Starting phenix.real_space_refine on Mon May 4 06:08:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.cif Found real_map, /net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.map" model { file = "/net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11nc_75856/05_2026/11nc_75856.cif" } resolution = 2.16 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= 0.010 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 5420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 18465 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, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, '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: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 598 Classifications: {'water': 598} Link IDs: {None: 597} Chain: "B" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 614 Classifications: {'water': 614} Link IDs: {None: 613} Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 602 Classifications: {'water': 602} Link IDs: {None: 601} Chain: "D" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 624 Classifications: {'water': 624} Link IDs: {None: 623} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 29.745 46.524 61.114 1.00 48.71 S ATOM 1170 SG CYS A 154 35.738 28.042 49.063 1.00 15.54 S ATOM 4552 SG CYS B 95 38.974 31.267 45.823 1.00 21.69 S ATOM 465 SG CYS A 62 36.289 34.152 51.449 1.00 10.15 S ATOM 652 SG CYS A 88 41.694 29.802 51.403 1.00 18.86 S ATOM 652 SG CYS A 88 41.694 29.802 51.403 1.00 18.86 S ATOM 5005 SG CYS B 153 40.156 25.880 47.402 1.00 23.16 S ATOM 4372 SG CYS B 70 45.761 30.302 45.780 1.00 16.87 S ATOM 4552 SG CYS B 95 38.974 31.267 45.823 1.00 21.69 S ATOM 10056 SG CYS C 275 106.898 58.083 61.382 1.00 26.69 S ATOM 12516 SG CYS D 95 97.564 73.055 45.794 1.00 18.81 S ATOM 9134 SG CYS C 154 100.883 76.320 49.103 1.00 17.56 S ATOM 8429 SG CYS C 62 100.407 70.188 51.450 1.00 13.99 S ATOM 8616 SG CYS C 88 94.931 74.352 51.451 1.00 17.76 S ATOM 8616 SG CYS C 88 94.931 74.352 51.451 1.00 17.76 S ATOM 12969 SG CYS D 153 96.482 78.403 47.391 1.00 20.35 S ATOM 12336 SG CYS D 70 90.805 73.987 45.790 1.00 15.68 S ATOM 12516 SG CYS D 95 97.564 73.055 45.794 1.00 18.81 S Time building chain proxies: 5.85, per 1000 atoms: 0.32 Number of scatterers: 18465 At special positions: 0 Unit cell: (136.71, 105.105, 102.165, 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 5420 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: 1.66 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: 105 helices and 12 sheets defined 59.0% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.999A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.812A 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: 3.735A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.766A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.282A 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: 4.081A 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 291 removed outlier: 6.164A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 removed outlier: 3.523A pdb=" N TYR A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.104A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 435 removed outlier: 4.414A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.722A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.533A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.043A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.194A 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 158 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 216 removed outlier: 5.763A pdb=" N ASP B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.815A 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 320 through 337 removed outlier: 4.206A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.108A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.965A 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: 3.555A 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: 4.437A 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 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.503A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) 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: 3.739A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 removed outlier: 3.664A pdb=" N VAL C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.225A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.616A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 211 " --> pdb=" O GLY C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.977A 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: 3.505A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.646A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 383 through 394 removed outlier: 4.399A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.593A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.654A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.831A 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 32 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: 4.078A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.990A 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 233 through 247 removed outlier: 3.779A 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: 5.066A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.995A 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: 3.840A 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: 4.365A 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: 3.813A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 401 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.348A 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: 6.891A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.130A 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: 