Starting phenix.real_space_refine on Mon May 4 04:35:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.map" model { file = "/net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nf_75859/05_2026/11nf_75859.cif" } resolution = 2.34 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= 0.000 sd= 0.009 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 Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 4825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17870 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 409 Classifications: {'water': 409} Link IDs: {None: 408} Chain: "B" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 497 Classifications: {'water': 497} Link IDs: {None: 496} Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 431 Classifications: {'water': 431} Link IDs: {None: 430} Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 506 Classifications: {'water': 506} Link IDs: {None: 505} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 29.638 45.002 60.584 1.00 27.00 S ATOM 1170 SG CYS A 154 35.662 26.579 48.446 1.00 35.72 S ATOM 4552 SG CYS B 95 38.945 29.893 45.205 1.00 35.18 S ATOM 465 SG CYS A 62 36.226 32.751 50.729 1.00 27.27 S ATOM 652 SG CYS A 88 41.674 28.413 50.653 1.00 33.37 S ATOM 652 SG CYS A 88 41.674 28.413 50.653 1.00 33.37 S ATOM 5005 SG CYS B 153 40.118 24.528 46.713 1.00 39.26 S ATOM 4372 SG CYS B 70 45.595 28.665 45.166 1.00 27.85 S ATOM 4552 SG CYS B 95 38.945 29.893 45.205 1.00 35.18 S ATOM 10056 SG CYS C 275 107.256 56.268 60.694 1.00 29.03 S ATOM 9134 SG CYS C 154 100.896 74.844 48.400 1.00 33.74 S ATOM 12516 SG CYS D 95 97.772 71.508 45.255 1.00 31.99 S ATOM 8429 SG CYS C 62 100.454 68.663 50.543 1.00 25.02 S ATOM 8616 SG CYS C 88 95.132 72.858 50.575 1.00 29.67 S ATOM 8616 SG CYS C 88 95.132 72.858 50.575 1.00 29.67 S ATOM 12969 SG CYS D 153 96.603 76.859 46.710 1.00 40.76 S ATOM 12336 SG CYS D 70 90.962 72.560 45.061 1.00 27.64 S ATOM 12516 SG CYS D 95 97.772 71.508 45.255 1.00 31.99 S Time building chain proxies: 5.82, per 1000 atoms: 0.33 Number of scatterers: 17870 At special positions: 0 Unit cell: (136.71, 104.37, 99.96, 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) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 4825 8.00 N 2702 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 58.5% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.179A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.830A pdb=" N LYS A 44 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.787A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.793A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.146A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.170A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.874A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.681A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 343 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 358 through 369 removed outlier: 3.768A pdb=" N HIS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 366 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.376A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.539A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.505A pdb=" N TYR A 446 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.705A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.518A pdb=" N LYS A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 31 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 3.990A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.968A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.847A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 321 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.087A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.974A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.416A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.650A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.875A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.787A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.148A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.044A pdb=" N LEU C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 275 through 291 removed outlier: 3.584A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.613A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 3.521A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.683A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.688A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 4.013A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.973A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.895A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.106A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.721A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.411A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.592A pdb=" N LYS A 349 " --> pdb=" O MET A 372 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 374 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.196A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.396A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 270 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 removed outlier: 8.548A pdb=" N VAL B 114 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.252A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.750A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 10.104A pdb=" N LEU C 399 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 375 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR C 401 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL C 351 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR C 377 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 353 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR C 379 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 421 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.971A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.319A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 removed outlier: 8.437A pdb=" N VAL D 114 " --> pdb=" O THR D 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.343A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.645A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.53: 