Starting phenix.real_space_refine on Thu Feb 5 14:56:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.map" model { file = "/net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hq4_52338/02_2026/9hq4_52338.cif" } resolution = 3.28 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= 0.001 sd= 0.021 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 12 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 11300 2.51 5 N 3019 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17848 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain: "C" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3372 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 20, 'TRANS': 409} Chain breaks: 1 Chain: "D" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3354 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain: "E" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4148 Classifications: {'peptide': 517} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 485} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {' MG': 1, 'G2P': 1, 'TA1': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.04, per 1000 atoms: 0.23 Number of scatterers: 17848 At special positions: 0 Unit cell: (126.806, 137.598, 130.853, 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 119 16.00 P 12 15.00 Mg 4 11.99 O 3394 8.00 N 3019 7.00 C 11300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 580 " - pdb=" SG CYS E 648 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 550.3 milliseconds 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4156 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 16 sheets defined 48.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.628A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.720A 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 110 through 113 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.823A pdb=" N VAL A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.392A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.508A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.862A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.506A pdb=" N GLU A 284 " --> pdb=" O ALA A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.572A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.511A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.091A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.278A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.326A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.589A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 74 " --> pdb=" O PRO B 70 " (cutoff:3.500A) 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 109 through 125 removed outlier: 4.381A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.993A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 190 removed outlier: 3.626A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.718A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.835A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.632A pdb=" N ASN B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.904A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN B 384 " --> pdb=" O ARG B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.467A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.385A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 removed outlier: 4.254A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 51 removed outlier: 3.902A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 81 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 143 through 160 removed outlier: 4.557A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.504A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.666A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.952A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.539A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.502A pdb=" N ALA C 281 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR C 282 " --> pdb=" O GLU C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 287 through 296 removed outlier: 3.699A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 301 removed outlier: 4.024A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 383 through 401 removed outlier: 4.003A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 3.704A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 436 removed outlier: 4.072A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 436 " --> pdb=" O TYR C 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.568A pdb=" N GLN D 43 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 69 through 78 removed outlier: 4.359A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 125 removed outlier: 4.332A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 157 Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.691A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 4.000A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.722A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 4.562A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 373 through 388 removed outlier: 4.116A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 427 removed outlier: 4.244A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN D 426 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 150 removed outlier: 3.678A pdb=" N SER E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.248A pdb=" N ASN E 175 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 193 through 208 Processing helix chain 'E' and resid 224 through 239 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 277 removed outlier: 4.225A pdb=" N SER E 276 " --> pdb=" O THR E 273 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 277 " --> pdb=" O LEU E 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 368 through 377 Processing helix chain 'E' and resid 381 through 412 Proline residue: E 402 - end of helix Processing helix chain 'E' and resid 466 through 484 removed outlier: 3.851A pdb=" N ALA E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET E 484 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 499 removed outlier: 4.352A pdb=" N LYS E 489 " --> pdb=" O ASP E 485 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS E 490 " --> pdb=" O PRO E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 4.370A pdb=" N ASN E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU E 555 " --> pdb=" O ARG E 551 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE E 557 " --> pdb=" O ALA E 553 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 559 " --> pdb=" O LEU E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 580 Processing helix chain 'E' and resid 588 through 607 Processing helix chain 'E' and resid 616 through 631 Processing helix chain 'E' and resid 638 through 657 removed outlier: 4.024A pdb=" N ALA E 642 " --> pdb=" O HIS E 638 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.961A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (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 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.517A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 137 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 4.081A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 349 through 354 removed outlier: 8.457A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 349 through 354 removed outlier: 8.457A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 368 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.025A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 272 removed outlier: 3.872A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.225A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA D 9 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB4, first strand: chain 'E' and resid 153 through 155 removed outlier: 6.850A pdb=" N VAL E 131 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER E 134 " --> pdb=" O TRP E 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 218 through 221 Processing sheet with id=AB6, first strand: chain 'E' and resid 290 through 291 removed outlier: 6.637A pdb=" N PHE E 296 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU E 431 " --> pdb=" O PHE E 296 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY E 426 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VAL E 442 " --> pdb=" O GLY E 426 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP E 428 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 365 through 367 removed outlier: 6.062A pdb=" N TYR E 301 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU E 311 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE E 314 " --> pdb=" O LYS E 533 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2193 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: 2.94 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3945 1.33 - 1.46: 5111 1.46 - 1.59: 8998 1.59 - 1.72: 14 1.72 - 1.84: 195 Bond restraints: 18263 Sorted by residual: bond pdb=" CA PHE D 294 " pdb=" C PHE D 294 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.34e-02 5.57e+03 2.37e+01 bond pdb=" CA SER D 78 " pdb=" CB SER D 78 " ideal model delta sigma weight residual 1.524 1.468 0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" CA SER B 275 " pdb=" CB SER B 275 " ideal model delta sigma weight residual 1.530 1.461 0.070 1.69e-02 3.50e+03 1.70e+01 bond pdb=" CA SER B 188 " pdb=" CB SER B 188 " ideal model delta sigma weight residual 1.533 1.470 0.063 1.60e-02 3.91e+03 1.54e+01 bond pdb=" CA SER C 158 " pdb=" CB SER C 158 " ideal model delta sigma weight residual 1.533 1.470 0.062 1.60e-02 3.91e+03 1.52e+01 ... (remaining 18258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 24522 3.37 - 6.74: 261 6.74 - 10.11: 25 10.11 - 13.48: 1 13.48 - 16.85: 1 Bond angle restraints: 24810 Sorted by residual: angle pdb=" N SER C 158 " pdb=" CA SER C 158 " pdb=" C SER C 158 " ideal model delta sigma weight residual 113.55 104.86 8.69 1.26e+00 6.30e-01 4.76e+01 angle pdb=" C PHE D 242 " pdb=" CA PHE D 242 " pdb=" CB PHE D 242 " ideal model delta sigma weight residual 108.91 119.19 -10.28 1.53e+00 4.27e-01 4.51e+01 angle pdb=" CA