 ARG cc_start: 0.8129 (ttp-110) cc_final: 0.7882 (ttp-110) REVERT: I 295 ASP cc_start: 0.8504 (t0) cc_final: 0.8147 (t0) REVERT: K 25 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8600 (mmpt) REVERT: K 57 TRP cc_start: 0.7210 (t-100) cc_final: 0.6769 (t-100) REVERT: K 145 SER cc_start: 0.7823 (m) cc_final: 0.7613 (p) REVERT: K 147 MET cc_start: 0.8542 (ptt) cc_final: 0.8298 (ptt) REVERT: K 153 ARG cc_start: 0.7425 (mpp-170) cc_final: 0.6982 (ptp-110) REVERT: K 253 GLU cc_start: 0.8323 (tt0) cc_final: 0.7851 (tt0) REVERT: N 20 MET cc_start: 0.8743 (mtm) cc_final: 0.8458 (mtm) REVERT: N 25 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8121 (mmtt) REVERT: N 30 MET cc_start: 0.6281 (mtm) cc_final: 0.5674 (mtm) REVERT: N 72 GLN cc_start: 0.7757 (tp40) cc_final: 0.7275 (tp-100) REVERT: N 108 MET cc_start: 0.7591 (mtt) cc_final: 0.6757 (ppp) REVERT: N 182 SER cc_start: 0.8843 (t) cc_final: 0.8511 (p) REVERT: N 183 LYS cc_start: 0.8962 (mtmm) cc_final: 0.8709 (mtpp) REVERT: N 197 ASP cc_start: 0.8872 (t70) cc_final: 0.8430 (m-30) REVERT: N 200 ASN cc_start: 0.8689 (m-40) cc_final: 0.8338 (m110) REVERT: N 201 LYS cc_start: 0.8587 (tptp) cc_final: 0.8041 (ttpt) REVERT: N 254 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6843 (ttp80) REVERT: N 256 ASP cc_start: 0.8353 (p0) cc_final: 0.8112 (p0) REVERT: N 355 ARG cc_start: 0.8044 (mmm160) cc_final: 0.7494 (tpm-80) outliers start: 37 outliers final: 16 residues processed: 318 average time/residue: 0.6267 time to fit residues: 225.1235 Evaluate side-chains 296 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 343 SER Chi-restraints excluded: chain N residue 242 SER Chi-restraints excluded: chain N residue 362 GLU Chi-restraints excluded: chain N residue 367 LYS Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN I 165 ASN K 16 ASN K 70 GLN K 190 ASN N 200 ASN N 318 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.121310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088016 restraints weight = 31122.012| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.84 r_work: 0.3115 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20139 Z= 0.181 Angle : 0.575 9.235 27333 Z= 0.293 Chirality : 0.045 0.231 3007 Planarity : 0.004 0.069 3543 Dihedral : 10.772 173.403 3070 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 3.28 % Allowed : 18.76 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.40 (0.17), residues: 2459 helix: 1.69 (0.16), residues: 1038 sheet: -0.38 (0.23), residues: 475 loop : -0.98 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 282 TYR 0.026 0.001 TYR A 24 PHE 0.016 0.001 PHE N 94 TRP 0.017 0.002 TRP A 21 HIS 0.003 0.001 HIS K 218 Details of bonding type rmsd covalent geometry : bond 0.00423 (20137) covalent geometry : angle 0.57496 (27333) hydrogen bonds : bond 0.05054 ( 927) hydrogen bonds : angle 4.45828 ( 2838) Misc. bond : bond 0.00090 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 295 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: A 253 THR cc_start: 0.8991 (m) cc_final: 0.8772 (p) REVERT: A 432 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.5695 (t80) REVERT: B 69 GLU cc_start: 0.8500 (pt0) cc_final: 0.7713 (pp20) REVERT: B 86 ARG cc_start: 0.5324 (tpt170) cc_final: 0.4563 (tpt170) REVERT: B 125 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: B 203 ASP cc_start: 0.8215 (t0) cc_final: 0.7905 (t0) REVERT: B 245 GLN cc_start: 0.8614 (mm110) cc_final: 0.8382 (mm-40) REVERT: B 288 GLU cc_start: 0.7769 (tp30) cc_final: 0.7462 (tp30) REVERT: B 295 ASP cc_start: 0.8415 (t0) cc_final: 0.8140 (t0) REVERT: B 297 LYS cc_start: 0.7990 (pttt) cc_final: 0.7497 (ttmt) REVERT: B 347 ASN cc_start: 0.8008 (t0) cc_final: 0.7666 (t0) REVERT: E 290 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7985 (mp0) REVERT: E 423 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8297 (mm-30) REVERT: E 432 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.6845 (t80) REVERT: I 124 SER cc_start: 0.8593 (t) cc_final: 0.8263 (p) REVERT: I 125 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7600 (pp20) REVERT: I 172 SER cc_start: 0.8814 (m) cc_final: 0.7876 (t) REVERT: I 205 GLU cc_start: 0.8766 (tp30) cc_final: 0.8125 (tp30) REVERT: I 211 CYS cc_start: 0.9399 (m) cc_final: 0.8970 (m) REVERT: I 295 ASP cc_start: 0.8284 (t0) cc_final: 0.7979 (t0) REVERT: K 57 TRP cc_start: 0.6746 (t-100) cc_final: 0.6120 (t-100) REVERT: K 145 SER cc_start: 0.8089 (m) cc_final: 0.7729 (p) REVERT: K 153 ARG cc_start: 0.7341 (mpp-170) cc_final: 0.6860 (tpp-160) REVERT: K 221 PHE cc_start: 0.8122 (t80) cc_final: 0.7359 (m-80) REVERT: K 253 GLU cc_start: 0.8178 (tt0) cc_final: 0.7768 (tt0) REVERT: N 13 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7748 (tmm-80) REVERT: N 20 MET cc_start: 0.8689 (mtm) cc_final: 0.8485 (mtm) REVERT: N 22 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7864 (ptm160) REVERT: N 25 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8032 (mmtt) REVERT: N 30 MET cc_start: 0.6158 (mtm) cc_final: 0.5651 (mtm) REVERT: N 72 GLN cc_start: 0.7597 (tp40) cc_final: 0.7149 (tp-100) REVERT: N 108 MET cc_start: 0.7545 (mtt) cc_final: 0.6838 (ppp) REVERT: N 182 SER cc_start: 0.8817 (t) cc_final: 0.8435 (p) REVERT: N 197 ASP cc_start: 0.8895 (t70) cc_final: 0.8401 (m-30) REVERT: N 200 ASN cc_start: 0.8714 (m110) cc_final: 0.8347 (m110) REVERT: N 367 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8970 (tmmt) outliers start: 70 outliers final: 30 residues processed: 335 average time/residue: 0.6203 time to fit residues: 235.1481 Evaluate side-chains 310 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 