15695 1.53 - 1.88: 652 1.88 - 2.23: 27 2.23 - 2.58: 91 2.58 - 2.93: 18 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 2.928 -0.728 2.00e-02 2.50e+03 1.33e+03 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 2.922 -0.722 2.00e-02 2.50e+03 1.30e+03 bond pdb="FE4 CLF B 602 " pdb="FE5 CLF B 602 " ideal model delta sigma weight residual 2.200 2.893 -0.693 2.00e-02 2.50e+03 1.20e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 2.887 -0.687 2.00e-02 2.50e+03 1.18e+03 bond pdb="FE6 CLF D 602 " pdb="FE7 CLF D 602 " ideal model delta sigma weight residual 2.200 2.854 -0.654 2.00e-02 2.50e+03 1.07e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 22230 6.87 - 13.74: 7 13.74 - 20.61: 2 20.61 - 27.48: 0 27.48 - 34.35: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.65 34.35 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.66 34.34 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 57.07 32.93 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 57.10 32.90 3.00e+00 1.11e-01 1.20e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 106.62 -16.62 3.00e+00 1.11e-01 3.07e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 9201 17.74 - 35.47: 714 35.47 - 53.21: 122 53.21 - 70.95: 35 70.95 - 88.69: 29 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA PHE B 367 " pdb=" C PHE B 367 " pdb=" N ALA B 368 " pdb=" CA ALA B 368 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C PHE A 431 " pdb=" N PHE A 431 " pdb=" CA PHE A 431 " pdb=" CB PHE A 431 " ideal model delta harmonic sigma weight residual -122.60 -133.61 11.01 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" CA PHE D 367 " pdb=" C PHE D 367 " pdb=" N ALA D 368 " pdb=" CA ALA D 368 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1784 0.059 - 0.118: 423 0.118 - 0.176: 99 0.176 - 0.235: 25 0.235 - 0.294: 5 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA SER C 397 " pdb=" N SER C 397 " pdb=" C SER C 397 " pdb=" CB SER C 397 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 404 " pdb=" CA VAL A 404 " pdb=" CG1 VAL A 404 " pdb=" CG2 VAL A 404 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 275 " -0.016 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C CYS C 275 " 0.058 2.00e-02 2.50e+03 pdb=" O CYS C 275 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR C 276 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 57 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.19e+00 pdb=" C PHE D 57 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE D 57 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN D 58 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 513 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C GLN D 513 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN D 513 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA D 514 " -0.015 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 529 2.59 - 3.16: 15270 3.16 - 3.74: 31481 3.74 - 4.32: 48273 4.32 - 4.90: 72525 Nonbonded interactions: 168078 Sorted by model distance: nonbonded pdb=" O ASN C 98 " pdb=" OD1 ASN C 98 " model vdw 2.007 3.040 nonbonded pdb=" OE2 GLU B 109 " pdb="FE FE D 601 " model vdw 2.056 2.260 nonbonded pdb=" OE2 GLU D 109 " pdb="FE FE B 601 " model vdw 2.163 2.260 nonbonded pdb=" OE1 GLN D 53 " pdb=" OG1 THR D 436 " model vdw 2.217 3.040 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.248 2.260 ... (remaining 168073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.43 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.830 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.025 0.889 16499 Z= 1.412 Angle : 0.977 34.347 22243 Z= 0.595 Chirality : 0.058 0.294 2336 Planarity : 0.005 0.038 2858 Dihedral : 14.074 88.686 6433 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 0.58 % Allowed : 2.03 % Favored : 97.39 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 1992 helix: 0.99 (0.17), residues: 980 sheet: -0.59 (0.42), residues: 138 loop : -0.78 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 277 TYR 0.024 0.003 TYR B 88 PHE 0.036 0.002 PHE C 118 TRP 0.026 0.002 TRP A 335 HIS 0.009 0.001 HIS D 90 Details of bonding type rmsd covalent geometry : bond 0.02377 (16483) covalent geometry : angle 0.97690 (22243) hydrogen bonds : bond 0.14936 ( 789) hydrogen bonds : angle 6.85130 ( 2274) Misc. bond : bond 0.24369 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 305 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7209 (mt-10) REVERT: A 23 LYS cc_start: 0.7809 (tttt) cc_final: 0.7567 (tttt) REVERT: A 26 LYS cc_start: 0.7886 (tttm) cc_final: 0.7130 (ttmt) REVERT: A 112 MET cc_start: 0.9280 (mtp) cc_final: 0.8822 (mtp) REVERT: A 120 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7341 (mp0) REVERT: A 121 LYS cc_start: 0.8251 (ptmt) cc_final: 0.7847 (pttm) REVERT: A 164 GLU cc_start: 0.7144 (tt0) cc_final: 0.6900 (mp0) REVERT: A 288 GLU cc_start: 0.7887 (tt0) cc_final: 0.7468 (pt0) REVERT: A 392 LYS cc_start: 0.8096 (pttt) cc_final: 0.7707 (pttp) REVERT: A 415 ARG cc_start: 0.7799 (tpp80) cc_final: 0.6745 (tmt170) REVERT: B 6 ASP cc_start: 0.6936 (m-30) cc_final: 0.6732 (p0) REVERT: B 60 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7832 (pt0) REVERT: B 120 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6957 (mt-10) REVERT: B 171 LYS cc_start: 0.7399 (tttm) cc_final: 0.7140 (mtpt) REVERT: B 268 GLN cc_start: 0.7825 (tt0) cc_final: 0.7326 (mt0) REVERT: B 330 MET cc_start: 0.8711 (mtp) cc_final: 0.8442 (mtp) REVERT: C 14 GLN cc_start: 0.7247 (mm110) cc_final: 0.7032 (mp10) REVERT: C 25 ARG cc_start: 0.7792 (ptp90) cc_final: 0.7533 (ptp-170) REVERT: C 26 LYS cc_start: 0.7954 (tttm) cc_final: 0.7133 (ttmt) REVERT: C 112 MET cc_start: 0.9277 (mtp) cc_final: 0.8876 (mtp) REVERT: C 120 GLU cc_start: 0.8333 (tp30) cc_final: 0.7835 (tt0) REVERT: C 168 LYS cc_start: 0.7776 (mmmt) cc_final: 0.7424 (mtmm) REVERT: C 288 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 318 GLU cc_start: 0.7953 (pt0) cc_final: 0.6896 (tp30) REVERT: C 322 LYS cc_start: 0.7046 (tttm) cc_final: 0.6776 (tttt) REVERT: C 397 SER cc_start: 0.8385 (p) cc_final: 0.8161 (m) REVERT: C 415 ARG cc_start: 0.7466 (tpp80) cc_final: 0.6841 (tmt170) REVERT: D 6 ASP cc_start: 0.7463 (m-30) cc_final: 0.7167 (p0) REVERT: D 54 GLU cc_start: 0.7999 (tt0) cc_final: 0.7733 (mp0) REVERT: D 60 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7880 (pt0) REVERT: D 125 PHE cc_start: 0.7112 (m-80) cc_final: 0.6728 (m-80) REVERT: D 222 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8174 (mtmt) REVERT: D 243 MET cc_start: 0.7931 (mtt) cc_final: 0.7729 (mtm) REVERT: D 330 MET cc_start: 0.8615 (mtp) cc_final: 0.8404 (mtp) outliers start: 10 outliers final: 3 residues processed: 313 average time/residue: 0.9273 time to fit residues: 314.1888 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 206 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain C residue 362 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 7.