PHE B 242 " pdb=" CB PHE B 242 " pdb=" CG PHE B 242 " ideal model delta sigma weight residual 113.80 120.39 -6.59 1.00e+00 1.00e+00 4.35e+01 angle pdb=" N PRO B 243 " pdb=" CA PRO B 243 " pdb=" CB PRO B 243 " ideal model delta sigma weight residual 103.38 96.48 6.90 1.05e+00 9.07e-01 4.32e+01 angle pdb=" N LEU B 240 " pdb=" CA LEU B 240 " pdb=" C LEU B 240 " ideal model delta sigma weight residual 113.38 105.32 8.06 1.23e+00 6.61e-01 4.29e+01 ... (remaining 24805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9407 17.92 - 35.84: 1171 35.84 - 53.76: 448 53.76 - 71.68: 80 71.68 - 89.60: 35 Dihedral angle restraints: 11141 sinusoidal: 4681 harmonic: 6460 Sorted by residual: dihedral pdb=" CD ARG D 241 " pdb=" NE ARG D 241 " pdb=" CZ ARG D 241 " pdb=" NH1 ARG D 241 " ideal model delta sinusoidal sigma weight residual 0.00 89.60 -89.60 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" C GLN B 292 " pdb=" N GLN B 292 " pdb=" CA GLN B 292 " pdb=" CB GLN B 292 " ideal model delta harmonic sigma weight residual -122.60 -108.86 -13.74 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" CA MET D 330 " pdb=" C MET D 330 " pdb=" N LEU D 331 " pdb=" CA LEU D 331 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 11138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2301 0.066 - 0.131: 369 0.131 - 0.197: 45 0.197 - 0.262: 13 0.262 - 0.328: 2 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA GLN B 292 " pdb=" N GLN B 292 " pdb=" C GLN B 292 " pdb=" CB GLN B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA GLU C 155 " pdb=" N GLU C 155 " pdb=" C GLU C 155 " pdb=" CB GLU C 155 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL D 365 " pdb=" CA VAL D 365 " pdb=" CG1 VAL D 365 " pdb=" CG2 VAL D 365 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2727 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 241 " 1.142 9.50e-02 1.11e+02 5.12e-01 1.58e+02 pdb=" NE ARG D 241 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D 241 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG D 241 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 241 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 241 " -0.655 9.50e-02 1.11e+02 2.94e-01 5.27e+01 pdb=" NE ARG B 241 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG B 241 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 241 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 241 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 46 " 0.641 9.50e-02 1.11e+02 2.87e-01 5.03e+01 pdb=" NE ARG B 46 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 46 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 46 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 46 " 0.021 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 86 2.46 - 3.07: 11782 3.07 - 3.68: 26825 3.68 - 4.29: 39670 4.29 - 4.90: 66798 Nonbonded interactions: 145161 Sorted by model distance: nonbonded pdb=" O2G G2P A 501 " pdb="MG MG A 502 " model vdw 1.855 2.170 nonbonded pdb=" O1G G2P C 501 " pdb="MG MG C 502 " model vdw 1.870 2.170 nonbonded pdb=" O3G G2P B 501 " pdb="MG MG B 502 " model vdw 1.984 2.170 nonbonded pdb=" O3G G2P D 501 " pdb="MG MG D 502 " model vdw 2.003 2.170 nonbonded pdb=" O1B G2P B 501 " pdb="MG MG B 502 " model vdw 2.048 2.170 ... (remaining 145156 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 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 1 through 426 or resid 501 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 0.070 18264 Z= 0.282 Angle : 0.820 16.847 24812 Z= 0.497 Chirality : 0.051 0.328 2730 Planarity : 0.015 0.512 3198 Dihedral : 18.591 89.604 6982 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 7.10 % Allowed : 29.84 % Favored : 63.06 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 1.82 % 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: -0.44 (0.18), residues: 2214 helix: 0.80 (0.17), residues: 956 sheet: 0.01 (0.29), residues: 327 loop : -1.57 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 214 TYR 0.021 0.001 TYR A 24 PHE 0.017 0.001 PHE E 576 TRP 0.039 0.002 TRP B 101 HIS 0.004 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00480 (18263) covalent geometry : angle 0.82003 (24810) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.97224 ( 2) hydrogen bonds : bond 0.16241 ( 761) hydrogen bonds : angle 6.12539 ( 2193) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 577 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8375 (m) REVERT: A 31 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 80 THR cc_start: 0.8013 (p) cc_final: 0.7750 (p) REVERT: A 102 ASN cc_start: 0.8081 (t0) cc_final: 0.7724 (t0) REVERT: A 120 ASP cc_start: 0.7467 (m-30) cc_final: 0.7185 (m-30) REVERT: A 172 TYR cc_start: 0.8611 (t80) cc_final: 0.8349 (t80) REVERT: A 196 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7367 (tp30) REVERT: A 211 ASP cc_start: 0.7966 (m-30) cc_final: 0.7397 (m-30) REVERT: A 233 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7938 (mm-40) REVERT: A 259 LEU cc_start: 0.8653 (tp) cc_final: 0.8138 (tt) REVERT: A 282 TYR cc_start: 0.7849 (m-10) cc_final: 0.7269 (m-10) REVERT: A 297 GLU cc_start: 0.8009 (tt0) cc_final: 0.7721 (tt0) REVERT: A 300 ASN cc_start: 0.8401 (t0) cc_final: 0.7872 (t0) REVERT: A 370 LYS cc_start: 0.8444 (tttt) cc_final: 0.8101 (ttmm) REVERT: A 415 GLU cc_start: 0.7896 (tp30) cc_final: 0.7499 (tp30) REVERT: A 429 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: A 431 ASP cc_start: 0.8379 (t0) cc_final: 0.8092 (t70) REVERT: A 432 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 27 GLU cc_start: 0.8404 (tt0) cc_final: 0.8204 (tt0) REVERT: B 78 SER cc_start: 0.8329 (t) cc_final: 0.8039 (p) REVERT: B 123 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6690 (mt-10) REVERT: B 203 ASP cc_start: 0.7787 (t0) cc_final: 0.7496 (t70) REVERT: B 218 THR cc_start: 0.8549 (p) cc_final: 0.8209 (p) REVERT: B 335 ASN cc_start: 0.7066 (m-40) cc_final: 0.6841 (m110) REVERT: B 344 TRP cc_start: 0.8769 (p-90) cc_final: 0.8542 (p-90) REVERT: B 366 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8164 (t) REVERT: B 412 GLU cc_start: 0.7476 (tp30) cc_final: 0.7086 (tp30) REVERT: B 417 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7486 (m-30) REVERT: B 422 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.6938 (t80) REVERT: C 91 GLN cc_start: 0.8118 (mt0) cc_final: 0.7827 (mt0) REVERT: C 119 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 123 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.7382 (ttp-170) REVERT: C 127 ASP cc_start: 0.7688 (m-30) cc_final: 0.7408 (m-30) REVERT: C 284 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6721 (mp0) REVERT: C 304 LYS cc_start: 0.8792 (tttt) cc_final: 0.8295 (tttt) REVERT: C 377 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7423 (tpt) REVERT: C 390 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7515 (mtm180) REVERT: C 432 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: D 44 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7894 (tp) REVERT: D 81 PHE cc_start: 0.8067 (m-80) cc_final: 0.7657 (m-80) REVERT: D 92 PHE cc_start: 0.8500 (p90) cc_final: 0.8085 (p90) REVERT: D 108 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7369 (tm-30) REVERT: D 151 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7860 (tt) REVERT: D 157 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: D 162 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8048 (mmp-170) REVERT: D 274 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8263 (p) REVERT: D 334 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8347 (mt0) REVERT: D 386 THR cc_start: 0.8845 (m) cc_final: 0.8574 (m) REVERT: D 391 ARG cc_start: 0.7742 (mmt180) cc_final: 0.5901 (ptt180) REVERT: D 423 GLN cc_start: 0.8219 (tt0) cc_final: 0.7984 (tp40) REVERT: E 199 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7488 (mtt180) REVERT: E 202 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6829 (mtp-110) REVERT: E 204 MET cc_start: 0.7361 (mmm) cc_final: 0.6823 (mmm) REVERT: E 316 LYS cc_start: 0.4453 (tppp) cc_final: 0.3912 (tppt) REVERT: E 388 ASP cc_start: 0.6213 (p0) cc_final: 0.5968 (p0) REVERT: E 448 MET cc_start: 0.4920 (mmm) cc_final: 0.4588 (mmm) REVERT: E 538 LYS cc_start: 0.8218 (mttt) cc_final: 0.7861 (mttt) REVERT: E 547 ARG cc_start: 0.7357 (mpp-170) cc_final: 0.6830 (mpp-170) REVERT: E 558 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7559 (mmm160) REVERT: E 559 PHE cc_start: 0.7574 (m-80) cc_final: 0.7244 (m-10) REVERT: E 578 ARG cc_start: 0.7505 (mtt90) cc_final: 0.7100 (mtt90) REVERT: E 609 ASP cc_start: 0.4874 (OUTLIER) cc_final: 0.4634 (p0) REVERT: E 612 ASP cc_start: 0.2273 (OUTLIER) cc_final: 0.2049 (m-30) REVERT: E 624 PHE cc_start: 0.8238 (t80) cc_final: 0.7913 (t80) REVERT: E 631 LYS cc_start: 0.7031 (mmmm) cc_final: 0.6453 (ttmm) REVERT: E 633 LYS cc_start: 0.7213 (mtmt) cc_final: 0.6981 (mtmt) REVERT: E 634 MET cc_start: 0.6279 (mmt) cc_final: 0.5947 (mmt) REVERT: E 646 ASP cc_start: 0.7445 (m-30) cc_final: 0.7198 (m-30) REVERT: E 654 LEU cc_start: 0.8118 (mm) cc_final: 0.7819 (mm) outliers start: 137 outliers final: 96 residues processed: 641 average time/residue: 0.1772 time to fit residues: 159.5756 Evaluate side-chains 678 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 563 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 429 GLU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 384 ILE Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 276 ARG Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 334 GLN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain E residue 384 LYS Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 574 ARG Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 611 ARG Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 638 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 0.0370 chunk 212 optimal weight: 5.