272 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 248 ASP Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 367 LYS Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 292 GLN E 301 GLN K 227 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.120912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.087569 restraints weight = 31362.500| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.86 r_work: 0.3112 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20139 Z= 0.169 Angle : 0.563 8.057 27333 Z= 0.286 Chirality : 0.044 0.228 3007 Planarity : 0.004 0.069 3543 Dihedral : 10.299 171.689 3048 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.05 % Favored : 96.91 % Rotamer: Outliers : 4.08 % Allowed : 18.62 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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 (0.17), residues: 2459 helix: 1.80 (0.16), residues: 1037 sheet: -0.15 (0.23), residues: 475 loop : -1.03 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 370 TYR 0.025 0.001 TYR A 24 PHE 0.019 0.001 PHE B 212 TRP 0.017 0.002 TRP A 21 HIS 0.003 0.001 HIS K 218 Details of bonding type rmsd covalent geometry : bond 0.00395 (20137) covalent geometry : angle 0.56311 (27333) hydrogen bonds : bond 0.04684 ( 927) hydrogen bonds : angle 4.24858 ( 2838) Misc. bond : bond 0.00092 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 302 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 253 THR cc_start: 0.9118 (m) cc_final: 0.8891 (p) REVERT: A 432 TYR cc_start: 0.8523 (OUTLIER) cc_final: 0.5754 (t80) REVERT: B 31 ASP cc_start: 0.8277 (t0) cc_final: 0.7910 (t0) REVERT: B 69 GLU cc_start: 0.8518 (pt0) cc_final: 0.7686 (pp20) REVERT: B 86 ARG cc_start: 0.5381 (tpt170) cc_final: 0.4980 (tpt170) REVERT: B 125 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 203 ASP cc_start: 0.8181 (t0) cc_final: 0.7825 (t0) REVERT: B 245 GLN cc_start: 0.8629 (mm110) cc_final: 0.8406 (mm-40) REVERT: B 282 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7866 (mtp180) REVERT: B 288 GLU cc_start: 0.7779 (tp30) cc_final: 0.7546 (tp30) REVERT: B 295 ASP cc_start: 0.8403 (t0) cc_final: 0.8012 (t0) REVERT: B 347 ASN cc_start: 0.7997 (t0) cc_final: 0.7661 (t0) REVERT: E 290 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8115 (mp0) REVERT: E 423 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8305 (mm-30) REVERT: E 432 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.6797 (t80) REVERT: I 124 SER cc_start: 0.8600 (t) cc_final: 0.8263 (p) REVERT: I 125 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: I 172 SER cc_start: 0.8867 (m) cc_final: 0.7853 (t) REVERT: I 205 GLU cc_start: 0.8776 (tp30) cc_final: 0.8079 (tp30) REVERT: I 211 CYS cc_start: 0.9385 (m) cc_final: 0.9000 (m) REVERT: I 245 GLN cc_start: 0.8413 (mm110) cc_final: 0.7810 (mt0) REVERT: I 295 ASP cc_start: 0.8322 (t0) cc_final: 0.7988 (t0) REVERT: I 297 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7770 (ttpt) REVERT: K 25 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8495 (mmpt) REVERT: K 153 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7086 (mmt90) REVERT: K 221 PHE cc_start: 0.8255 (t80) cc_final: 0.7413 (m-80) REVERT: K 253 GLU cc_start: 0.8283 (tt0) cc_final: 0.7890 (tt0) REVERT: N 13 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7667 (tmm-80) REVERT: N 22 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7884 (ptm160) REVERT: N 25 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8030 (mmtt) REVERT: N 30 MET cc_start: 0.6229 (mtm) cc_final: 0.5767 (mtm) REVERT: N 72 GLN cc_start: 0.7622 (tp40) cc_final: 0.7161 (tp-100) REVERT: N 108 MET cc_start: 0.7554 (mtt) cc_final: 0.6881 (ppp) REVERT: N 182 SER cc_start: 0.8851 (t) cc_final: 0.8399 (p) REVERT: N 193 GLN cc_start: 0.5388 (OUTLIER) cc_final: 0.4409 (mp10) REVERT: N 197 ASP cc_start: 0.8890 (t70) cc_final: 0.8385 (m-30) REVERT: N 200 ASN cc_start: 0.8734 (m110) cc_final: 0.8378 (m110) REVERT: N 254 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7310 (tpp80) REVERT: N 288 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8849 (ttp) REVERT: N 355 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7571 (tpm-80) REVERT: N 361 ASN cc_start: 0.6035 (OUTLIER) cc_final: 0.5803 (p0) outliers start: 87 outliers final: 41 residues processed: 357 average time/residue: 0.6264 time to fit residues: 253.1911 Evaluate side-chains 325 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 22 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 361 ASN Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 234 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 301 GLN E 301 GLN K 115 GLN K 227 GLN K 235 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.088418 restraints weight = 31274.422| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.85 r_work: 0.3118 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20139 Z= 0.147 Angle : 0.548 7.401 27333 Z= 0.277 Chirality : 0.043 0.225 3007 Planarity : 0.004 0.067 3543 Dihedral : 10.037 171.657 3039 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 4.03 % Allowed : 20.12 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.67 (0.17), residues: 2459 helix: 1.93 (0.16), residues: 1027 sheet: -0.04 (0.23), residues: 485 loop : -0.94 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 84 TYR 0.025 0.001 TYR A 24 PHE 0.014 0.001 PHE K 303 TRP 0.016 0.001 TRP A 21 HIS 0.003 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00337 (20137) covalent geometry : angle 0.54826 (27333) hydrogen bonds : bond 0.04348 ( 927) hydrogen bonds : angle 