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 145 ASN A 196 HIS B 18 GLN B 45 GLN B 58 GLN B 136 GLN B 168 ASN B 518 ASN C 29 ASN C 98 ASN C 252 GLN D 45 GLN D 518 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.096770 restraints weight = 18127.710| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.32 r_work: 0.3017 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 16499 Z= 0.181 Angle : 0.745 28.774 22243 Z= 0.358 Chirality : 0.047 0.172 2336 Planarity : 0.005 0.040 2858 Dihedral : 5.358 50.728 2524 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.39 % Allowed : 8.01 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 1992 helix: 1.25 (0.16), residues: 990 sheet: -0.34 (0.43), residues: 126 loop : -0.68 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 277 TYR 0.023 0.002 TYR B 102 PHE 0.032 0.002 PHE C 118 TRP 0.018 0.002 TRP A 335 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00382 (16483) covalent geometry : angle 0.74489 (22243) hydrogen bonds : bond 0.05539 ( 789) hydrogen bonds : angle 5.54711 ( 2274) Misc. bond : bond 0.09743 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7105 (mt-10) REVERT: A 22 GLU cc_start: 0.7722 (tp30) cc_final: 0.7429 (mm-30) REVERT: A 23 LYS cc_start: 0.7755 (tttt) cc_final: 0.7501 (tttt) REVERT: A 26 LYS cc_start: 0.7779 (tttm) cc_final: 0.6988 (ttmt) REVERT: A 112 MET cc_start: 0.9165 (mtp) cc_final: 0.8637 (mtp) REVERT: A 120 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7128 (mp0) REVERT: A 168 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7268 (mttt) REVERT: A 288 GLU cc_start: 0.7776 (tt0) cc_final: 0.7214 (pt0) REVERT: A 318 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: A 391 MET cc_start: 0.8079 (mmm) cc_final: 0.7857 (mmm) REVERT: A 392 LYS cc_start: 0.8163 (pttt) cc_final: 0.7700 (pttp) REVERT: A 415 ARG cc_start: 0.7753 (tpp80) cc_final: 0.6656 (tmt170) REVERT: B 6 ASP cc_start: 0.7021 (m-30) cc_final: 0.6755 (p0) REVERT: B 54 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: B 60 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7732 (pt0) REVERT: B 120 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6722 (mt-10) REVERT: B 171 LYS cc_start: 0.7309 (tttm) cc_final: 0.7007 (mtpt) REVERT: B 268 GLN cc_start: 0.7671 (tt0) cc_final: 0.7145 (mt0) REVERT: B 330 MET cc_start: 0.8645 (mtp) cc_final: 0.8338 (mtp) REVERT: B 389 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: C 26 LYS cc_start: 0.7830 (tttm) cc_final: 0.6972 (ttmt) REVERT: C 112 MET cc_start: 0.9176 (mtp) cc_final: 0.8688 (mtp) REVERT: C 120 GLU cc_start: 0.8238 (tp30) cc_final: 0.7775 (tt0) REVERT: C 168 LYS cc_start: 0.7565 (mmmt) cc_final: 0.7119 (mtmm) REVERT: C 288 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7149 (mt-10) REVERT: C 322 LYS cc_start: 0.6854 (tttm) cc_final: 0.6598 (tttt) REVERT: C 397 SER cc_start: 0.8338 (p) cc_final: 0.8055 (m) REVERT: C 415 ARG cc_start: 0.7625 (tpp80) cc_final: 0.6912 (tmt170) REVERT: C 467 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8692 (tp) REVERT: D 6 ASP cc_start: 0.7528 (m-30) cc_final: 0.7092 (p0) REVERT: D 7 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7445 (mmtt) REVERT: D 54 GLU cc_start: 0.7817 (tt0) cc_final: 0.7556 (mp0) REVERT: D 60 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7706 (pt0) REVERT: D 125 PHE cc_start: 0.7049 (m-80) cc_final: 0.6710 (m-80) REVERT: D 171 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6725 (mttp) REVERT: D 222 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8137 (mtmt) REVERT: D 243 MET cc_start: 0.7934 (mtt) cc_final: 0.7630 (mtm) REVERT: D 330 MET cc_start: 0.8633 (mtp) cc_final: 0.8352 (mtp) outliers start: 24 outliers final: 7 residues processed: 212 average time/residue: 0.8826 time to fit residues: 204.2868 Evaluate side-chains 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 212 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 160 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.098309 restraints weight = 22916.548| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.52 r_work: 0.3037 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 16499 Z= 0.136 Angle : 0.674 29.071 22243 Z= 0.315 Chirality : 0.044 0.142 2336 Planarity : 0.004 0.040 2858 Dihedral : 4.940 57.573 2518 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.57 % Allowed : 9.11 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 1992 helix: 1.51 (0.17), residues: 992 sheet: -0.67 (0.41), residues: 142 loop : -0.56 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 277 TYR 0.015 0.001 TYR B 102 PHE 0.021 0.001 PHE C 118 TRP 0.014 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00268 (16483) covalent geometry : angle 0.67432 (22243) hydrogen bonds : bond 0.04376 ( 789) hydrogen bonds : angle 5.23205 ( 2274) Misc. bond : bond 0.08380 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 10 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6596 (mt-10) REVERT: A 22 GLU cc_start: 0.7671 (tp30) cc_final: 0.7379 (mm-30) REVERT: A 23 LYS cc_start: 0.7596 (tttt) cc_final: 0.7344 (tttt) REVERT: A 26 LYS cc_start: 0.7735 (tttm) cc_final: 0.6962 (ttmt) REVERT: A 35 ASN cc_start: 0.8550 (t0) cc_final: 0.8255 (t0) REVERT: A 112 MET cc_start: 0.9127 (mtp) cc_final: 0.8611 (mtp) REVERT: A 120 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7124 (mp0) REVERT: A 168 LYS