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 GLN D 247 ASN D 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120011 restraints weight = 24463.040| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.01 r_work: 0.3222 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18264 Z= 0.160 Angle : 0.574 12.100 24812 Z= 0.296 Chirality : 0.044 0.208 2730 Planarity : 0.005 0.102 3198 Dihedral : 10.608 85.282 2999 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.75 % Allowed : 28.45 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.16 (0.18), residues: 2214 helix: 1.14 (0.17), residues: 972 sheet: -0.19 (0.29), residues: 352 loop : -1.47 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 241 TYR 0.016 0.001 TYR E 301 PHE 0.021 0.001 PHE D 242 TRP 0.018 0.002 TRP B 101 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00353 (18263) covalent geometry : angle 0.57349 (24810) SS BOND : bond 0.00216 ( 1) SS BOND : angle 0.87191 ( 2) hydrogen bonds : bond 0.04976 ( 761) hydrogen bonds : angle 4.62824 ( 2193) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 567 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7555 (mm-40) REVERT: A 80 THR cc_start: 0.7843 (p) cc_final: 0.7587 (p) REVERT: A 102 ASN cc_start: 0.8366 (t0) cc_final: 0.7857 (t0) REVERT: A 120 ASP cc_start: 0.7470 (m-30) cc_final: 0.7206 (m-30) REVERT: A 123 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7356 (mmt-90) REVERT: A 155 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: A 172 TYR cc_start: 0.8591 (t80) cc_final: 0.8366 (t80) REVERT: A 196 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7300 (tp30) REVERT: A 211 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: A 233 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8058 (mm-40) REVERT: A 259 LEU cc_start: 0.8697 (tp) cc_final: 0.8186 (tt) REVERT: A 280 LYS cc_start: 0.8251 (mttm) cc_final: 0.7988 (mttp) REVERT: A 282 TYR cc_start: 0.7888 (m-10) cc_final: 0.7304 (m-10) REVERT: A 300 ASN cc_start: 0.8337 (t0) cc_final: 0.7838 (t0) REVERT: A 306 ASP cc_start: 0.7408 (t0) cc_final: 0.7066 (t0) REVERT: A 311 LYS cc_start: 0.8069 (mttm) cc_final: 0.7848 (mttm) REVERT: A 370 LYS cc_start: 0.8447 (tttt) cc_final: 0.8111 (ttmm) REVERT: A 392 ASP cc_start: 0.7815 (t0) cc_final: 0.7476 (t0) REVERT: A 415 GLU cc_start: 0.7777 (tp30) cc_final: 0.7436 (tp30) REVERT: A 429 GLU cc_start: 0.8067 (tp30) cc_final: 0.7572 (mm-30) REVERT: A 431 ASP cc_start: 0.8352 (t0) cc_final: 0.8079 (t70) REVERT: A 432 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7810 (t80) REVERT: B 123 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: B 130 LEU cc_start: 0.8666 (tt) cc_final: 0.8390 (tt) REVERT: B 138 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 218 THR cc_start: 0.8915 (p) cc_final: 0.8670 (p) REVERT: B 257 MET cc_start: 0.8315 (mmt) cc_final: 0.8106 (mmt) REVERT: B 262 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8278 (ptm160) REVERT: B 267 MET cc_start: 0.8380 (mtm) cc_final: 0.8172 (mtm) REVERT: B 278 SER cc_start: 0.8106 (OUTLIER) cc_final: 0.7468 (p) REVERT: B 282 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7532 (ttt180) REVERT: B 293 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8315 (t) REVERT: B 335 ASN cc_start: 0.8268 (m-40) cc_final: 0.8056 (m110) REVERT: B 344 TRP cc_start: 0.8813 (p-90) cc_final: 0.8561 (p-90) REVERT: B 366 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8111 (t) REVERT: B 391 ARG cc_start: 0.8664 (mtm180) cc_final: 0.6648 (ptt90) REVERT: B 417 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 422 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.6902 (t80) REVERT: C 90 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7665 (mp0) REVERT: C 91 GLN cc_start: 0.8096 (mt0) cc_final: 0.7888 (mt0) REVERT: C 105 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8426 (mmm160) REVERT: C 123 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7398 (ttp-170) REVERT: C 127 ASP cc_start: 0.7636 (m-30) cc_final: 0.7373 (m-30) REVERT: C 196 GLU cc_start: 0.7834 (pt0) cc_final: 0.7469 (pm20) REVERT: C 214 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7567 (ttp-110) REVERT: C 304 LYS cc_start: 0.8853 (tttt) cc_final: 0.8523 (tppt) REVERT: C 342 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6886 (pt0) REVERT: C 377 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7771 (tpt) REVERT: C 396 ASP cc_start: 0.8288 (m-30) cc_final: 0.8037 (m-30) REVERT: C 423 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7739 (mt-10) REVERT: C 432 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: D 76 VAL cc_start: 0.8380 (t) cc_final: 0.8135 (p) REVERT: D 81 PHE cc_start: 0.8119 (m-80) cc_final: 0.7704 (m-80) REVERT: D 92 PHE cc_start: 0.8426 (p90) cc_final: 0.8003 (p90) REVERT: D 108 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 157 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: D 162 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7925 (mmp-170) REVERT: D 209 ASP cc_start: 0.8382 (t70) cc_final: 0.7647 (t0) REVERT: D 249 ASP cc_start: 0.8130 (p0) cc_final: 0.7789 (p0) REVERT: D 274 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8024 (p) REVERT: D 293 VAL cc_start: 0.8370 (p) cc_final: 0.7857 (t) REVERT: D 297 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7678 (mtmt) REVERT: D 325 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7717 (mt-10) REVERT: D 390 ARG cc_start: 0.8144 (pmm-80) cc_final: 0.7738 (ptm-80) REVERT: D 391 ARG cc_start: 0.7761 (mmt180) cc_final: 0.5920 (ptt180) REVERT: D 415 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7434 (ttp) REVERT: E 199 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7570 (mtt180) REVERT: E 316 LYS cc_start: 0.3936 (tppp) cc_final: 0.3564 (tppt) REVERT: E 388 ASP cc_start: 0.6671 (p0) cc_final: 0.6459 (p0) REVERT: E 538 LYS cc_start: 0.8160 (mttt) cc_final: 0.7803 (mttt) REVERT: E 547 ARG cc_start: 0.7392 (mpp-170) cc_final: 0.7031 (mpp-170) REVERT: E 558 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7593 (mmm160) REVERT: E 573 PHE cc_start: 0.7284 (t80) cc_final: 0.6818 (t80) REVERT: E 578 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7110 (mtt90) REVERT: E 579 SER cc_start: 0.7651 (t) cc_final: 0.7424 (p) REVERT: E 624 PHE cc_start: 0.8272 (t80) cc_final: 0.7931 (t80) REVERT: E 633 LYS cc_start: 0.7105 (mtmt) cc_final: 0.6884 (mtmt) REVERT: E 634 MET cc_start: 0.6166 (mmt) cc_final: 0.5849 (mmt) REVERT: E 646 ASP cc_start: 0.7382 (m-30) cc_final: 0.7131 (m-30) REVERT: E 654 LEU cc_start: 0.8200 (mm) cc_final: 0.7856 (mm) outliers start: 111 outliers final: 63 residues processed: 622 average time/residue: 0.1697 time to fit residues: 147.5110 Evaluate side-chains 622 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 537 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 278 SER Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 586 SER Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 655 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 128 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 145 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS D 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119064 restraints weight = 24618.352| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.05 r_work: 0.3199 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18264 Z= 0.178 Angle : 0.564 8.249 24812 Z= 0.291 Chirality : 0.044 0.209 2730 Planarity : 0.005 0.071 3198 Dihedral : 9.189 82.305 2850 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.58 % Allowed : 28.19 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.06 (0.18), residues: 2214 helix: 1.21 (0.17), residues: 972 sheet: -0.06 (0.29), residues: 348 loop : -1.44 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 213 TYR 0.015 0.001 TYR D 159 PHE 0.016 0.001 PHE D 20 TRP 0.013 0.002 TRP B 101 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00405 (18263) covalent geometry : angle 0.56374 (24810) SS BOND : bond 0.00267 ( 1) SS BOND : angle 1.84906 ( 2) hydrogen bonds : bond 0.04884 ( 761) hydrogen bonds : angle 4.47020 ( 2193) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 572 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 80 THR cc_start: 0.7830 (p) cc_final: 0.7588 (p) REVERT: A 102 ASN cc_start: 0.8459 (t0) cc_final: 0.7989 (t0) REVERT: A 120 ASP cc_start: 0.7616 (m-30) cc_final: 0.7363 (m-30) REVERT: A 123 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7350 (mmt-90) REVERT: A 155 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: A 160 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (t0) REVERT: A 166 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7759 (mtmm) REVERT: A 196 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7310 (tp30) REVERT: A 211 ASP cc_start: 0.8031 (m-30) cc_final: 0.7420 (m-30) REVERT: A 233 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8119 (mm-40) REVERT: A 259 LEU cc_start: 0.8690 (tp) cc_final: 0.8104 (tt) REVERT: A 282 TYR cc_start: 0.7892 (m-10) cc_final: 0.7298 (m-10) REVERT: A 300 ASN cc_start: 0.8396 (t0) cc_final: 0.7861 (t0) REVERT: A 306 ASP cc_start: 0.7468 (t0) cc_final: 0.7168 (t0) REVERT: A 370 LYS cc_start: 0.8436 (tttt) cc_final: 0.8102 (ttmm) REVERT: A 390 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7837 (mtm180) REVERT: A 415 GLU cc_start: 0.7793 (tp30) cc_final: 0.7438 (tp30) REVERT: A 429 GLU cc_start: 0.8093 (tp30) cc_final: 0.7615 (mm-30) REVERT: A 431 ASP cc_start: 0.8359 (t0) cc_final: 0.8103 (t70) REVERT: A 432 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.7839 (t80) REVERT: B 31 ASP cc_start: 0.7937 (t0) cc_final: 0.7657 (t0) REVERT: B 48 SER cc_start: 0.8733 (OUTLIER) cc_final: 0.8212 (p) REVERT: B 158 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: B 175 VAL cc_start: 0.8467 (t) cc_final: 0.8178 (m) REVERT: B 218 THR cc_start: 0.8900 (p) cc_final: 0.8658 (p) REVERT: B 262 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8288 (ptm160) REVERT: B 282 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7316 (ttt180) REVERT: B 288 GLU cc_start: 0.7644 (pp20) cc_final: 0.7040 (pp20) REVERT: B 328 GLU cc_start: 0.7424 (tp30) cc_final: 0.7195 (tp30) REVERT: B 344 TRP cc_start: 0.8826 (p-90) cc_final: 0.8600 (p-90) REVERT: B 366 THR cc_start: 0.8564 (m) cc_final: 0.8169 (t) REVERT: B 391 ARG cc_start: 0.8663 (mtm180) cc_final: 0.6716 (ptt90) REVERT: B 417 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: B 422 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.6865 (t80) REVERT: C 90 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7669 (mp0) REVERT: C 91 GLN cc_start: 0.8114 (mt0) cc_final: 0.7901 (mt0) REVERT: C 119 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8601 (mt) REVERT: C 123 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7433 (ttp-170) REVERT: C 127 ASP cc_start: 0.7630 (m-30) cc_final: 0.7397 (m-30) REVERT: C 284 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6918 (mp0) REVERT: C 304 LYS cc_start: 0.8876 (tttt) cc_final: 0.8584 (ttmm) REVERT: C 306 ASP cc_start: 0.8418 (t0) cc_final: 0.8213 (t0) REVERT: C 377 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7563 (tpt) REVERT: C 432 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8247 (m-80) REVERT: D 19 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7869 (tmtm) REVERT: D 92 PHE cc_start: 0.8485 (p90) cc_final: 0.8027 (p90) REVERT: D 108 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7172 (tm-30) REVERT: D 157 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7657 (tp30) REVERT: D 162 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7797 (mmp-170) REVERT: D 190 HIS cc_start: 0.8311 (t-170) cc_final: 0.7595 (t70) REVERT: D 209 ASP cc_start: 0.8176 (t70) cc_final: 0.7707 (t0) REVERT: D 274 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8068 (p) REVERT: D 291 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 293 VAL cc_start: 0.8533 (p) cc_final: 0.7964 (t) REVERT: D 324 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8367 (tttm) REVERT: D 325 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 390 ARG cc_start: 0.8215 (pmm-80) cc_final: 0.7808 (ptm-80) REVERT: D 391 ARG cc_start: 0.7809 (mmt180) cc_final: 0.5886 (ptt180) REVERT: D 415 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7487 (ttp) REVERT: D 421 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7410 (tp30) REVERT: E 199 ARG cc_start: 0.8139 (mtt180) cc_final: 0.7515 (mtt180) REVERT: E 316 LYS cc_start: 0.3378 (tppp) cc_final: 0.3135 (tppp) REVERT: E 388 ASP cc_start: 0.6579 (p0) cc_final: 0.6360 (p0) REVERT: E 538 LYS cc_start: 0.8245 (mttt) cc_final: 0.7907 (mttt) REVERT: E 558 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7619 (mmm160) REVERT: E 573 PHE cc_start: 0.7313 (t80) cc_final: 0.6964 (t80) REVERT: E 578 ARG cc_start: 0.7509 (mtt90) cc_final: 0.7121 (mtt90) REVERT: E 589 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7125 (mpt) REVERT: E 624 PHE cc_start: 0.8276 (t80) cc_final: 0.7933 (t80) REVERT: E 634 MET cc_start: 0.6237 (mmt) cc_final: 0.5893 (mmt) REVERT: E 646 ASP cc_start: 0.7350 (m-30) cc_final: 0.7100 (m-30) REVERT: E 654 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7823 (mm) outliers start: 127 outliers final: 78 residues processed: 632 average time/residue: 0.1732 time to fit residues: 153.9219 Evaluate side-chains 640 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 541 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 342 GLN Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 386 THR Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 581 LYS Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Chi-restraints excluded: chain E residue 655 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 12 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 307 HIS B 335 ASN C 301 GLN D 347 ASN E 542 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.159194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119130 restraints weight = 24526.467| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.98 r_work: 0.3204 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18264 Z= 0.167 Angle : 0.559 7.936 24812 Z= 0.288 Chirality : 0.044 0.205 2730 Planarity : 0.004 0.058 3198 Dihedral : 8.692 64.499 2832 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.89 % Allowed : 27.93 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.03 (0.18), residues: 2214 helix: 1.21 (0.17), residues: 977 sheet: 0.01 (0.29), residues: 342 loop : -1.41 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 121 TYR 0.017 0.001 TYR A 172 PHE 0.016 0.001 PHE D 20 TRP 0.011 0.002 TRP B 101 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00383 (18263) covalent geometry : angle 0.55841 (24810) SS BOND : bond 0.00075 ( 1) SS BOND : angle 1.75275 ( 2) hydrogen bonds : bond 0.04586 ( 761) hydrogen bonds : angle 4.37309 ( 2193) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 550 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7579 (mm-40) REVERT: A 80 THR cc_start: 0.7841 (p) cc_final: 0.7580 (p) REVERT: A 102 ASN cc_start: 0.8470 (t0) cc_final: 0.7965 (t0) REVERT: A 120 ASP cc_start: 0.7431 (m-30) cc_final: 0.7142 (m-30) REVERT: A 123 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7364 (mmt-90) REVERT: A 155 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: A 160 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7998 (t0) REVERT: A 166 LYS cc_start: 0.8170 (mtmm) cc_final: 0.7799 (mtmm) REVERT: A 196 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7301 (tp30) REVERT: A 211 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: A 233 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 259 LEU cc_start: 0.8683 (tp) cc_final: 0.8102 (tt) REVERT: A 282 TYR cc_start: 0.7843 (m-10) cc_final: 0.7256 (m-10) REVERT: A 300 ASN cc_start: 0.8384 (t0) cc_final: 0.7863 (t0) REVERT: A 306 ASP cc_start: 0.7493 (t0) cc_final: 0.7123 (t0) REVERT: A 370 LYS cc_start: 0.8466 (tttt) cc_final: 0.8133 (ttmm) REVERT: A 415 GLU cc_start: 0.7773 (tp30) cc_final: 0.7427 (tp30) REVERT: A 429 GLU cc_start: 0.8089 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 432 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.7859 (t80) REVERT: B 48 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8207 (p) REVERT: B 138 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7944 (p) REVERT: B 158 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 218 THR cc_start: 0.8892 (p) cc_final: 0.8593 (p) REVERT: B 219 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 262 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8265 (ptm160) REVERT: B 282 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7370 (ttt180) REVERT: B 288 GLU cc_start: 0.7707 (pp20) cc_final: 0.7089 (pp20) REVERT: B 328 GLU cc_start: 0.7390 (tp30) cc_final: 0.7171 (tp30) REVERT: B 366 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8112 (t) REVERT: B 391 ARG cc_start: 0.8647 (mtm180) cc_final: 0.6678 (ptt-90) REVERT: B 417 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: B 422 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.6848 (t80) REVERT: C 90 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7672 (mp0) REVERT: C 105 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8595 (mmm160) REVERT: C 123 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7479 (ttp-170) REVERT: C 127 ASP cc_start: 0.7612 (m-30) cc_final: 0.7377 (m-30) REVERT: C 196 GLU cc_start: 0.7832 (pt0) cc_final: 0.7353 (pm20) REVERT: C 214 ARG cc_start: 0.8017 (ttt-90) cc_final: 0.7565 (ttp-110) REVERT: C 284 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6724 (mp0) REVERT: C 304 LYS cc_start: 0.8851 (tttt) cc_final: 0.8546 (ttmm) REVERT: C 306 ASP cc_start: 0.8466 (t0) cc_final: 0.8188 (t0) REVERT: C 432 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: D 19 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7873 (tmtm) REVERT: D 92 PHE cc_start: 0.8487 (p90) cc_final: 0.8028 (p90) REVERT: D 108 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 157 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: D 162 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7723 (mmp-170) REVERT: D 209 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7759 (t0) REVERT: D 213 ARG cc_start: 0.8094 (ttm110) cc_final: 0.7842 (ttm110) REVERT: D 306 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.7342 (mmm160) REVERT: D 324 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8496 (tttm) REVERT: D 325 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7811 (mt-10) REVERT: D 390 ARG cc_start: 0.8223 (pmm-80) cc_final: 0.7813 (ptm-80) REVERT: D 391 ARG cc_start: 0.7849 (mmt180) cc_final: 0.5897 (ptt90) REVERT: D 412 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6730 (tm-30) REVERT: E 148 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7691 (mmm160) REVERT: E 199 ARG cc_start: 0.8007 (mtt180) cc_final: 0.7373 (mtt180) REVERT: E 316 LYS cc_start: 0.3675 (tppp) cc_final: 0.3441 (tppp) REVERT: E 431 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7105 (tm) REVERT: E 538 LYS cc_start: 0.8209 (mttt) cc_final: 0.7854 (mttt) REVERT: E 558 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7643 (mmm160) REVERT: E 573 PHE cc_start: 0.7225 (t80) cc_final: 0.6997 (t80) REVERT: E 578 ARG cc_start: 0.7454 (mtt90) cc_final: 0.7079 (mtt90) REVERT: E 589 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7088 (mpt) REVERT: E 612 ASP cc_start: 0.2424 (OUTLIER) cc_final: 0.2148 (m-30) REVERT: E 624 PHE cc_start: 0.8290 (t80) cc_final: 0.7930 (t80) REVERT: E 634 MET cc_start: 0.6283 (mmt) cc_final: 0.5929 (mmt) REVERT: E 654 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7788 (mm) outliers start: 133 outliers final: 87 residues processed: 618 average time/residue: 0.1610 time to fit residues: 139.0789 Evaluate side-chains 643 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 530 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 301 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 432 TYR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 148 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 192 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 335 ASN C 91 GLN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.158955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118844 restraints weight = 24508.366| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.95 r_work: 0.3204 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18264 Z= 0.181 Angle : 0.569 8.097 24812 Z= 0.292 Chirality : 0.045 0.206 2730 Planarity : 0.005 