4.11628 ( 2838) Misc. bond : bond 0.00070 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 288 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 432 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.5809 (t80) REVERT: B 31 ASP cc_start: 0.8294 (t0) cc_final: 0.7926 (t0) REVERT: B 86 ARG cc_start: 0.5371 (tpt170) cc_final: 0.4942 (tpt170) REVERT: B 125 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7333 (mp0) REVERT: B 203 ASP cc_start: 0.8149 (t0) cc_final: 0.7841 (t0) REVERT: B 245 GLN cc_start: 0.8624 (mm110) cc_final: 0.8405 (mm-40) REVERT: B 288 GLU cc_start: 0.7780 (tp30) cc_final: 0.7543 (tp30) REVERT: B 295 ASP cc_start: 0.8416 (t0) cc_final: 0.7998 (t0) REVERT: B 347 ASN cc_start: 0.8005 (t0) cc_final: 0.7670 (t0) REVERT: E 290 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8116 (mp0) REVERT: E 386 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8441 (mt-10) REVERT: E 423 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8303 (mm-30) REVERT: E 432 TYR cc_start: 0.8713 (OUTLIER) cc_final: 0.6714 (t80) REVERT: I 124 SER cc_start: 0.8530 (t) cc_final: 0.8181 (p) REVERT: I 125 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: I 172 SER cc_start: 0.8893 (m) cc_final: 0.7894 (t) REVERT: I 205 GLU cc_start: 0.8777 (tp30) cc_final: 0.8082 (tp30) REVERT: I 211 CYS cc_start: 0.9375 (m) cc_final: 0.9011 (m) REVERT: I 245 GLN cc_start: 0.8407 (mm110) cc_final: 0.7830 (mt0) REVERT: I 295 ASP cc_start: 0.8285 (t0) cc_final: 0.7948 (t0) REVERT: I 297 LYS cc_start: 0.8172 (ttpt) cc_final: 0.7757 (ttpt) REVERT: K 25 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8506 (mmpt) REVERT: K 153 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.7089 (mmp80) REVERT: K 221 PHE cc_start: 0.8153 (t80) cc_final: 0.7349 (m-80) REVERT: K 253 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: N 13 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7706 (tmm-80) REVERT: N 20 MET cc_start: 0.8548 (mtm) cc_final: 0.8314 (mtm) REVERT: N 72 GLN cc_start: 0.7605 (tp40) cc_final: 0.7145 (tp-100) REVERT: N 108 MET cc_start: 0.7602 (mtt) cc_final: 0.6998 (ppp) REVERT: N 113 LYS cc_start: 0.8088 (mttp) cc_final: 0.7808 (pptt) REVERT: N 182 SER cc_start: 0.8848 (t) cc_final: 0.8382 (p) REVERT: N 193 GLN cc_start: 0.5369 (OUTLIER) cc_final: 0.4358 (mp10) REVERT: N 197 ASP cc_start: 0.8892 (t70) cc_final: 0.8388 (m-30) REVERT: N 200 ASN cc_start: 0.8759 (m110) cc_final: 0.8420 (m110) REVERT: N 210 MET cc_start: 0.7016 (tpp) cc_final: 0.6739 (tpp) REVERT: N 288 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8978 (ttt) REVERT: N 355 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7525 (tpm-80) outliers start: 86 outliers final: 47 residues processed: 336 average time/residue: 0.6211 time to fit residues: 236.6745 Evaluate side-chains 333 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 26 CYS Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 288 MET Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 42 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 242 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN B 348 ASN B 375 GLN B 426 GLN E 301 GLN I 165 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.119714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.086752 restraints weight = 31207.796| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.83 r_work: 0.3093 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20139 Z= 0.190 Angle : 0.578 7.949 27333 Z= 0.294 Chirality : 0.044 0.231 3007 Planarity : 0.004 0.069 3543 Dihedral : 10.091 170.526 3039 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 4.55 % Allowed : 20.59 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.63 (0.17), residues: 2459 helix: 1.83 (0.16), residues: 1031 sheet: 0.09 (0.23), residues: 475 loop : -0.97 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 215 TYR 0.024 0.001 TYR A 24 PHE 0.022 0.002 PHE N 221 TRP 0.017 0.002 TRP A 21 HIS 0.003 0.001 HIS K 218 Details of bonding type rmsd covalent geometry : bond 0.00444 (20137) covalent geometry : angle 0.57801 (27333) hydrogen bonds : bond 0.04719 ( 927) hydrogen bonds : angle 4.17628 ( 2838) Misc. bond : bond 0.00114 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 284 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7082 (p0) REVERT: A 113 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: A 215 ARG cc_start: 0.7712 (tpt90) cc_final: 0.7269 (ttm110) REVERT: A 417 GLU cc_start: 0.8863 (mp0) cc_final: 0.8398 (mp0) REVERT: A 432 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.5818 (t80) REVERT: B 31 ASP cc_start: 0.8321 (t0) cc_final: 0.7972 (t0) REVERT: B 69 GLU cc_start: 0.8478 (pt0) cc_final: 0.7613 (pp20) REVERT: B 86 ARG cc_start: 0.5460 (tpt170) cc_final: 0.4972 (tpt170) REVERT: B 125 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 203 ASP cc_start: 0.8175 (t0) cc_final: 0.7865 (t0) REVERT: B 245 GLN cc_start: 0.8633 (mm110) cc_final: 0.8414 (mm-40) REVERT: B 288 GLU cc_start: 0.7819 (tp30) cc_final: 0.7577 (tp30) REVERT: B 295 ASP cc_start: 0.8277 (t0) cc_final: 0.7881 (t0) REVERT: B 347 ASN cc_start: 0.8028 (t0) cc_final: 0.7699 (t0) REVERT: E 230 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8473 (mp) REVERT: E 290 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8139 (mp0) REVERT: E 386 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: E 423 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8258 (mm-30) REVERT: E 432 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.6788 (t80) REVERT: I 124 SER cc_start: 0.8609 (t) cc_final: 0.8270 (p) REVERT: I 125 