cc_start: 0.7817 (mtmm) cc_final: 0.7404 (mttt) REVERT: A 243 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: A 288 GLU cc_start: 0.7814 (tt0) cc_final: 0.7211 (pt0) REVERT: A 391 MET cc_start: 0.8113 (mmm) cc_final: 0.7879 (mmm) REVERT: A 392 LYS cc_start: 0.8210 (pttt) cc_final: 0.7848 (ptmm) REVERT: A 415 ARG cc_start: 0.7742 (tpp80) cc_final: 0.6612 (tmt170) REVERT: A 473 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7449 (mptt) REVERT: B 6 ASP cc_start: 0.7013 (m-30) cc_final: 0.6740 (p0) REVERT: B 54 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 60 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7786 (pt0) REVERT: B 120 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6702 (mt-10) REVERT: B 171 LYS cc_start: 0.7311 (tttm) cc_final: 0.6968 (mtpt) REVERT: B 222 LYS cc_start: 0.8562 (mttt) cc_final: 0.7990 (mtmt) REVERT: B 268 GLN cc_start: 0.7696 (tt0) cc_final: 0.7068 (mt0) REVERT: B 330 MET cc_start: 0.8592 (mtp) cc_final: 0.8295 (mtp) REVERT: C 15 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6594 (mm-30) REVERT: C 26 LYS cc_start: 0.7842 (tttm) cc_final: 0.6900 (mtmt) REVERT: C 112 MET cc_start: 0.9141 (mtp) cc_final: 0.8638 (mtp) REVERT: C 120 GLU cc_start: 0.8258 (tp30) cc_final: 0.7798 (tt0) REVERT: C 168 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7140 (mtmm) REVERT: C 288 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 368 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8194 (mt-10) REVERT: C 397 SER cc_start: 0.8297 (p) cc_final: 0.8026 (m) REVERT: C 415 ARG cc_start: 0.7711 (tpp80) cc_final: 0.6891 (tmt170) REVERT: C 467 LEU cc_start: 0.8932 (tt) cc_final: 0.8636 (tp) REVERT: D 6 ASP cc_start: 0.7631 (m-30) cc_final: 0.7142 (p0) REVERT: D 54 GLU cc_start: 0.7827 (tt0) cc_final: 0.7526 (mp0) REVERT: D 60 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7743 (pt0) REVERT: D 172 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: D 222 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8097 (mtmt) REVERT: D 243 MET cc_start: 0.7894 (mtt) cc_final: 0.7606 (mtm) REVERT: D 312 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: D 330 MET cc_start: 0.8605 (mtp) cc_final: 0.8317 (mtp) REVERT: D 417 LYS cc_start: 0.8285 (tptp) cc_final: 0.7623 (tppt) outliers start: 27 outliers final: 6 residues processed: 220 average time/residue: 0.8789 time to fit residues: 211.0928 Evaluate side-chains 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 312 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 113 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN A 383 HIS C 98 ASN C 432 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092116 restraints weight = 27516.254| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.64 r_work: 0.2933 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.240 16499 Z= 0.220 Angle : 0.761 29.170 22243 Z= 0.367 Chirality : 0.049 0.159 2336 Planarity : 0.005 0.047 2858 Dihedral : 5.069 51.292 2518 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.09 % Allowed : 9.52 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.49 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1002 sheet: -0.37 (0.43), residues: 130 loop : -0.63 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 277 TYR 0.022 0.002 TYR B 88 PHE 0.028 0.002 PHE C 118 TRP 0.013 0.002 TRP C 335 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00483 (16483) covalent geometry : angle 0.76078 (22243) hydrogen bonds : bond 0.06121 ( 789) hydrogen bonds : angle 5.42013 ( 2274) Misc. bond : bond 0.11493 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 22 GLU cc_start: 0.7766 (tp30) cc_final: 0.7458 (mm-30) REVERT: A 23 LYS cc_start: 0.7805 (tttt) cc_final: 0.7464 (tttt) REVERT: A 26 LYS cc_start: 0.7819 (tttm) cc_final: 0.7060 (ttmt) REVERT: A 112 MET cc_start: 0.9220 (mtp) cc_final: 0.8696 (mtp) REVERT: A 120 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7178 (mp0) REVERT: A 168 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7658 (mtmt) REVERT: A 243 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: A 288 GLU cc_start: 0.7808 (tt0) cc_final: 0.7200 (pt0) REVERT: A 318 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6659 (tp30) REVERT: A 391 MET cc_start: 0.8189 (mmm) cc_final: 0.7967 (mmm) REVERT: A 392 LYS cc_start: 0.8230 (pttt) cc_final: 0.7758 (pttp) REVERT: A 415 ARG cc_start: 0.7843 (tpp80) cc_final: 0.6620 (tmt170) REVERT: B 6 ASP cc_start: 0.7257 (m-30) cc_final: 0.6831 (p0) REVERT: B 54 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: B 60 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7760 (pt0) REVERT: B 120 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 171 LYS cc_start: 0.7345 (tttm) cc_final: 0.7034 (mtpt) REVERT: B 222 LYS cc_start: 0.8563 (mttt) cc_final: 0.8014 (mtmt) REVERT: B 268 GLN cc_start: 0.7743 (tt0) cc_final: 0.7134 (mt0) REVERT: C 26 LYS cc_start: 0.7914 (tttm) cc_final: 0.7031 (ttmt) REVERT: C 112 MET cc_start: 0.9222 (mtp) cc_final: 0.8771 (mtp) REVERT: C 120 GLU cc_start: 0.8309 (tp30) cc_final: 0.7800 (tt0) REVERT: C 161 ASP cc_start: 0.7559 (m-30) cc_final: 0.7348 (m-30) REVERT: C 168 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7183 (mtmm) REVERT: C 287 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: C 288 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7144 (mt-10) REVERT: C 318 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: C 397 SER cc_start: 0.8372 (p) cc_final: 0.8018 (m) REVERT: C 415 ARG cc_start: 0.7802 (tpp80) cc_final: 0.6745 (tmt170) REVERT: D 6 ASP cc_start: 0.7705 (m-30) cc_final: 0.7208 (p0) REVERT: D 7 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7461 (mmtt) REVERT: D 54 GLU cc_start: 0.7904 (tt0) cc_final: 0.7597 (mp0) REVERT: D 60 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7727 (pt0) REVERT: D 172 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: D 222 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8154 (mtmt) REVERT: D 243 MET cc_start: 0.7919 (mtt) cc_final: 0.7598 (mtm) REVERT: D 312 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: D 330 MET cc_start: 0.8709 (mtp) cc_final: 0.8439 (mtp) outliers start: 36 outliers final: 13 residues