0.083 3198 Dihedral : 8.590 63.919 2825 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 7.25 % Allowed : 27.46 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.03 (0.18), residues: 2214 helix: 1.17 (0.17), residues: 983 sheet: 0.09 (0.29), residues: 342 loop : -1.42 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 121 TYR 0.014 0.001 TYR D 159 PHE 0.016 0.001 PHE D 20 TRP 0.011 0.002 TRP C 21 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00416 (18263) covalent geometry : angle 0.56898 (24810) SS BOND : bond 0.00160 ( 1) SS BOND : angle 1.43821 ( 2) hydrogen bonds : bond 0.04663 ( 761) hydrogen bonds : angle 4.37555 ( 2193) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 539 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7583 (mm-40) REVERT: A 47 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8413 (t0) REVERT: A 80 THR cc_start: 0.7845 (p) cc_final: 0.7599 (p) REVERT: A 102 ASN cc_start: 0.8481 (t0) cc_final: 0.7984 (t0) REVERT: A 120 ASP cc_start: 0.7483 (m-30) cc_final: 0.7196 (m-30) REVERT: A 123 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7421 (mmt-90) REVERT: A 155 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: A 160 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8017 (t0) REVERT: A 166 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7784 (mtmm) REVERT: A 196 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7307 (tp30) REVERT: A 211 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: A 233 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8106 (mm-40) REVERT: A 259 LEU cc_start: 0.8690 (tp) cc_final: 0.8138 (tt) REVERT: A 282 TYR cc_start: 0.7861 (m-10) cc_final: 0.7269 (m-10) REVERT: A 300 ASN cc_start: 0.8394 (t0) cc_final: 0.7831 (t0) REVERT: A 306 ASP cc_start: 0.7466 (t0) cc_final: 0.7091 (t0) REVERT: A 370 LYS cc_start: 0.8457 (tttt) cc_final: 0.8124 (ttmm) REVERT: A 415 GLU cc_start: 0.7713 (tp30) cc_final: 0.7470 (tp30) REVERT: A 429 GLU cc_start: 0.8073 (tp30) cc_final: 0.7605 (mm-30) REVERT: A 431 ASP cc_start: 0.8383 (t0) cc_final: 0.8132 (t70) REVERT: A 432 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7858 (t80) REVERT: B 31 ASP cc_start: 0.7896 (t0) cc_final: 0.7678 (t0) REVERT: B 48 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 138 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7946 (p) REVERT: B 158 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: B 194 GLU cc_start: 0.7637 (pm20) cc_final: 0.7366 (pm20) REVERT: B 218 THR cc_start: 0.8893 (p) cc_final: 0.8669 (p) REVERT: B 262 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8268 (ptm160) REVERT: B 282 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7384 (ttt180) REVERT: B 288 GLU cc_start: 0.7713 (pp20) cc_final: 0.7119 (pp20) REVERT: B 328 GLU cc_start: 0.7430 (tp30) cc_final: 0.7219 (tp30) REVERT: B 366 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8103 (t) REVERT: B 391 ARG cc_start: 0.8645 (mtm180) cc_final: 0.6677 (ptt-90) REVERT: B 417 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7519 (m-30) REVERT: B 422 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.6746 (t80) REVERT: C 90 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7681 (mp0) REVERT: C 105 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8592 (mmm160) REVERT: C 123 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7395 (ttp-170) REVERT: C 127 ASP cc_start: 0.7611 (m-30) cc_final: 0.7388 (m-30) REVERT: C 196 GLU cc_start: 0.7776 (pt0) cc_final: 0.7343 (pm20) REVERT: C 214 ARG cc_start: 0.8027 (ttt-90) cc_final: 0.7570 (ttp-110) REVERT: C 304 LYS cc_start: 0.8858 (tttt) cc_final: 0.8537 (tppt) REVERT: C 306 ASP cc_start: 0.8463 (t0) cc_final: 0.8240 (t0) REVERT: C 377 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7406 (tpt) REVERT: D 19 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7861 (tmtm) REVERT: D 92 PHE cc_start: 0.8483 (p90) cc_final: 0.8023 (p90) REVERT: D 108 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 162 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7806 (mmp-170) REVERT: D 209 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.7648 (t0) REVERT: D 213 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7632 (ttm110) REVERT: D 324 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8509 (tttm) REVERT: D 325 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 390 ARG cc_start: 0.8226 (pmm-80) cc_final: 0.7801 (ptm-80) REVERT: D 391 ARG cc_start: 0.7842 (mmt180) cc_final: 0.5901 (ptt180) REVERT: E 148 ARG cc_start: 0.8110 (mmp80) cc_final: 0.7788 (mmm160) REVERT: E 199 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7420 (mtt180) REVERT: E 218 SER cc_start: 0.6823 (p) cc_final: 0.6291 (m) REVERT: E 299 ARG cc_start: 0.6284 (ttp80) cc_final: 0.5468 (ttp80) REVERT: E 316 LYS cc_start: 0.3657 (tppp) cc_final: 0.3436 (tppp) REVERT: E 431 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7069 (tm) REVERT: E 448 MET cc_start: 0.5103 (mmm) cc_final: 0.4766 (mmm) REVERT: E 538 LYS cc_start: 0.8218 (mttt) cc_final: 0.7845 (mttt) REVERT: E 558 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7674 (mmm160) REVERT: E 578 ARG cc_start: 0.7375 (mtt90) cc_final: 0.6995 (mtt90) REVERT: E 589 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7073 (mpt) REVERT: E 612 ASP cc_start: 0.2413 (OUTLIER) cc_final: 0.2131 (m-30) REVERT: E 624 PHE cc_start: 0.8293 (t80) cc_final: 0.7927 (t80) REVERT: E 634 MET cc_start: 0.6362 (mmt) cc_final: 0.6007 (mmt) REVERT: E 654 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7777 (mm) outliers start: 140 outliers final: 97 residues processed: 611 average time/residue: 0.1642 time to fit residues: 141.0403 Evaluate side-chains 641 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 520 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 324 LYS Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 162 optimal weight: 0.2980 chunk 150 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 158 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 186 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 335 ASN C 91 GLN D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.159847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119595 restraints weight = 24256.209| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.89 r_work: 0.3218 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18264 Z= 0.139 Angle : 0.551 8.873 24812 Z= 0.282 Chirality : 0.044 0.200 2730 Planarity : 0.004 0.075 3198 Dihedral : 8.334 65.058 2819 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 6.74 % Allowed : 28.19 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.11 (0.18), residues: 2214 helix: 1.30 (0.17), residues: 976 sheet: 0.14 (0.29), residues: 342 loop : -1.35 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 121 TYR 0.020 0.001 TYR D 340 PHE 0.015 0.001 PHE D 20 TRP 0.013 0.002 TRP C 21 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00317 (18263) covalent geometry : angle 0.55049 (24810) SS BOND : bond 0.00171 ( 1) SS BOND : angle 1.31913 ( 2) hydrogen bonds : bond 0.04264 ( 761) hydrogen bonds : angle 4.29593 ( 2193) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 546 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7580 (mm-40) REVERT: A 80 THR cc_start: 0.7844 (p) cc_final: 0.7567 (p) REVERT: A 102 ASN cc_start: 0.8471 (t0) cc_final: 0.7955 (t0) REVERT: A 120 ASP cc_start: 0.7603 (m-30) cc_final: 0.7301 (m-30) REVERT: A 123 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7242 (mmt-90) REVERT: A 155 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: A 160 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8019 (t0) REVERT: A 166 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7771 (mtmm) REVERT: A 196 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7263 (tp30) REVERT: A 211 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7432 (m-30) REVERT: A 214 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8191 (ttp80) REVERT: A 233 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8055 (mm-40) REVERT: A 259 LEU cc_start: 0.8730 (tp) cc_final: 0.8121 (tt) REVERT: A 282 TYR cc_start: 0.7863 (m-10) cc_final: 0.7284 (m-10) REVERT: A 300 ASN cc_start: 0.8332 (t0) cc_final: 0.7862 (t0) REVERT: A 306 ASP cc_start: 0.7469 (t0) cc_final: 0.7097 (t0) REVERT: A 370 LYS cc_start: 0.8451 (tttt) cc_final: 0.8111 (ttmm) REVERT: A 415 GLU cc_start: 0.7679 (tp30) cc_final: 0.7459 (tp30) REVERT: A 431 ASP cc_start: 0.8372 (t0) cc_final: 0.8143 (t70) REVERT: A 432 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7812 (t80) REVERT: B 138 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7970 (p) REVERT: B 194 GLU cc_start: 0.7652 (pm20) cc_final: 0.7237 (pm20) REVERT: B 218 THR cc_start: 0.8879 (p) cc_final: 0.8580 (p) REVERT: B 219 THR cc_start: 0.8833 (t) cc_final: 0.8424 (p) REVERT: B 262 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8242 (ptm160) REVERT: B 282 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7372 (ttt180) REVERT: B 288 GLU cc_start: 0.7716 (pp20) cc_final: 0.7161 (pp20) REVERT: B 328 GLU cc_start: 0.7428 (tp30) cc_final: 0.7212 (tp30) REVERT: B 417 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: B 422 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 105 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8532 (mmm160) REVERT: C 123 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7453 (ttp-170) REVERT: C 127 ASP cc_start: 0.7618 (m-30) cc_final: 0.7391 (m-30) REVERT: C 196 GLU cc_start: 0.7777 (pt0) cc_final: 0.7296 (pm20) REVERT: C 304 LYS cc_start: 0.8812 (tttt) cc_final: 0.8520 (ttmm) REVERT: C 338 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8326 (ptpp) REVERT: C 423 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7738 (mt-10) REVERT: D 92 PHE cc_start: 0.8500 (p90) cc_final: 0.8031 (p90) REVERT: D 108 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 162 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7828 (mmp-170) REVERT: D 209 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7650 (t0) REVERT: D 213 ARG cc_start: 0.8033 (ttm110) cc_final: 0.7561 (ttm110) REVERT: D 291 