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7593 (pp20) REVERT: I 170 MET cc_start: 0.8569 (mtm) cc_final: 0.8185 (mtt) REVERT: I 172 SER cc_start: 0.8934 (m) cc_final: 0.7912 (t) REVERT: I 205 GLU cc_start: 0.8755 (tp30) cc_final: 0.8034 (tp30) REVERT: I 211 CYS cc_start: 0.9357 (m) cc_final: 0.8987 (m) REVERT: I 245 GLN cc_start: 0.8420 (mm110) cc_final: 0.7833 (mt0) REVERT: I 295 ASP cc_start: 0.8300 (t0) cc_final: 0.7912 (t0) REVERT: I 297 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7557 (ttmt) REVERT: K 25 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8493 (mmpt) REVERT: K 138 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5342 (mmm) REVERT: K 153 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7092 (mmp80) REVERT: K 221 PHE cc_start: 0.8228 (t80) cc_final: 0.7410 (m-80) REVERT: K 253 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: N 13 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7672 (tmm-80) REVERT: N 30 MET cc_start: 0.6257 (mtm) cc_final: 0.5752 (mtm) REVERT: N 72 GLN cc_start: 0.7604 (tp40) cc_final: 0.7114 (tp-100) REVERT: N 108 MET cc_start: 0.7577 (mtt) cc_final: 0.7029 (ppp) REVERT: N 148 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: N 182 SER cc_start: 0.8870 (t) cc_final: 0.8378 (p) REVERT: N 193 GLN cc_start: 0.5347 (OUTLIER) cc_final: 0.4361 (mp10) REVERT: N 197 ASP cc_start: 0.8883 (t70) cc_final: 0.8378 (m-30) REVERT: N 200 ASN cc_start: 0.8776 (m110) cc_final: 0.8430 (m110) REVERT: N 210 MET cc_start: 0.6988 (tpp) cc_final: 0.6654 (tpp) REVERT: N 355 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7644 (tpm-80) outliers start: 97 outliers final: 53 residues processed: 340 average time/residue: 0.6336 time to fit residues: 242.8550 Evaluate side-chains 338 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 271 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 113 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 275 SER Chi-restraints excluded: chain I residue 293 MET Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain K residue 335 ASP Chi-restraints excluded: chain N residue 6 VAL Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 44 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 206 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 237 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 156 optimal weight: 0.0370 chunk 119 optimal weight: 5.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN B 426 GLN E 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.122456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.089366 restraints weight = 30854.229| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.86 r_work: 0.3137 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20139 Z= 0.121 Angle : 0.552 9.862 27333 Z= 0.277 Chirality : 0.043 0.224 3007 Planarity : 0.004 0.064 3543 Dihedral : 9.917 171.758 3039 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.56 % Allowed : 21.72 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.77 (0.17), residues: 2459 helix: 2.01 (0.17), residues: 1029 sheet: 0.20 (0.23), residues: 484 loop : -1.01 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 339 TYR 0.028 0.001 TYR A 24 PHE 0.022 0.001 PHE B 212 TRP 0.016 0.001 TRP E 21 HIS 0.003 0.001 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00274 (20137) covalent geometry : angle 0.55160 (27333) hydrogen bonds : bond 0.03927 ( 927) hydrogen bonds : angle 3.98339 ( 2838) Misc. bond : bond 0.00040 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 309 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 120 ASP cc_start: 0.8913 (t70) cc_final: 0.8534 (m-30) REVERT: A 215 ARG cc_start: 0.7730 (tpt90) cc_final: 0.7280 (ttm110) REVERT: A 290 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: A 417 GLU cc_start: 0.8879 (mp0) cc_final: 0.8429 (mp0) REVERT: A 432 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.5782 (t80) REVERT: B 31 ASP cc_start: 0.8309 (t0) cc_final: 0.7962 (t0) REVERT: B 69 GLU cc_start: 0.8452 (pt0) cc_final: 0.7609 (pp20) REVERT: B 86 ARG cc_start: 0.5397 (tpt170) cc_final: 0.4870 (tpt170) REVERT: B 125 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 203 ASP cc_start: 0.8145 (t0) cc_final: 0.7844 (t0) REVERT: B 245 GLN cc_start: 0.8644 (mm110) cc_final: 0.8407 (mm-40) REVERT: B 288 GLU cc_start: 0.7774 (tp30) cc_final: 0.7484 (OUTLIER) REVERT: B 295 ASP cc_start: 0.8433 (t0) cc_final: 0.8020 (t0) REVERT: B 312 THR cc_start: 0.9225 (m) cc_final: 0.8764 (p) REVERT: B 347 ASN cc_start: 0.7969 (t0) cc_final: 0.7624 (t0) REVERT: E 230 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8438 (mp) REVERT: E 290 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8129 (mp0) REVERT: E 423 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8265 (mm-30) REVERT: E 432 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.6761 (t80) REVERT: I 124 SER cc_start: 0.8503 (t) cc_final: 0.8164 (p) REVERT: I 125 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7541 (pp20) REVERT: I 172 SER cc_start: 0.8939 (m) cc_final: 0.7927 (t) REVERT: I 205 GLU cc_start: 0.8764 (tp30) cc_final: 0.8056 (tp30) REVERT: I 211 CYS cc_start: 0.9337 (m) cc_final: 0.8987 (m) REVERT: I 245 GLN cc_start: 0.8395 (mm110) cc_final: 0.7844 (mt0) REVERT: I 295 ASP cc_start: 0.8238 (t0) cc_final: 0.7865 (t0) REVERT: I 297 LYS cc_start: 0.8208 (ttpt) cc_final: 0.7610 (ttmt) REVERT: I 343 GLU cc_start: 0.8947 (pm20) cc_final: 0.8466 (pm20) REVERT: K 25 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8541 (mmpt) REVERT: K 138 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5590 (mmm) REVERT: K 153 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7089 (mmp80) REVERT: K 161 LYS cc_start: 0.9185 (mppt) cc_final: 0.8862 (ptpp) REVERT: K 221 PHE cc_start: 0.8186 (t80) cc_final: 0.7451 (m-80) REVERT: K 253 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: N 13 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7684 (tmm-80) REVERT: N 20 MET cc_start: 0.8553 (mtm) cc_final: 0.8297 (mtm) REVERT: N 72 GLN cc_start: 0.7586 (tp40) cc_final: 0.7112 (tp-100) REVERT: N 108 MET cc_start: 0.7628 (mtt) cc_final: 0.7017 (ppp) REVERT: N 115 GLN cc_start: 0.8361 (mp10) cc_final: 0.8110 (mp10) REVERT: N 182 SER cc_start: 0.8882 (t) cc_final: 0.8370 (p) REVERT: N 193 GLN cc_start: 0.5351 (OUTLIER) cc_final: 0.4334 (mp10) REVERT: N 197 ASP cc_start: 0.8892 (t70) cc_final: 0.8396 (m-30) REVERT: N 200 ASN cc_start: 0.8739 (m110) cc_final: 0.8407 (m110) REVERT: N 210 MET cc_start: 0.7011 (tpp) cc_final: 0.6680 (tpp) REVERT: N 355 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7689 (tpm-80) outliers start: 76 outliers final: 40 residues processed: 356 average time/residue: 0.6188 time to fit residues: 250.3594 Evaluate side-chains 333 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 282 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 60 THR Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 241 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 GLN E 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.120706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.087611 restraints weight = 31237.549| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.86 r_work: 0.3105 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20139 Z= 0.172 Angle : 0.588 9.645 27333 Z= 0.296 Chirality : 0.044 0.241 3007 Planarity : 0.004 0.064 3543 Dihedral : 9.975 170.896 3039 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.75 % Allowed : 22.28 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.69 (0.17), residues: 2459 helix: 1.91 (0.16), residues: 1029 sheet: 0.20 (0.23), residues: 489 loop : -1.03 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 339 TYR 0.026 0.001 TYR A 24 PHE 0.028 0.001 PHE N 221 TRP 0.042 0.002 TRP K 57 HIS 0.003 0.001 HIS K 218 Details of bonding type rmsd covalent geometry : bond 0.00402 (20137) covalent geometry : angle 0.58757 (27333) hydrogen bonds : bond 0.04402 ( 927) hydrogen bonds : angle 4.08187 ( 2838) Misc. bond : bond 0.00101 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 283 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7086 (p0) REVERT: A 120 ASP cc_start: 0.8921 (t70) cc_final: 0.8530 (m-30) REVERT: A 215 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7582 (tpp80) REVERT: A 290 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8610 (pm20) REVERT: A 432 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.5805 (t80) REVERT: B 31 ASP cc_start: 0.8291 (t0) cc_final: 0.7912 (t0) REVERT: B 69 GLU cc_start: 0.8570 (pt0) cc_final: 0.7639 (pp20) REVERT: B 86 ARG cc_start: 0.5359 (tpt170) cc_final: 0.4795 (tpt170) REVERT: B 125 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: B 203 ASP cc_start: 0.8179 (t0) cc_final: 0.7840 (t0) REVERT: B 245 GLN cc_start: 0.8637 (mm110) cc_final: 0.8401 (mm-40) REVERT: B 288 GLU cc_start: 0.7808 (tp30) cc_final: 0.7562 (tp30) REVERT: B 295 ASP cc_start: 0.8282 (t0) cc_final: 0.7883 (t0) REVERT: B 347 ASN cc_start: 0.8004 (t0) cc_final: 0.7661 (t0) REVERT: E 230 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8457 (mp) REVERT: E 290 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8129 (mp0) REVERT: E 386 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8450 (mt-10) REVERT: E 423 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8279 (mm-30) REVERT: E 432 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.6762 (t80) REVERT: I 124 SER cc_start: 0.8530 (t) cc_final: 0.8180 (p) REVERT: I 125 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7566 (pp20) REVERT: I 205 GLU cc_start: 0.8745 (tp30) cc_final: 0.8232 (tp30) REVERT: I 211 CYS cc_start: 0.9348 (m) cc_final: 0.8997 (m) REVERT: I 245 GLN cc_start: 0.8414 (mm110) cc_final: 0.7851 (mt0) REVERT: I 295 ASP cc_start: 0.8265 (t0) cc_final: 0.7846 (t0) REVERT: I 297 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7610 (ttmt) REVERT: I 343 GLU cc_start: 0.8954 (pm20) cc_final: 0.8427 (pm20) REVERT: K 25 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8541 (mmpt) REVERT: K 138 MET cc_start: 0.5893 (OUTLIER) cc_final: 0.5535 (mmm) REVERT: K 153 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6930 (tpp-160) REVERT: K 161 LYS cc_start: 0.9243 (mppt) cc_final: 0.8960 (ptpp) REVERT: K 221 PHE cc_start: 0.8157 (t80) cc_final: 0.7387 (m-80) REVERT: K 253 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: N 13 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7655 (tmm-80) REVERT: N 20 MET cc_start: 0.8545 (mtm) cc_final: 0.8256 (mtm) REVERT: N 30 MET cc_start: 0.6360 (mtm) cc_final: 0.5733 (mtm) REVERT: N 42 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8178 (mm110) REVERT: N 72 GLN cc_start: 0.7585 (tp40) cc_final: 0.7088 (tp-100) REVERT: N 108 MET cc_start: 0.7603 (mtt) cc_final: 0.7005 (ppp) REVERT: N 148 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: N 182 SER cc_start: 0.8850 (t) cc_final: 0.8334 (p) REVERT: N 193 GLN cc_start: 0.5335 (OUTLIER) cc_final: 0.4336 (mp10) REVERT: N 197 ASP cc_start: 0.8882 (t70) cc_final: 0.8376 (m-30) REVERT: N 200 ASN cc_start: 0.8742 (m110) cc_final: 0.8412 (m110) REVERT: N 355 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7723 (tpm-80) outliers start: 