processed: 211 average time/residue: 0.8865 time to fit residues: 204.1380 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 312 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 104 optimal weight: 0.0980 chunk 84 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 457 HIS C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094844 restraints weight = 27370.699| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.65 r_work: 0.2981 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 16499 Z= 0.150 Angle : 0.690 29.060 22243 Z= 0.324 Chirality : 0.044 0.144 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.858 51.076 2518 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 10.74 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.64 (0.18), residues: 1992 helix: 1.43 (0.16), residues: 994 sheet: -0.62 (0.41), residues: 142 loop : -0.54 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 25 TYR 0.014 0.002 TYR B 102 PHE 0.018 0.001 PHE C 118 TRP 0.013 0.001 TRP A 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00304 (16483) covalent geometry : angle 0.69049 (22243) hydrogen bonds : bond 0.04801 ( 789) hydrogen bonds : angle 5.24021 ( 2274) Misc. bond : bond 0.09234 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 22 GLU cc_start: 0.7744 (tp30) cc_final: 0.7451 (mm-30) REVERT: A 23 LYS cc_start: 0.7709 (tttt) cc_final: 0.7430 (tttt) REVERT: A 26 LYS cc_start: 0.7793 (tttm) cc_final: 0.7018 (ttmt) REVERT: A 112 MET cc_start: 0.9181 (mtp) cc_final: 0.8674 (mtp) REVERT: A 168 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7646 (mtmt) REVERT: A 243 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: A 288 GLU cc_start: 0.7814 (tt0) cc_final: 0.7155 (pt0) REVERT: A 391 MET cc_start: 0.8073 (mmm) cc_final: 0.7851 (mmm) REVERT: A 392 LYS cc_start: 0.8250 (pttt) cc_final: 0.7883 (ptmm) REVERT: A 415 ARG cc_start: 0.7831 (tpp80) cc_final: 0.6622 (tmt170) REVERT: B 6 ASP cc_start: 0.7226 (m-30) cc_final: 0.6815 (p0) REVERT: B 54 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 60 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7707 (pt0) REVERT: B 120 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6761 (mt-10) REVERT: B 171 LYS cc_start: 0.7348 (tttm) cc_final: 0.6995 (mtpt) REVERT: B 222 LYS cc_start: 0.8547 (mttt) cc_final: 0.7997 (mtmt) REVERT: B 268 GLN cc_start: 0.7747 (tt0) cc_final: 0.7094 (mt0) REVERT: B 312 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: C 15 GLU cc_start: 0.7713 (mt-10) cc_final: 0.6602 (mm-30) REVERT: C 26 LYS cc_start: 0.7874 (tttm) cc_final: 0.6959 (ttmt) REVERT: C 112 MET cc_start: 0.9180 (mtp) cc_final: 0.8703 (mtp) REVERT: C 120 GLU cc_start: 0.8303 (tp30) cc_final: 0.7812 (tt0) REVERT: C 168 LYS cc_start: 0.7608 (mmmt) cc_final: 0.7134 (mtmm) REVERT: C 288 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7138 (mt-10) REVERT: C 397 SER cc_start: 0.8319 (p) cc_final: 0.8018 (m) REVERT: C 415 ARG cc_start: 0.7802 (tpp80) cc_final: 0.6722 (tmt170) REVERT: C 467 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8637 (tp) REVERT: C 476 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 6 ASP cc_start: 0.7691 (m-30) cc_final: 0.7165 (p0) REVERT: D 54 GLU cc_start: 0.7890 (tt0) cc_final: 0.7556 (mp0) REVERT: D 60 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7768 (pt0) REVERT: D 171 LYS cc_start: 0.7433 (mtpt) cc_final: 0.6750 (mttp) REVERT: D 172 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 222 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8111 (mtmt) REVERT: D 243 MET cc_start: 0.7966 (mtt) cc_final: 0.7636 (mtm) REVERT: D 312 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: D 330 MET cc_start: 0.8685 (mtp) cc_final: 0.8422 (mtp) outliers start: 29 outliers final: 12 residues processed: 211 average time/residue: 0.8688 time to fit residues: 200.4937 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 185 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.093537 restraints weight = 29680.979| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.71 r_work: 0.2959 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.206 16499 Z= 0.166 Angle : 0.706 29.119 22243 Z= 0.333 Chirality : 0.045 0.146 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.813 51.415 2518 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 10.80 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1992 helix: 1.39 (0.16), residues: 1002 sheet: -0.75 (0.40), residues: 156 loop : -0.49 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.016 0.002 TYR B 88 PHE 0.018 0.002 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00347 (16483) covalent geometry : angle 0.70643 (22243) hydrogen bonds : bond 0.05144 ( 789) hydrogen bonds : angle 5.24715 ( 2274) Misc. bond : bond 0.09836 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6992 (mt-10) REVERT: A 22 GLU cc_start: 0.7766 (tp30) cc_final: 0.7460 (mm-30) REVERT: A 23 LYS cc_start: 0.7733 (tttt) cc_final: 0.7426 (tttt) REVERT: A 26 LYS cc_start: 0.7794 (tttm) cc_final: 0.7025 (ttmt) REVERT: A 112 MET cc_start: 0.9199 (mtp) cc_final: 0.8713 (mtp) REVERT: A 168 LYS cc_start: 0.8045 (mtmm) cc_final: 0.7689 (mtmt) REVERT: A 243 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: A 288 GLU cc_start: 0.7842 (tt0) cc_final: 0.7144 (pt0) REVERT: A 391 MET cc_start: 0.8061 (mmm) cc_final: 0.7853 (mmm) REVERT: A 392 LYS cc_start: 0.8268 (pttt) cc_final: 0.7897 (ptmm) REVERT: A 415 ARG cc_start: 0.7865 (tpp80) cc_final: 0.6634 (tmt170) REVERT: B 6 ASP cc_start: 0.7252 (m-30) cc_final: 0.6777 (p0) REVERT: B 54 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: B 60 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7712 (pt0) REVERT: B 120 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6791 (mt-10) REVERT: B 171 LYS cc_start: 0.7333 (tttm) cc_final: 0.6984 (mtpt) REVERT: B 222 LYS cc_start: 0.8557 (mttt) cc_final: 0.7969 (mtmt) REVERT: B 268 GLN cc_start: 0.7785 (tt0) cc_final: 0.7150 (mt0) REVERT: B 312 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: C 26 LYS cc_start: 0.7906 (tttm) cc_final: 0.7006 (ttmt) REVERT: C 112 MET cc_start: 0.9194 (mtp) cc_final: 0.8730 (mtp) REVERT: C 120 GLU cc_start: 0.8278 (tp30) cc_final: 