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7928 (tm-30) REVERT: D 325 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7820 (mt-10) REVERT: D 390 ARG cc_start: 0.8273 (pmm-80) cc_final: 0.7852 (ptm-80) REVERT: D 391 ARG cc_start: 0.7828 (mmt180) cc_final: 0.5885 (ptt90) REVERT: D 421 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7426 (tp30) REVERT: E 148 ARG cc_start: 0.7956 (mmp80) cc_final: 0.7701 (mmm160) REVERT: E 193 ARG cc_start: 0.6330 (mtt180) cc_final: 0.6115 (mtt180) REVERT: E 199 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7323 (mtt180) REVERT: E 299 ARG cc_start: 0.6384 (ttp80) cc_final: 0.5547 (ttp80) REVERT: E 389 ILE cc_start: 0.6781 (mm) cc_final: 0.6562 (mm) REVERT: E 431 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7092 (tm) REVERT: E 448 MET cc_start: 0.5079 (mmm) cc_final: 0.4801 (mmm) REVERT: E 538 LYS cc_start: 0.8183 (mttt) cc_final: 0.7828 (mttt) REVERT: E 558 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7537 (mmm160) REVERT: E 559 PHE cc_start: 0.7849 (m-80) cc_final: 0.7558 (m-10) REVERT: E 578 ARG cc_start: 0.7383 (mtt90) cc_final: 0.7011 (mtt90) REVERT: E 589 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7079 (mpt) REVERT: E 612 ASP cc_start: 0.2429 (OUTLIER) cc_final: 0.2117 (m-30) REVERT: E 624 PHE cc_start: 0.8301 (t80) cc_final: 0.7938 (t80) REVERT: E 634 MET cc_start: 0.6313 (mmt) cc_final: 0.5958 (mmt) REVERT: E 654 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7783 (mm) outliers start: 130 outliers final: 94 residues processed: 608 average time/residue: 0.1643 time to fit residues: 139.8657 Evaluate side-chains 639 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 528 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 402 ARG Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 554 ASN Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 153 optimal weight: 0.9990 chunk 172 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 102 optimal weight: 0.2980 chunk 61 optimal weight: 0.5980 chunk 126 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 335 ASN D 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.161076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119644 restraints weight = 24374.547| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.60 r_work: 0.3241 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18264 Z= 0.112 Angle : 0.532 8.351 24812 Z= 0.271 Chirality : 0.043 0.197 2730 Planarity : 0.004 0.056 3198 Dihedral : 8.107 66.929 2811 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.17 % Allowed : 28.81 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.24 (0.18), residues: 2214 helix: 1.40 (0.17), residues: 978 sheet: 0.20 (0.30), residues: 342 loop : -1.28 (0.20), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 121 TYR 0.019 0.001 TYR B 36 PHE 0.034 0.001 PHE E 576 TRP 0.014 0.001 TRP B 344 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00254 (18263) covalent geometry : angle 0.53212 (24810) SS BOND : bond 0.00119 ( 1) SS BOND : angle 1.34952 ( 2) hydrogen bonds : bond 0.03812 ( 761) hydrogen bonds : angle 4.17018 ( 2193) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 553 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7937 (mp0) cc_final: 0.7130 (mp0) REVERT: A 31 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7568 (mm-40) REVERT: A 80 THR cc_start: 0.7852 (p) cc_final: 0.7583 (p) REVERT: A 102 ASN cc_start: 0.8464 (t0) cc_final: 0.7991 (t0) REVERT: A 120 ASP cc_start: 0.7597 (m-30) cc_final: 0.7302 (m-30) REVERT: A 121 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6879 (tpp80) REVERT: A 123 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7190 (mmt-90) REVERT: A 160 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8006 (t0) REVERT: A 166 LYS cc_start: 0.8140 (mtmm) cc_final: 0.7798 (mtmm) REVERT: A 196 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7624 (mm-30) REVERT: A 211 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: A 214 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8234 (ttp80) REVERT: A 233 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8058 (mm-40) REVERT: A 259 LEU cc_start: 0.8745 (tp) cc_final: 0.8067 (tt) REVERT: A 282 TYR cc_start: 0.7800 (m-10) cc_final: 0.7258 (m-10) REVERT: A 300 ASN cc_start: 0.8286 (t0) cc_final: 0.7871 (t0) REVERT: A 306 ASP cc_start: 0.7452 (t0) cc_final: 0.7080 (t0) REVERT: A 370 LYS cc_start: 0.8439 (tttt) cc_final: 0.8100 (ttmm) REVERT: A 429 GLU cc_start: 0.8088 (tp30) cc_final: 0.7593 (mp0) REVERT: A 431 ASP cc_start: 0.8325 (t0) cc_final: 0.8090 (t70) REVERT: A 432 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7869 (t80) REVERT: B 88 ASP cc_start: 0.7902 (p0) cc_final: 0.7556 (p0) REVERT: B 194 GLU cc_start: 0.7641 (pm20) cc_final: 0.7275 (pm20) REVERT: B 218 THR cc_start: 0.8876 (p) cc_final: 0.8579 (p) REVERT: B 219 THR cc_start: 0.8831 (t) cc_final: 0.8432 (p) REVERT: B 262 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8235 (ptm160) REVERT: B 282 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7296 (ttt180) REVERT: B 288 GLU cc_start: 0.7724 (pp20) cc_final: 0.7216 (pp20) REVERT: B 328 GLU cc_start: 0.7414 (tp30) cc_final: 0.7178 (tp30) REVERT: B 392 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7970 (mttp) REVERT: B 405 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7787 (mt-10) REVERT: B 417 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: B 422 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.6830 (t80) REVERT: C 113 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 119 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 123 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7520 (ttp-170) REVERT: C 127 ASP cc_start: 0.7606 (m-30) cc_final: 0.7393 (m-30) REVERT: C 256 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: C 304 LYS cc_start: 0.8752 (tttt) cc_final: 0.8440 (tppt) REVERT: C 338 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8297 (ptpp) REVERT: C 377 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7331 (tpt) REVERT: C 423 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7761 (mt-10) REVERT: D 19 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7980 (tmtm) REVERT: D 92 PHE cc_start: 0.8517 (p90) cc_final: 0.8070 (p90) REVERT: D 108 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 209 ASP cc_start: 0.8370 (t70) cc_final: 0.7635 (t0) REVERT: D 213 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7751 (ttm110) REVERT: D 311 LEU cc_start: 0.8215 (mp) cc_final: 0.7857 (mt) REVERT: D 312 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.7789 (m) REVERT: D 325 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7754 (mt-10) REVERT: D 390 ARG cc_start: 0.8282 (pmm-80) cc_final: 0.7853 (ptm-80) REVERT: D 391 ARG cc_start: 0.7794 (mmt180) cc_final: 0.5914 (ptt90) REVERT: D 421 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7381 (tp30) REVERT: E 193 ARG cc_start: 0.6310 (mtt180) cc_final: 0.6102 (mtt180) REVERT: E 199 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7017 (mtt180) REVERT: E 202 ARG cc_start: 0.7210 (mtp-110) cc_final: 0.6723 (mtp-110) REVERT: E 299 ARG cc_start: 0.6442 (ttp80) cc_final: 0.5657 (ttp80) REVERT: E 431 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7075 (tm) REVERT: E 448 MET cc_start: 0.5052 (mmm) cc_final: 0.4674 (mmm) REVERT: E 538 LYS cc_start: 0.8161 (mttt) cc_final: 0.7805 (mttt) REVERT: E 559 PHE cc_start: 0.7884 (m-80) cc_final: 0.7207 (m-80) REVERT: E 566 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6281 (mmt) REVERT: E 578 ARG cc_start: 0.7422 (mtt90) cc_final: 0.7059 (mtt90) REVERT: E 589 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7043 (mpt) REVERT: E 612 ASP cc_start: 0.2438 (OUTLIER) cc_final: 0.2129 (m-30) REVERT: E 624 PHE cc_start: 0.8336 (t80) cc_final: 0.7960 (t80) REVERT: E 634 MET cc_start: 0.6258 (mmt) cc_final: 0.5913 (mmt) REVERT: E 654 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7818 (mm) outliers start: 119 outliers final: 82 residues processed: 609 average time/residue: 0.1845 time to fit residues: 155.7739 Evaluate side-chains 644 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 542 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 192 HIS Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 554 ASN Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 25 optimal weight: 0.0980 chunk 132 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 191 optimal weight: 40.0000 chunk 135 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 335 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.161062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.118744 restraints weight = 24215.152| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.68 r_work: 0.3207 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18264 Z= 0.166 Angle : 0.568 9.415 24812 Z= 0.291 Chirality : 0.044 0.204 2730 Planarity : 0.004 0.064 3198 Dihedral : 8.098 66.453 2802 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 6.11 % Allowed : 28.55 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.18), residues: 2214 helix: 1.38 (0.17), residues: 977 sheet: 0.20 (0.30), residues: 342 loop : -1.26 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 121 TYR 0.022 0.001 TYR B 36 PHE 0.022 0.001 PHE E 576 TRP 0.015 0.002 TRP B 344 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00384 (18263) covalent geometry : angle 0.56820 (24810) SS BOND : bond 0.00147 ( 1) SS BOND : angle 1.29709 ( 2) hydrogen bonds : bond 0.04355 ( 761) hydrogen bonds : angle 4.23664 ( 2193) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 538 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7974 (mp0) cc_final: 0.7141 (mp0) REVERT: A 31 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7569 (mm-40) REVERT: A 80 THR cc_start: 0.7854 (p) cc_final: 0.7606 (p) REVERT: A 102 ASN cc_start: 0.8490 (t0) cc_final: 0.8049 (t0) REVERT: A 120 ASP cc_start: 0.7660 (m-30) cc_final: 0.7345 (m-30) REVERT: A 121 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6868 (tpp80) REVERT: A 123 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7266 (mmt-90) REVERT: A 160 