80 outliers final: 46 residues processed: 332 average time/residue: 0.6607 time to fit residues: 247.1520 Evaluate side-chains 336 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 168 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 81 MET Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 301 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 0 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 86 optimal weight: 0.0570 chunk 133 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 192 optimal weight: 10.0000 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 GLN E 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.123288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.090308 restraints weight = 30951.293| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.86 r_work: 0.3152 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20139 Z= 0.116 Angle : 0.566 10.309 27333 Z= 0.283 Chirality : 0.043 0.220 3007 Planarity : 0.004 0.061 3543 Dihedral : 9.817 171.972 3039 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.24 % Allowed : 22.80 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.78 (0.17), residues: 2459 helix: 1.98 (0.16), residues: 1041 sheet: 0.31 (0.23), residues: 483 loop : -1.07 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 339 TYR 0.031 0.001 TYR A 24 PHE 0.023 0.001 PHE B 212 TRP 0.039 0.002 TRP K 57 HIS 0.003 0.000 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00261 (20137) covalent geometry : angle 0.56556 (27333) hydrogen bonds : bond 0.03717 ( 927) hydrogen bonds : angle 3.92371 ( 2838) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 39 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7089 (p0) REVERT: A 120 ASP cc_start: 0.8902 (t70) cc_final: 0.8520 (m-30) REVERT: A 215 ARG cc_start: 0.7779 (tpt90) cc_final: 0.7282 (ttm110) REVERT: A 290 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8640 (pm20) REVERT: A 417 GLU cc_start: 0.8903 (mp0) cc_final: 0.8231 (mp0) REVERT: A 432 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.5907 (t80) REVERT: B 31 ASP cc_start: 0.8317 (t0) cc_final: 0.7968 (t0) REVERT: B 69 GLU cc_start: 0.8525 (pt0) cc_final: 0.7611 (pp20) REVERT: B 86 ARG cc_start: 0.5315 (tpt170) cc_final: 0.4772 (tpt170) REVERT: B 125 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: B 203 ASP cc_start: 0.8163 (t0) cc_final: 0.7837 (t0) REVERT: B 245 GLN cc_start: 0.8616 (mm110) cc_final: 0.8392 (mm-40) REVERT: B 288 GLU cc_start: 0.7760 (tp30) cc_final: 0.7386 (tt0) REVERT: B 295 ASP cc_start: 0.8330 (t0) cc_final: 0.7946 (t0) REVERT: B 312 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 347 ASN cc_start: 0.7960 (t0) cc_final: 0.7628 (t0) REVERT: E 230 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8410 (mp) REVERT: E 290 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8130 (mp0) REVERT: E 423 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8254 (mm-30) REVERT: E 432 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.6746 (t80) REVERT: I 124 SER cc_start: 0.8544 (t) cc_final: 0.8167 (p) REVERT: I 125 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7561 (pp20) REVERT: I 205 GLU cc_start: 0.8769 (tp30) cc_final: 0.8279 (tp30) REVERT: I 211 CYS cc_start: 0.9327 (m) cc_final: 0.8986 (m) REVERT: I 245 GLN cc_start: 0.8402 (mm110) cc_final: 0.7882 (mt0) REVERT: I 295 ASP cc_start: 0.8203 (t0) cc_final: 0.7814 (t0) REVERT: I 297 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7555 (ttmt) REVERT: I 343 GLU cc_start: 0.8953 (pm20) cc_final: 0.8439 (pm20) REVERT: K 25 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8566 (mmpt) REVERT: K 71 LYS cc_start: 0.7042 (pttt) cc_final: 0.6082 (pptt) REVERT: K 75 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7708 (mtt180) REVERT: K 138 MET cc_start: 0.5980 (OUTLIER) cc_final: 0.5656 (mmm) REVERT: K 153 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6946 (tpp-160) REVERT: K 221 PHE cc_start: 0.8183 (t80) cc_final: 0.7476 (m-80) REVERT: K 253 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7782 (tt0) REVERT: N 13 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7675 (tmm-80) REVERT: N 20 MET cc_start: 0.8608 (mtm) cc_final: 0.8339 (mtm) REVERT: N 30 MET cc_start: 0.6352 (mtm) cc_final: 0.5844 (mtm) REVERT: N 72 GLN cc_start: 0.7584 (tp40) cc_final: 0.7109 (tp-100) REVERT: N 108 MET cc_start: 0.7563 (mtt) cc_final: 0.6939 (ppp) REVERT: N 148 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: N 182 SER cc_start: 0.8839 (t) cc_final: 0.8342 (p) REVERT: N 193 GLN cc_start: 0.5282 (OUTLIER) cc_final: 0.4306 (mp10) REVERT: N 197 ASP cc_start: 0.8920 (t70) cc_final: 0.8427 (m-30) REVERT: N 200 ASN cc_start: 0.8683 (m110) cc_final: 0.8384 (m110) REVERT: N 201 LYS cc_start: 0.8545 (tptp) cc_final: 0.8013 (ttpt) REVERT: N 264 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7895 (tpp-160) REVERT: N 355 ARG cc_start: 0.8067 (mmm160) cc_final: 0.7769 (tpm-80) outliers start: 69 outliers final: 34 residues processed: 339 average time/residue: 0.6347 time to fit residues: 243.4862 Evaluate side-chains 323 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 275 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 220 VAL Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 37 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 0.0070 chunk 159 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 301 GLN I 396 HIS ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.125578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092535 restraints weight = 30795.670| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.87 