0.7776 (tt0) REVERT: C 161 ASP cc_start: 0.7561 (m-30) cc_final: 0.7359 (m-30) REVERT: C 168 LYS cc_start: 0.7605 (mmmt) cc_final: 0.7128 (mtmm) REVERT: C 287 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: C 288 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7121 (mt-10) REVERT: C 322 LYS cc_start: 0.7036 (ptmm) cc_final: 0.6344 (ptpt) REVERT: C 397 SER cc_start: 0.8343 (p) cc_final: 0.8004 (m) REVERT: C 415 ARG cc_start: 0.7796 (tpp80) cc_final: 0.6655 (tmt170) REVERT: C 467 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8618 (tp) REVERT: D 2 SER cc_start: 0.8534 (m) cc_final: 0.8224 (t) REVERT: D 6 ASP cc_start: 0.7712 (m-30) cc_final: 0.7166 (p0) REVERT: D 7 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7479 (mmtt) REVERT: D 54 GLU cc_start: 0.7900 (tt0) cc_final: 0.7552 (mp0) REVERT: D 60 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7749 (pt0) REVERT: D 171 LYS cc_start: 0.7470 (mtpt) cc_final: 0.6807 (mttp) REVERT: D 222 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8146 (mtmt) REVERT: D 238 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7654 (mtt180) REVERT: D 243 MET cc_start: 0.7931 (mtt) cc_final: 0.7588 (mtm) REVERT: D 312 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7520 (mt-10) outliers start: 32 outliers final: 15 residues processed: 211 average time/residue: 0.8908 time to fit residues: 205.0680 Evaluate side-chains 212 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 22 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 189 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095819 restraints weight = 31039.443| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.76 r_work: 0.2991 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2884 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 16499 Z= 0.134 Angle : 0.671 29.049 22243 Z= 0.312 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.632 51.134 2518 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.63 % Allowed : 10.97 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.79 (0.18), residues: 1992 helix: 1.55 (0.17), residues: 996 sheet: -0.59 (0.42), residues: 142 loop : -0.45 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.013 0.001 TYR A 229 PHE 0.014 0.001 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00264 (16483) covalent geometry : angle 0.67058 (22243) hydrogen bonds : bond 0.04351 ( 789) hydrogen bonds : angle 5.12534 ( 2274) Misc. bond : bond 0.08262 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 22 GLU cc_start: 0.7751 (tp30) cc_final: 0.7471 (mm-30) REVERT: A 23 LYS cc_start: 0.7655 (tttt) cc_final: 0.7415 (tttt) REVERT: A 26 LYS cc_start: 0.7794 (tttm) cc_final: 0.7029 (ttmt) REVERT: A 112 MET cc_start: 0.9147 (mtp) cc_final: 0.8633 (mtp) REVERT: A 168 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7687 (mtmt) REVERT: A 288 GLU cc_start: 0.7843 (tt0) cc_final: 0.7148 (pt0) REVERT: A 391 MET cc_start: 0.8032 (mmm) cc_final: 0.7828 (mmm) REVERT: A 392 LYS cc_start: 0.8241 (pttt) cc_final: 0.7867 (ptmm) REVERT: A 415 ARG cc_start: 0.7822 (tpp80) cc_final: 0.6580 (tmt170) REVERT: A 476 GLN cc_start: 0.8252 (tt0) cc_final: 0.7966 (tm-30) REVERT: B 6 ASP cc_start: 0.7213 (m-30) cc_final: 0.6784 (p0) REVERT: B 54 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: B 60 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7739 (pt0) REVERT: B 120 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 171 LYS cc_start: 0.7309 (tttm) cc_final: 0.6957 (mtpt) REVERT: B 222 LYS cc_start: 0.8562 (mttt) cc_final: 0.7989 (mtmt) REVERT: B 268 GLN cc_start: 0.7799 (tt0) cc_final: 0.7119 (mt0) REVERT: C 10 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6723 (mt-10) REVERT: C 15 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6578 (mm-30) REVERT: C 26 LYS cc_start: 0.7894 (tttm) cc_final: 0.7012 (ttmt) REVERT: C 112 MET cc_start: 0.9161 (mtp) cc_final: 0.8677 (mtp) REVERT: C 120 GLU cc_start: 0.8301 (tp30) cc_final: 0.7813 (tt0) REVERT: C 168 LYS cc_start: 0.7584 (mmmt) cc_final: 0.7121 (mtmm) REVERT: C 287 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: C 288 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7141 (mt-10) REVERT: C 322 LYS cc_start: 0.6965 (ptmm) cc_final: 0.6257 (ptpt) REVERT: C 397 SER cc_start: 0.8298 (p) cc_final: 0.7966 (m) REVERT: C 415 ARG cc_start: 0.7783 (tpp80) cc_final: 0.6684 (tmt170) REVERT: C 467 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8585 (tp) REVERT: C 476 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: D 2 SER cc_start: 0.8549 (m) cc_final: 0.8268 (t) REVERT: D 6 ASP cc_start: 0.7701 (m-30) cc_final: 0.7167 (p0) REVERT: D 7 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7470 (mmtt) REVERT: D 54 GLU cc_start: 0.7891 (tt0) cc_final: 0.7541 (mp0) REVERT: D 60 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7747 (pt0) REVERT: D 171 LYS cc_start: 0.7485 (mtpt) cc_final: 0.6807 (mttp) REVERT: D 222 LYS cc_start: 0.8518 (mtpt) cc_final: 0.8093 (mtmt) REVERT: D 238 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7648 (mtt180) REVERT: D 243 MET cc_start: 0.7932 (mtt) cc_final: 0.7623 (mtm) REVERT: D 268 GLN cc_start: 0.8410 (pt0) cc_final: 0.8138 (pt0) REVERT: D 312 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7190 (mp0) outliers start: 28 outliers final: 15 residues processed: 209 average time/residue: 0.8984 time to fit residues: 204.9996 Evaluate side-chains 209 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 194 optimal weight: 0.0070 chunk 127 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097255 restraints weight = 21691.888| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.45 r_work: 0.3025 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 16499 Z= 0.133 Angle : 0.668 29.086 22243 Z= 0.309 Chirality : 0.043 0.145 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.545 50.763 2518 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.57 % Allowed : 11.32 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.86 (0.19), residues: 1992 helix: 1.61 (0.17), residues: 996 sheet: -0.53 (0.42), residues: 142 loop : -0.43 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.013 0.001 TYR