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 166 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7850 (mtmm) REVERT: A 172 TYR cc_start: 0.8604 (t80) cc_final: 0.8326 (t80) REVERT: A 196 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7597 (mm-30) REVERT: A 211 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: A 214 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8183 (ttp80) REVERT: A 233 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8028 (mm-40) REVERT: A 259 LEU cc_start: 0.8721 (tp) cc_final: 0.8113 (tt) REVERT: A 282 TYR cc_start: 0.7905 (m-10) cc_final: 0.7359 (m-10) REVERT: A 300 ASN cc_start: 0.8367 (t0) cc_final: 0.7937 (t0) REVERT: A 306 ASP cc_start: 0.7507 (t0) cc_final: 0.7118 (t0) REVERT: A 370 LYS cc_start: 0.8416 (tttt) cc_final: 0.8060 (ttmm) REVERT: A 415 GLU cc_start: 0.7788 (tp30) cc_final: 0.7504 (tp30) REVERT: A 429 GLU cc_start: 0.8082 (tp30) cc_final: 0.7599 (mp0) REVERT: A 431 ASP cc_start: 0.8374 (t0) cc_final: 0.8144 (t70) REVERT: A 432 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7826 (t80) REVERT: B 88 ASP cc_start: 0.7994 (p0) cc_final: 0.7657 (p0) REVERT: B 194 GLU cc_start: 0.7725 (pm20) cc_final: 0.7315 (pm20) REVERT: B 203 ASP cc_start: 0.7915 (t0) cc_final: 0.7510 (t70) REVERT: B 218 THR cc_start: 0.8883 (p) cc_final: 0.8590 (p) REVERT: B 219 THR cc_start: 0.8791 (t) cc_final: 0.8396 (p) REVERT: B 257 MET cc_start: 0.8443 (mmt) cc_final: 0.7984 (mmt) REVERT: B 262 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8266 (ptm160) REVERT: B 282 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7426 (ttt180) REVERT: B 288 GLU cc_start: 0.7729 (pp20) cc_final: 0.7268 (pp20) REVERT: B 328 GLU cc_start: 0.7453 (tp30) cc_final: 0.7216 (tp30) REVERT: B 412 GLU cc_start: 0.7408 (tp30) cc_final: 0.7011 (tp30) REVERT: B 417 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: B 422 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.6838 (t80) REVERT: C 90 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7642 (mp0) REVERT: C 121 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7585 (mmm160) REVERT: C 123 ARG cc_start: 0.7922 (ttp-170) cc_final: 0.7458 (ttp-170) REVERT: C 127 ASP cc_start: 0.7684 (m-30) cc_final: 0.7467 (m-30) REVERT: C 196 GLU cc_start: 0.7760 (pt0) cc_final: 0.7333 (pm20) REVERT: C 214 ARG cc_start: 0.8032 (ttt-90) cc_final: 0.7535 (ttp-110) REVERT: C 304 LYS cc_start: 0.8844 (tttt) cc_final: 0.8534 (ttmm) REVERT: C 377 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7306 (tpt) REVERT: D 19 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7885 (tmtm) REVERT: D 92 PHE cc_start: 0.8527 (p90) cc_final: 0.8088 (p90) REVERT: D 101 TRP cc_start: 0.9043 (t60) cc_final: 0.8552 (t60) REVERT: D 108 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7496 (tm-30) REVERT: D 209 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7574 (t0) REVERT: D 213 ARG cc_start: 0.8132 (ttm110) cc_final: 0.7678 (ttm110) REVERT: D 293 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.7977 (t) REVERT: D 311 LEU cc_start: 0.8205 (mp) cc_final: 0.7982 (mt) REVERT: D 325 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7828 (mt-10) REVERT: D 390 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7854 (ptm-80) REVERT: D 391 ARG cc_start: 0.7838 (mmt180) cc_final: 0.5853 (ptt180) REVERT: D 421 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7403 (tp30) REVERT: E 199 ARG cc_start: 0.8010 (mtt180) cc_final: 0.7048 (mtt180) REVERT: E 202 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6699 (mtp-110) REVERT: E 218 SER cc_start: 0.6869 (p) cc_final: 0.6342 (m) REVERT: E 299 ARG cc_start: 0.6450 (ttp80) cc_final: 0.5689 (ttp80) REVERT: E 431 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7073 (tm) REVERT: E 538 LYS cc_start: 0.8177 (mttt) cc_final: 0.7828 (mttt) REVERT: E 558 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7240 (tmm160) REVERT: E 559 PHE cc_start: 0.7897 (m-80) cc_final: 0.6880 (m-80) REVERT: E 566 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6300 (mmt) REVERT: E 578 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7151 (mtt90) REVERT: E 589 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7033 (mpt) REVERT: E 612 ASP cc_start: 0.2431 (OUTLIER) cc_final: 0.2125 (m-30) REVERT: E 624 PHE cc_start: 0.8356 (t80) cc_final: 0.7967 (t80) REVERT: E 634 MET cc_start: 0.6269 (mmt) cc_final: 0.5843 (mmt) REVERT: E 654 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7827 (mm) outliers start: 118 outliers final: 88 residues processed: 594 average time/residue: 0.1652 time to fit residues: 137.5231 Evaluate side-chains 636 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 528 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 359 ARG Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 554 ASN Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 335 ASN C 91 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118120 restraints weight = 24179.597| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.69 r_work: 0.3198 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18264 Z= 0.166 Angle : 0.577 10.202 24812 Z= 0.295 Chirality : 0.045 0.202 2730 Planarity : 0.004 0.057 3198 Dihedral : 8.120 66.223 2802 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.96 % Allowed : 28.96 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.16 (0.18), residues: 2214 helix: 1.32 (0.17), residues: 983 sheet: 0.13 (0.29), residues: 342 loop : -1.28 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 121 TYR 0.017 0.001 TYR B 36 PHE 0.024 0.001 PHE E 576 TRP 0.017 0.002 TRP B 344 HIS 0.004 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00383 (18263) covalent geometry : angle 0.57644 (24810) SS BOND : bond 0.00157 ( 1) SS BOND : angle 1.28246 ( 2) hydrogen bonds : bond 0.04370 ( 761) hydrogen bonds : angle 4.27535 ( 2193) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 539 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7570 (mm-40) REVERT: A 80 THR cc_start: 0.7848 (p) cc_final: 0.7595 (p) REVERT: A 102 ASN cc_start: 0.8470 (t0) cc_final: 0.8004 (t0) REVERT: A 120 ASP cc_start: 0.7618 (m-30) cc_final: 0.7351 (m-30) REVERT: A 121 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6847 (tpp80) REVERT: A 123 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7191 (mmt-90) REVERT: A 160 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8056 (t0) REVERT: A 166 LYS cc_start: 0.8227 (mtmm) cc_final: 0.7856 (mtmm) REVERT: A 196 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7657 (mm-30) REVERT: A 211 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7426 (m-30) REVERT: A 214 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8199 (ttp80) REVERT: A 233 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8009 (mm-40) REVERT: A 259 LEU cc_start: 0.8704 (tp) cc_final: 0.8113 (tt) REVERT: A 282 TYR cc_start: 0.7911 (m-10) cc_final: 0.7381 (m-10) REVERT: A 300 ASN cc_start: 0.8353 (t0) cc_final: 0.7959 (t0) REVERT: A 306 ASP cc_start: 0.7511 (t0) cc_final: 0.7119 (t0) REVERT: A 370 LYS cc_start: 0.8428 (tttt) cc_final: 0.8074 (ttmm) REVERT: A 377 MET cc_start: 0.7693 (tpp) cc_final: 0.7155 (mmm) REVERT: A 415 GLU cc_start: 0.7765 (tp30) cc_final: 0.7491 (tp30) REVERT: A 429 GLU cc_start: 0.8062 (tp30) cc_final: 0.7584 (mp0) REVERT: A 431 ASP cc_start: 0.8380 (t0) cc_final: 0.8164 (t70) REVERT: A 432 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.7840 (t80) REVERT: B 48 SER cc_start: 0.8702 (m) cc_final: 0.8188 (p) REVERT: B 88 ASP cc_start: 0.8016 (p0) cc_final: 0.7682 (p0) REVERT: B 194 GLU cc_start: 0.7721 (pm20) cc_final: 0.7318 (pm20) REVERT: B 203 ASP cc_start: 0.7912 (t0) cc_final: 0.7500 (t70) REVERT: B 218 THR cc_start: 0.8884 (p) cc_final: 0.8666 (p) REVERT: B 262 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8264 (ptm160) REVERT: B 282 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7241 (ttt180) REVERT: B 288 GLU cc_start: 0.7740 (pp20) cc_final: 0.6888 (pp20) REVERT: B 328 GLU cc_start: 0.7476 (tp30) cc_final: 0.7242 (tp30) REVERT: B 412 GLU cc_start: 0.7415 (tp30) cc_final: 0.7039 (tp30) REVERT: B 417 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7522 (m-30) REVERT: B 422 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.6819 (t80) REVERT: C 90 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7652 (mp0) REVERT: C 91 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7468 (tt0) REVERT: C 121 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: C 123 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7460 (ttp-170) REVERT: C 127 ASP cc_start: 0.7692 (m-30) cc_final: 0.7466 (m-30) REVERT: C 196 GLU cc_start: 0.7775 (pt0) cc_final: 0.7342 (pm20) REVERT: C 214 ARG cc_start: 0.8031 (ttt-90) cc_final: 0.7535 (ttp-110) REVERT: C 304 LYS cc_start: 0.8862 (tttt) cc_final: 0.8543 (ttmm) REVERT: C 306 ASP cc_start: 0.8426 (t0) cc_final: 0.8226 (t0) REVERT: C 332 ILE cc_start: 0.8514 (mp) cc_final: 0.8311 (mt) REVERT: C 338 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8315 (ptpp) REVERT: C 377 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7295 (tpt) REVERT: D 92 PHE cc_start: 0.8535 (p90) cc_final: 0.8077 (p90) REVERT: D 101 TRP cc_start: 0.9055 (t60) cc_final: 0.8461 (t60) REVERT: D 108 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7519 (tm-30) REVERT: D 209 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.7655 (t0) REVERT: D 213 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7609 (ttp-110) REVERT: D 291 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 293 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.7980 (t) REVERT: D 311 LEU cc_start: 0.8224 (mp) cc_final: 0.7994 (mt) REVERT: D 325 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7809 (mt-10) REVERT: D 390 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7851 (ptm-80) REVERT: D 391 ARG cc_start: 0.7848 (mmt180) cc_final: 0.5866 (ptt180) REVERT: D 421 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7399 (tp30) REVERT: E 193 ARG cc_start: 0.6303 (mtt180) cc_final: 0.5978 (mtt180) REVERT: E 199 ARG cc_start: 0.7973 (mtt180) cc_final: 0.6987 (mtt180) REVERT: E 202 ARG cc_start: 0.7190 (mtp-110) cc_final: 0.6660 (mtp-110) REVERT: E 218 SER cc_start: 0.6897 (p) cc_final: 0.6377 (m) REVERT: E 299 ARG cc_start: 0.6510 (ttp80) cc_final: 0.5689 (ttp80) REVERT: E 431 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7092 (tm) REVERT: E 538 LYS cc_start: 0.8244 (mttt) cc_final: 0.7918 (mttt) REVERT: E 558 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7637 (mmm160) REVERT: E 566 MET cc_start: 0.6695 (OUTLIER) cc_final: 0.6307 (mmt) REVERT: E 578 ARG cc_start: 0.7546 (mtt90) cc_final: 0.7183 (mtt90) REVERT: E 589 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7075 (mpt) REVERT: E 612 ASP cc_start: 0.2431 (OUTLIER) cc_final: 0.2135 (m-30) REVERT: E 624 PHE cc_start: 0.8330 (t80) cc_final: 0.7964 (t80) REVERT: E 634 MET cc_start: 0.6266 (mmt) cc_final: 0.5826 (mmt) REVERT: E 654 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7845 (mm) outliers start: 115 outliers final: 88 residues processed: 595 average time/residue: 0.1647 time to fit residues: 136.9023 Evaluate side-chains 647 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 539 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 554 ASN Chi-restraints excluded: chain E residue 557 ILE Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 180 optimal weight: 40.0000 chunk 2 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 125 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 chunk 190 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS B 37 HIS B 307 HIS B 335 ASN C 91 GLN D 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.160915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.120571 restraints weight = 24082.230| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.21 r_work: 0.3194 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18264 Z= 0.133 Angle : 0.569 10.632 24812 Z= 0.289 Chirality : 0.044 0.338 2730 Planarity : 0.004 0.053 3198 Dihedral : 8.052 67.486 2802 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.65 % Allowed : 28.96 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.26 (0.18), residues: 2214 helix: 1.37 (0.17), residues: 983 sheet: 0.34 (0.30), residues: 326 loop : -1.24 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 121 TYR 0.016 0.001 TYR B 36 PHE 0.022 0.001 PHE E 576 TRP 0.019 0.002 TRP B 344 HIS 0.003 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00306 (18263) covalent geometry : angle 0.56927 (24810) SS BOND : bond 0.00145 ( 1) SS BOND : angle 1.24998 ( 2) hydrogen bonds : bond 0.04061 ( 761) hydrogen bonds : angle 4.21995 ( 2193) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4428 Ramachandran restraints generated. 2214 Oldfield, 0 Emsley, 2214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 542 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.8002 (mp0) cc_final: 0.7147 (mp0) REVERT: A 31 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7588 (mm-40) REVERT: A 80 THR cc_start: 0.7849 (p) cc_final: 0.7596 (p) REVERT: A 102 ASN cc_start: 0.8505 (t0) cc_final: 0.8058 (t0) REVERT: A 120 ASP cc_start: 0.7700 (m-30) cc_final: 0.7415 (m-30) REVERT: A 121 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6959 (tpp80) REVERT: A 123 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7251 (mmt-90) REVERT: A 160 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8038 (t0) REVERT: A 166 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7871 (mtmm) REVERT: A 172 TYR cc_start: 0.8597 (t80) cc_final: 0.8319 (t80) REVERT: A 196 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7756 (mm-30) REVERT: A 211 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: A 214 ARG cc_start: 0.8485 (ttp80) cc_final: 0.8221 (ttp80) REVERT: A 233 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8015 (mm-40) REVERT: A 259 LEU cc_start: 0.8728 (tp) cc_final: 0.8138 (tt) REVERT: A 282 TYR cc_start: 0.7909 (m-10) cc_final: 0.7380 (m-10) REVERT: A 300 ASN cc_start: 0.8337 (t0) cc_final: 0.7969 (t0) REVERT: A 306 ASP cc_start: 0.7489 (t0) cc_final: 0.7080 (t0) REVERT: A 370 LYS cc_start: 0.8447 (tttt) cc_final: 0.8090 (ttmm) REVERT: A 429 GLU cc_start: 0.8063 (tp30) cc_final: 0.7583 (mp0) REVERT: A 431 ASP cc_start: 0.8381 (t0) cc_final: 0.8142 (t70) REVERT: A 432 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 88 ASP cc_start: 0.8010 (p0) cc_final: 0.7679 (p0) REVERT: B 194 GLU cc_start: 0.7712 (pm20) cc_final: 0.7355 (pm20) REVERT: B 203 ASP cc_start: 0.7869 (t0) cc_final: 0.7455 (t70) REVERT: B 218 THR cc_start: 0.8866 (p) cc_final: 0.8651 (p) REVERT: B 262 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8305 (ptm160) REVERT: B 282 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7208 (ttt180) REVERT: B 288 GLU cc_start: 0.7740 (pp20) cc_final: 0.6900 (pp20) REVERT: B 328 GLU cc_start: 0.7475 (tp30) cc_final: 0.7239 (tp30) REVERT: B 335 ASN cc_start: 0.8199 (m-40) cc_final: 0.7932 (m110) REVERT: B 412 GLU cc_start: 0.7430 (tp30) cc_final: 0.7036 (tp30) REVERT: B 417 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 422 TYR cc_start: 0.8483 (OUTLIER) cc_final: 0.6859 (t80) REVERT: C 90 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7695 (mp0) REVERT: C 113 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7573 (mt-10) REVERT: C 121 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: C 123 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7496 (ttp-170) REVERT: C 127 ASP cc_start: 0.7703 (m-30) cc_final: 0.7477 (m-30) REVERT: C 196 GLU cc_start: 0.7777 (pt0) cc_final: 0.7342 (pm20) REVERT: C 214 ARG cc_start: 0.8028 (ttt-90) cc_final: 0.7543 (ttp-110) REVERT: C 304 LYS cc_start: 0.8850 (tttt) cc_final: 0.8534 (ttmm) REVERT: C 338 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8351 (ptpp) REVERT: C 377 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7302 (tpt) REVERT: D 92 PHE cc_start: 0.8554 (p90) cc_final: 0.8132 (p90) REVERT: D 101 TRP cc_start: 0.9026 (t60) cc_final: 0.8430 (t60) REVERT: D 108 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 209 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7688 (t0) REVERT: D 213 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7599 (ttp-110) REVERT: D 291 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 293 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.7962 (t) REVERT: D 311 LEU cc_start: 0.8219 (mp) cc_final: 0.7999 (mt) REVERT: D 325 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 390 ARG cc_start: 0.8312 (pmm-80) cc_final: 0.7886 (ptm-80) REVERT: D 391 ARG cc_start: 0.7849 (mmt180) cc_final: 0.5861 (ptt90) REVERT: D 421 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7379 (tp30) REVERT: E 193 ARG cc_start: 0.6237 (mtt180) cc_final: 0.5971 (mtt180) REVERT: E 199 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7001 (mtt180) REVERT: E 202 ARG cc_start: 0.7177 (mtp-110) cc_final: 0.6661 (mtp-110) REVERT: E 218 SER cc_start: 0.6859 (p) cc_final: 0.6347 (m) REVERT: E 299 ARG cc_start: 0.6365 (ttp80) cc_final: 0.5576 (ttp80) REVERT: E 431 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7056 (tm) REVERT: E 538 LYS cc_start: 0.8231 (mttt) cc_final: 0.7881 (mttt) REVERT: E 558 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7646 (mmm160) REVERT: E 566 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6281 (mmt) REVERT: E 573 PHE cc_start: 0.7463 (t80) cc_final: 0.7071 (t80) REVERT: E 578 ARG cc_start: 0.7543 (mtt90) cc_final: 0.7179 (mtt90) REVERT: E 589 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7053 (mpt) REVERT: E 612 ASP cc_start: 0.2437 (OUTLIER) cc_final: 0.2135 (m-30) REVERT: E 624 PHE cc_start: 0.8301 (t80) cc_final: 0.7934 (t80) REVERT: E 634 MET cc_start: 0.6309 (mmt) cc_final: 0.5874 (mmt) REVERT: E 654 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7859 (mm) outliers start: 109 outliers final: 89 residues processed: 595 average time/residue: 0.1726 time to fit residues: 143.7969 Evaluate side-chains 639 residues out of total 1930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 532 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 123 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 282 ARG Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 422 TYR Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 256 GLN Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 425 MET Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 329 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 392 LYS Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 488 LYS Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 554 ASN Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain E residue 579 SER Chi-restraints excluded: chain E residue 585 SER Chi-restraints excluded: chain E residue 589 MET Chi-restraints excluded: chain E residue 598 ASP Chi-restraints excluded: chain E residue 609 ASP Chi-restraints excluded: chain E residue 612 ASP Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 638 HIS Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 183 optimal weight: 50.0000 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 307 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.118332 restraints weight = 24371.825| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.68 r_work: 0.3200 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18264 Z= 0.171 Angle : 0.589 11.064 24812 Z= 0.301 Chirality : 0.045 0.327 2730 Planarity : 0.004 0.051 3198 Dihedral : 8.094 66.810 2802 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.01 % Allowed : 28.86 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: 0.21 (0.18), residues: 2214 helix: 1.31 (0.17), residues: 984 sheet: 0.31 (0.30), residues: 326 loop : -1.25 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 121 TYR 0.015 0.001 TYR B 36 PHE 0.023 0.001 PHE E 576 TRP 0.039 0.002 TRP B 344 HIS 0.005 0.001 HIS B 264 Details of bonding type rmsd covalent geometry : bond 0.00393 (18263) covalent geometry : angle 0.58922 (24810) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.25856 ( 2) hydrogen bonds : bond 0.04364 ( 761) hydrogen bonds : angle 4.27690 ( 2193) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6027.16 seconds wall clock time: 103 minutes 25.76 seconds (6205.76 seconds total)