r_work: 0.3190 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20139 Z= 0.106 Angle : 0.569 11.025 27333 Z= 0.282 Chirality : 0.043 0.216 3007 Planarity : 0.004 0.071 3543 Dihedral : 9.710 172.224 3039 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.35 % Allowed : 24.25 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.82 (0.17), residues: 2459 helix: 2.01 (0.17), residues: 1047 sheet: 0.30 (0.23), residues: 489 loop : -1.04 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 359 TYR 0.031 0.001 TYR A 24 PHE 0.032 0.001 PHE N 221 TRP 0.027 0.002 TRP K 57 HIS 0.003 0.000 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00235 (20137) covalent geometry : angle 0.56949 (27333) hydrogen bonds : bond 0.03429 ( 927) hydrogen bonds : angle 3.85103 ( 2838) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 308 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8913 (t70) cc_final: 0.8531 (m-30) REVERT: A 215 ARG cc_start: 0.7807 (tpt90) cc_final: 0.7323 (ttm110) REVERT: A 417 GLU cc_start: 0.8896 (mp0) cc_final: 0.8167 (mp0) REVERT: A 432 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.5633 (t80) REVERT: B 31 ASP cc_start: 0.8319 (t0) cc_final: 0.8000 (t0) REVERT: B 69 GLU cc_start: 0.8379 (pt0) cc_final: 0.8021 (mm-30) REVERT: B 86 ARG cc_start: 0.5230 (tpt170) cc_final: 0.4579 (tpt170) REVERT: B 125 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 203 ASP cc_start: 0.8151 (t0) cc_final: 0.7833 (t0) REVERT: B 213 ARG cc_start: 0.8274 (ttp80) cc_final: 0.8060 (ttp-170) REVERT: B 245 GLN cc_start: 0.8581 (mm110) cc_final: 0.8361 (mm-40) REVERT: B 288 GLU cc_start: 0.7678 (tp30) cc_final: 0.7413 (tm-30) REVERT: B 295 ASP cc_start: 0.8537 (t0) cc_final: 0.8117 (t0) REVERT: B 312 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8788 (p) REVERT: B 320 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8686 (ttm-80) REVERT: B 347 ASN cc_start: 0.7951 (t0) cc_final: 0.7625 (t0) REVERT: E 168 GLU cc_start: 0.8980 (pt0) cc_final: 0.8662 (pt0) REVERT: E 230 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8366 (mp) REVERT: E 290 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8150 (mp0) REVERT: E 423 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8297 (mm-30) REVERT: E 432 TYR cc_start: 0.8381 (OUTLIER) cc_final: 0.6635 (t80) REVERT: E 434 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: I 125 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7617 (pp20) REVERT: I 211 CYS cc_start: 0.9268 (m) cc_final: 0.8944 (m) REVERT: I 245 GLN cc_start: 0.8381 (mm110) cc_final: 0.7927 (mt0) REVERT: I 295 ASP cc_start: 0.8166 (t0) cc_final: 0.7756 (t0) REVERT: I 297 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7545 (ttmt) REVERT: I 343 GLU cc_start: 0.8941 (pm20) cc_final: 0.8436 (pm20) REVERT: K 25 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8590 (mmpt) REVERT: K 67 TYR cc_start: 0.7281 (t80) cc_final: 0.6913 (t80) REVERT: K 71 LYS cc_start: 0.7021 (pttt) cc_final: 0.6528 (pptt) REVERT: K 138 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5550 (mmm) REVERT: K 153 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6989 (tpp-160) REVERT: K 161 LYS cc_start: 0.9254 (mppt) cc_final: 0.8897 (ptpp) REVERT: K 221 PHE cc_start: 0.8173 (t80) cc_final: 0.7497 (m-80) REVERT: K 253 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: K 256 ASP cc_start: 0.8162 (p0) cc_final: 0.7699 (m-30) REVERT: N 13 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7651 (tmm-80) REVERT: N 20 MET cc_start: 0.8580 (mtm) cc_final: 0.8350 (mtm) REVERT: N 30 MET cc_start: 0.6276 (mtm) cc_final: 0.5781 (mtm) REVERT: N 72 GLN cc_start: 0.7498 (tp40) cc_final: 0.7017 (tp-100) REVERT: N 108 MET cc_start: 0.7447 (mtt) cc_final: 0.6776 (ppp) REVERT: N 148 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: N 182 SER cc_start: 0.8861 (t) cc_final: 0.8282 (p) REVERT: N 193 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4276 (mp10) REVERT: N 197 ASP cc_start: 0.8915 (t70) cc_final: 0.8415 (m-30) REVERT: N 200 ASN cc_start: 0.8655 (m110) cc_final: 0.8363 (m110) REVERT: N 201 LYS cc_start: 0.8528 (tptp) cc_final: 0.8011 (ttpt) REVERT: N 355 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7785 (tpm-80) outliers start: 50 outliers final: 26 residues processed: 337 average time/residue: 0.6521 time to fit residues: 248.1262 Evaluate side-chains 320 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 371 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 178 optimal weight: 5.9990 chunk 157 optimal weight: 0.6980 chunk 140 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 ASN B 426 GLN E 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.125062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.092025 restraints weight = 30817.348| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.85 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20139 Z= 0.115 Angle : 0.590 11.959 27333 Z= 0.291 Chirality : 0.043 0.211 3007 Planarity : 0.004 0.066 3543 Dihedral : 9.656 171.543 3039 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.25 % Allowed : 24.77 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.88 (0.17), residues: 2459 helix: 2.06 (0.17), residues: 1039 sheet: 0.40 (0.23), residues: 481 loop : -1.02 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 339 TYR 0.033 0.001 TYR A 24 PHE 0.034 0.001 PHE N 221 TRP 0.025 0.001 TRP K 57 HIS 0.003 0.000 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00264 (20137) covalent geometry : angle 0.58971 (27333) hydrogen bonds : bond 0.03553 ( 927) hydrogen bonds : angle 3.85995 ( 2838) Misc. bond : bond 0.00034 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8884 (t70) cc_final: 0.8589 (m-30) REVERT: A 215 ARG cc_start: 0.7813 (tpt90) cc_final: 0.7606 (tpp80) REVERT: A 417 GLU cc_start: 0.8875 (mp0) cc_final: 0.8493 (mp0) REVERT: A 432 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.5591 (t80) REVERT: B 31 ASP cc_start: 0.8305 (t0) cc_final: 0.8001 (t0) REVERT: B 69 GLU cc_start: 0.8311 (pt0) cc_final: 0.8032 (mm-30) REVERT: B 86 ARG cc_start: 0.5343 (tpt170) cc_final: 0.4708 (tpt170) REVERT: B 125 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: B 143 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 203 ASP cc_start: 0.8174 (t0) cc_final: 0.7856 (t0) REVERT: B 213 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8076 (ttp-170) REVERT: B 245 GLN cc_start: 0.8539 (mm110) cc_final: 0.8325 (mm-40) REVERT: B 288 GLU cc_start: 0.7753 (tp30) cc_final: 0.7487 (tm-30) REVERT: B 295 ASP cc_start: 0.8620 (t0) cc_final: 0.8201 (t0) REVERT: B 312 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8801 (p) REVERT: B 347 ASN cc_start: 0.7975 (t0) cc_final: 0.7623 (t0) REVERT: E 168 GLU cc_start: 0.8965 (pt0) cc_final: 0.8611 (pt0) REVERT: E 230 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8424 (mp) REVERT: E 290 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8172 (mp0) REVERT: E 423 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8335 (mm-30) REVERT: E 432 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.6671 (t80) REVERT: I 125 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7647 (pp20) REVERT: I 205 GLU cc_start: 0.8768 (tp30) cc_final: 0.8274 (tp30) REVERT: I 211 CYS cc_start: 0.9272 (m) cc_final: 0.8954 (m) REVERT: I 245 GLN cc_start: 0.8375 (mm110) cc_final: 0.7906 (mt0) REVERT: I 295 ASP cc_start: 0.8208 (t0) cc_final: 0.7783 (t0) REVERT: I 297 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7522 (ttmt) REVERT: I 343 GLU cc_start: 0.8921 (pm20) cc_final: 0.8439 (pm20) REVERT: K 25 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8610 (mmpt) REVERT: K 67 TYR cc_start: 0.7234 (t80) cc_final: 0.6875 (t80) REVERT: K 71 LYS cc_start: 0.7038 (pttt) cc_final: 0.6098 (pptt) REVERT: K 75 ARG cc_start: 0.8171 (mtt180) cc_final: 0.7815 (mtt180) REVERT: K 138 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5579 (mmm) REVERT: K 153 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7107 (mmt90) REVERT: K 161 LYS cc_start: 0.9252 (mppt) cc_final: 0.8930 (ptpp) REVERT: K 221 PHE cc_start: 0.8191 (t80) cc_final: 0.7530 (m-80) REVERT: K 253 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7827 (tt0) REVERT: K 256 ASP cc_start: 0.8153 (p0) cc_final: 0.7654 (m-30) REVERT: N 13 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7692 (tmm-80) REVERT: N 20 MET cc_start: 0.8583 (mtm) cc_final: 0.8345 (mtm) REVERT: N 30 MET cc_start: 0.6518 (mtm) cc_final: 0.6066 (mtm) REVERT: N 72 GLN cc_start: 0.7500 (tp40) cc_final: 0.7013 (tp-100) REVERT: N 108 MET cc_start: 0.7363 (mtt) cc_final: 0.6839 (mmm) REVERT: N 148 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: N 182 SER cc_start: 0.8858 (t) cc_final: 0.8309 (p) REVERT: N 193 GLN cc_start: 0.5333 (OUTLIER) cc_final: 0.4319 (mp10) REVERT: N 197 ASP cc_start: 0.8914 (t70) cc_final: 0.8420 (m-30) REVERT: N 200 ASN cc_start: 0.8661 (m110) cc_final: 0.8369 (m110) REVERT: N 201 LYS cc_start: 0.8489 (tptp) cc_final: 0.7960 (tmmm) REVERT: N 264 ARG cc_start: 0.8165 (tpp-160) cc_final: 0.7949 (tpp-160) REVERT: N 355 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7815 (tpm-80) outliers start: 48 outliers final: 24 residues processed: 320 average time/residue: 0.6652 time to fit residues: 240.3160 Evaluate side-chains 320 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 283 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 432 TYR Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 33 SER Chi-restraints excluded: chain K residue 138 MET Chi-restraints excluded: chain K residue 153 ARG Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 122 LEU Chi-restraints excluded: chain N residue 148 GLU Chi-restraints excluded: chain N residue 189 TYR Chi-restraints excluded: chain N residue 193 GLN Chi-restraints excluded: chain N residue 220 VAL Chi-restraints excluded: chain N residue 263 THR Chi-restraints excluded: chain N residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 64 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 0.0040 chunk 3 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 426 GLN E 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091811 restraints weight = 30917.133| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.90 r_work: 0.3192 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20139 Z= 0.123 Angle : 0.599 12.131 27333 Z= 0.294 Chirality : 0.044 0.318 3007 Planarity : 0.004 0.064 3543 Dihedral : 9.631 170.881 3037 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.20 % Allowed : 25.28 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: 0.85 (0.17), residues: 2459 helix: 2.01 (0.17), residues: 1039 sheet: 0.39 (0.23), residues: 487 loop : -1.03 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 282 TYR 0.033 0.001 TYR A 24 PHE 0.023 0.001 PHE B 212 TRP 0.024 0.001 TRP K 57 HIS 0.003 0.000 HIS E 8 Details of bonding type rmsd covalent geometry : bond 0.00284 (20137) covalent geometry : angle 0.59895 (27333) hydrogen bonds : bond 0.03660 ( 927) hydrogen bonds : angle 3.88607 ( 2838) Misc. bond : bond 0.00045 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6637.47 seconds wall clock time: 114 minutes 13.05 seconds (6853.05 seconds total)