A 229 PHE 0.013 0.001 PHE C 118 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00265 (16483) covalent geometry : angle 0.66777 (22243) hydrogen bonds : bond 0.04296 ( 789) hydrogen bonds : angle 5.08464 ( 2274) Misc. bond : bond 0.08138 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6941 (mt-10) REVERT: A 22 GLU cc_start: 0.7688 (tp30) cc_final: 0.7411 (mm-30) REVERT: A 23 LYS cc_start: 0.7622 (tttt) cc_final: 0.7383 (tttt) REVERT: A 26 LYS cc_start: 0.7762 (tttm) cc_final: 0.7007 (ttmt) REVERT: A 112 MET cc_start: 0.9124 (mtp) cc_final: 0.8608 (mtp) REVERT: A 168 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7718 (mtmt) REVERT: A 288 GLU cc_start: 0.7803 (tt0) cc_final: 0.7123 (pt0) REVERT: A 391 MET cc_start: 0.7997 (mmm) cc_final: 0.7792 (mmm) REVERT: A 392 LYS cc_start: 0.8248 (pttt) cc_final: 0.7858 (ptmm) REVERT: A 415 ARG cc_start: 0.7786 (tpp80) cc_final: 0.6605 (tmt170) REVERT: B 6 ASP cc_start: 0.7158 (m-30) cc_final: 0.6773 (p0) REVERT: B 60 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7733 (pt0) REVERT: B 120 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6757 (mt-10) REVERT: B 171 LYS cc_start: 0.7307 (tttm) cc_final: 0.6981 (mtpt) REVERT: B 222 LYS cc_start: 0.8558 (mttt) cc_final: 0.7983 (mtmt) REVERT: B 268 GLN cc_start: 0.7775 (tt0) cc_final: 0.7104 (mt0) REVERT: C 10 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6709 (mt-10) REVERT: C 15 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6572 (mm-30) REVERT: C 26 LYS cc_start: 0.7858 (tttm) cc_final: 0.6979 (ttmt) REVERT: C 112 MET cc_start: 0.9142 (mtp) cc_final: 0.8655 (mtp) REVERT: C 120 GLU cc_start: 0.8245 (tp30) cc_final: 0.7782 (tt0) REVERT: C 168 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7100 (mtmm) REVERT: C 287 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: C 288 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7092 (mt-10) REVERT: C 322 LYS cc_start: 0.6956 (ptmm) cc_final: 0.6259 (ptpt) REVERT: C 397 SER cc_start: 0.8284 (p) cc_final: 0.7937 (m) REVERT: C 415 ARG cc_start: 0.7774 (tpp80) cc_final: 0.6679 (tmt170) REVERT: C 467 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8561 (tp) REVERT: C 476 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: D 2 SER cc_start: 0.8538 (m) cc_final: 0.8257 (t) REVERT: D 6 ASP cc_start: 0.7642 (m-30) cc_final: 0.7156 (p0) REVERT: D 7 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7463 (mmtt) REVERT: D 54 GLU cc_start: 0.7824 (tt0) cc_final: 0.7531 (mp0) REVERT: D 60 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7717 (pt0) REVERT: D 171 LYS cc_start: 0.7489 (mtpt) cc_final: 0.6817 (mttp) REVERT: D 222 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8120 (mtmt) REVERT: D 238 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7637 (mtt180) REVERT: D 243 MET cc_start: 0.7925 (mtt) cc_final: 0.7613 (mtm) REVERT: D 268 GLN cc_start: 0.8394 (pt0) cc_final: 0.8182 (pt0) REVERT: D 312 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7160 (mp0) outliers start: 27 outliers final: 16 residues processed: 207 average time/residue: 0.8890 time to fit residues: 201.5148 Evaluate side-chains 213 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097217 restraints weight = 22104.712| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.47 r_work: 0.3022 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 16499 Z= 0.135 Angle : 0.669 29.086 22243 Z= 0.311 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.522 50.704 2518 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.74 % Allowed : 11.20 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.90 (0.19), residues: 1992 helix: 1.62 (0.16), residues: 994 sheet: -0.52 (0.42), residues: 142 loop : -0.37 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.012 0.001 TYR D 88 PHE 0.013 0.001 PHE C 118 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00269 (16483) covalent geometry : angle 0.66936 (22243) hydrogen bonds : bond 0.04325 ( 789) hydrogen bonds : angle 5.07445 ( 2274) Misc. bond : bond 0.08185 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6919 (mt-10) REVERT: A 22 GLU cc_start: 0.7685 (tp30) cc_final: 0.7413 (mm-30) REVERT: A 23 LYS cc_start: 0.7566 (tttt) cc_final: 0.7326 (tttt) REVERT: A 26 LYS cc_start: 0.7742 (tttm) cc_final: 0.6992 (ttmt) REVERT: A 35 ASN cc_start: 0.8512 (t0) cc_final: 0.8136 (t0) REVERT: A 112 MET cc_start: 0.9126 (mtp) cc_final: 0.8611 (mtp) REVERT: A 168 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7744 (mtmt) REVERT: A 287 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: A 288 GLU cc_start: 0.7815 (tt0) cc_final: 0.7164 (pt0) REVERT: A 334 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: A 391 MET cc_start: 0.7981 (mmm) cc_final: 0.7760 (mmm) REVERT: A 392 LYS cc_start: 0.8203 (pttt) cc_final: 0.7823 (ptmm) REVERT: A 415 ARG cc_start: 0.7785 (tpp80) cc_final: 0.6601 (tmt170) REVERT: B 6 ASP cc_start: 0.7151 (m-30) cc_final: 0.6757 (p0) REVERT: B 60 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7721 (pt0) REVERT: B 120 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6764 (mt-10) REVERT: B 171 LYS cc_start: 0.7314 (tttm) cc_final: 0.7016 (mtpt) REVERT: B 222 LYS cc_start: 0.8569 (mttt) cc_final: 0.8010 (mtmt) REVERT: B 268 GLN cc_start: 0.7784 (tt0) cc_final: 0.7106 (mt0) REVERT: C 10 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6647 (mt-10) REVERT: C 15 GLU cc_start: 0.7612 (mt-10) cc_final: 0.6568 (mm-30) REVERT: C 26 LYS cc_start: 0.7867 (tttm) cc_final: 0.6981 (ttmt) REVERT: C 112 MET cc_start: 0.9146 (mtp) cc_final: 0.8661 (mtp) REVERT: C 120 GLU cc_start: 0.8227 (tp30) cc_final: 0.7755 (tt0) REVERT: C 168 LYS cc_start: 0.7548 (mmmt) cc_final: 0.7093 (mtmm) REVERT: C 287 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7832 (tp30) REVERT: C 288 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7109 (mt-10) REVERT: C 322 LYS cc_start: 0.6996 (ptmm) cc_final: 0.6189 (pttt) REVERT: C 415 ARG cc_start: 0.7742 (tpp80) cc_final: 0.6629 (tmt170) REVERT: C 467 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8544 (tp) REVERT: C 476 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: D 2 SER cc_start: 0.8526 (m) cc_final: 0.8257 (t) REVERT: D 6 ASP cc_start: 0.7673 (m-30) cc_final: 0.7136 (p0) REVERT: D 7 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7449 (mmtt) REVERT: D 54 GLU cc_start: 0.7820 (tt0) cc_final: 0.7523 (mp0) REVERT: D 60 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7711 (pt0) REVERT: D 171 LYS cc_start: 0.7489 (mtpt) cc_final: 0.6809 (mttp) REVERT: D 222 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8105 (mtmt) REVERT: D 238 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7655 (mtt180) REVERT: D 243 MET cc_start: 0.7926 (mtt) cc_final: 0.7615 (mtm) REVERT: D 268 GLN cc_start: 0.8387 (pt0) cc_final: 0.8125 (pt0) REVERT: D 312 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7170 (mp0) outliers start: 30 outliers final: 14 residues processed: 210 average time/residue: 0.8441 time to fit residues: 193.2464 Evaluate side-chains 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 0.0770 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 173 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097881 restraints weight = 22756.351| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.49 r_work: 0.3030 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.164 16499 Z= 0.128 Angle : 0.663 29.077 22243 Z= 0.307 Chirality : 0.043 0.145 2336 Planarity : 0.004 0.041 2858 Dihedral : 4.453 50.541 2518 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.28 % Allowed : 11.55 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.91 (0.19), residues: 1992 helix: 1.63 (0.16), residues: 998 sheet: -0.51 (0.42), residues: 142 loop : -0.37 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.012 0.001 TYR A 401 PHE 0.012 0.001 PHE C 118 TRP 0.012 0.001 TRP C 335 HIS 0.009 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00254 (16483) covalent geometry : angle 0.66301 (22243) hydrogen bonds : bond 0.04127 ( 789) hydrogen bonds : angle 5.03659 ( 2274) Misc. bond : bond 0.07771 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 0.740 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6978 (mt-10) REVERT: A 22 GLU cc_start: 0.7655 (tp30) cc_final: 0.7389 (mm-30) REVERT: A 23 LYS cc_start: 0.7515 (tttt) cc_final: 0.7295 (tttt) REVERT: A 26 LYS cc_start: 0.7750 (tttm) cc_final: 0.6993 (ttmt) REVERT: A 35 ASN cc_start: 0.8514 (t0) cc_final: 0.8155 (t0) REVERT: A 112 MET cc_start: 0.9114 (mtp) cc_final: 0.8593 (mtp) REVERT: A 168 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7748 (mtmt) REVERT: A 287 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: A 288 GLU cc_start: 0.7812 (tt0) cc_final: 0.7177 (pt0) REVERT: A 334 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: A 391 MET cc_start: 0.7985 (mmm) cc_final: 0.7772 (mmm) REVERT: A 392 LYS cc_start: 0.8186 (pttt) cc_final: 0.7812 (ptmm) REVERT: A 415 ARG cc_start: 0.7768 (tpp80) cc_final: 0.6581 (tmt170) REVERT: B 6 ASP cc_start: 0.7101 (m-30) cc_final: 0.6713 (p0) REVERT: B 60 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7721 (pt0) REVERT: B 120 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6768 (mt-10) REVERT: B 171 LYS cc_start: 0.7318 (tttm) cc_final: 0.7033 (mtpt) REVERT: B 222 LYS cc_start: 0.8560 (mttt) cc_final: 0.8007 (mtmt) REVERT: B 268 GLN cc_start: 0.7799 (tt0) cc_final: 0.7091 (mt0) REVERT: C 15 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6573 (mm-30) REVERT: C 26 LYS cc_start: 0.7859 (tttm) cc_final: 0.6975 (ttmt) REVERT: C 112 MET cc_start: 0.9130 (mtp) cc_final: 0.8635 (mtp) REVERT: C 120 GLU cc_start: 0.8251 (tp30) cc_final: 0.7783 (tt0) REVERT: C 168 LYS cc_start: 0.7550 (mmmt) cc_final: 0.7099 (mtmm) REVERT: C 284 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.6776 (mtm110) REVERT: C 287 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: C 288 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7105 (mt-10) REVERT: C 322 LYS cc_start: 0.7010 (ptmm) cc_final: 0.6243 (pttt) REVERT: C 415 ARG cc_start: 0.7764 (tpp80) cc_final: 0.6684 (tmt170) REVERT: C 467 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 476 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: D 2 SER cc_start: 0.8523 (m) cc_final: 0.8256 (t) REVERT: D 6 ASP cc_start: 0.7667 (m-30) cc_final: 0.7159 (p0) REVERT: D 54 GLU cc_start: 0.7820 (tt0) cc_final: 0.7515 (mp0) REVERT: D 60 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7713 (pt0) REVERT: D 171 LYS cc_start: 0.7480 (mtpt) cc_final: 0.6797 (mttp) REVERT: D 222 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8104 (mtmt) REVERT: D 243 MET cc_start: 0.7928 (mtt) cc_final: 0.7609 (mtm) REVERT: D 268 GLN cc_start: 0.8383 (pt0) cc_final: 0.8112 (pt0) outliers start: 22 outliers final: 13 residues processed: 201 average time/residue: 0.8959 time to fit residues: 196.4161 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 MET Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 360 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 0.7980 chunk 139 optimal weight: 0.0570 chunk 80 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN C 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095047 restraints weight = 31988.933| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.79 r_work: 0.2979 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2866 r_free = 0.2866 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 16499 Z= 0.146 Angle : 0.683 29.108 22243 Z= 0.319 Chirality : 0.044 0.145 2336 Planarity : 0.004 0.042 2858 Dihedral : 4.559 51.111 2518 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 11.38 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.10 % 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: 0.90 (0.19), residues: 1992 helix: 1.57 (0.16), residues: 996 sheet: -0.19 (0.40), residues: 162 loop : -0.38 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 25 TYR 0.014 0.002 TYR D 88 PHE 0.014 0.001 PHE C 118 TRP 0.013 0.001 TRP C 335 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00299 (16483) covalent geometry : angle 0.68304 (22243) hydrogen bonds : bond 0.04586 ( 789) hydrogen bonds : angle 5.09882 ( 2274) Misc. bond : bond 0.08838 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7874.43 seconds wall clock time: 134 minutes 58.96 seconds (8098.96 seconds total)