7.008A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.385A 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: 8.631A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.609A 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: 6.127A pdb=" N VAL C 351 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 376 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.351A 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: 6.974A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.155A 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: 7.139A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.540A 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 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.361A 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: 8.530A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2283 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: 3.75 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.82: 16347 1.82 - 2.47: 103 2.47 - 3.11: 26 3.11 - 3.75: 5 3.75 - 4.39: 2 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 4.387 -2.187 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.935 -1.735 2.00e-02 2.50e+03 7.53e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.710 -1.510 2.00e-02 2.50e+03 5.70e+03 bond pdb="FE4 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.707 -1.507 2.00e-02 2.50e+03 5.68e+03 bond pdb=" S1 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.663 -1.463 2.00e-02 2.50e+03 5.35e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.91: 22232 6.91 - 13.82: 5 13.82 - 20.74: 2 20.74 - 27.65: 0 27.65 - 34.56: 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 55.44 34.56 3.00e+00 1.11e-01 1.33e+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 55.56 34.44 3.00e+00 1.11e-01 1.32e+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 56.86 33.14 3.00e+00 1.11e-01 1.22e+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 60.80 29.20 3.00e+00 1.11e-01 9.47e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.21 -18.21 3.00e+00 1.11e-01 3.69e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 9256 18.03 - 36.06: 669 36.06 - 54.09: 100 54.09 - 72.12: 47 72.12 - 90.15: 29 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: 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 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C SER A 5 " pdb=" N SER A 5 " pdb=" CA SER A 5 " pdb=" CB SER A 5 " ideal model delta harmonic sigma weight residual -122.60 -131.31 8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1721 0.054 - 0.109: 464 0.109 - 0.163: 117 0.163 - 0.218: 25 0.218 - 0.272: 9 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA SER A 423 " pdb=" N SER A 423 " pdb=" C SER A 423 " pdb=" CB SER A 423 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA SER A 5 " pdb=" N SER A 5 " pdb=" C SER A 5 " pdb=" CB SER A 5 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB VAL A 351 " pdb=" CA VAL A 351 " pdb=" CG1 VAL A 351 " pdb=" CG2 VAL A 351 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP C 479 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C TRP C 479 " 0.050 2.00e-02 2.50e+03 pdb=" O TRP C 479 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU C 480 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 358 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C LEU A 358 " 0.047 2.00e-02 2.50e+03 pdb=" O LEU A 358 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 359 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 379 " 0.027 2.00e-02 2.50e+03 1.77e-02 6.28e+00 pdb=" CG TYR A 379 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 379 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 379 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 379 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 379 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 379 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 379 " 0.029 2.00e-02 2.50e+03 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 979 2.64 - 3.21: 17924 3.21 - 3.77: 34312 3.77 - 4.34: 50098 4.34 - 4.90: 73351 Nonbonded interactions: 176664 Sorted by model distance: nonbonded pdb=" OE1 GLU D 109 " pdb="FE FE B 601 " model vdw 2.080 2.260 nonbonded pdb=" O ASN C 98 " pdb=" OD1 ASN C 98 " model vdw 2.111 3.040 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.134 2.260 nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.152 2.260 nonbonded pdb=" O ARG D 108 " pdb="FE FE B 601 " model vdw 2.255 2.260 ... (remaining 176659 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=0.47 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: 3.590 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.100 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.039 2.187 16499 Z= 1.951 Angle : 0.942 34.561 22243 Z= 0.571 Chirality : 0.056 0.272 2336 Planarity : 0.005 0.066 2858 Dihedral : 13.972 90.147 6433 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.94 % Rotamer: Outliers : 0.58 % Allowed : 1.63 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.39 (0.18), residues: 1992 helix: 1.13 (0.17), residues: 964 sheet: -0.33 (0.38), residues: 166 loop : -0.56 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 310 TYR 0.029 0.002 TYR A 379 PHE 0.019 0.002 PHE A 118 TRP 0.022 0.002 TRP C 444 HIS 0.012 0.002 HIS C 442 Details of bonding type rmsd covalent geometry : bond 0.03849 (16483) covalent geometry : angle 0.94206 (22243) hydrogen bonds : bond 0.15118 ( 797) hydrogen bonds : angle 6.72120 ( 2283) Misc. bond : bond 0.12592 ( 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 294 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 284 time to evaluate : 0.688 Fit side-chains REVERT: A 218 SER cc_start: 0.8577 (p) cc_final: 0.8106 (m) REVERT: A 318 GLU cc_start: 0.6538 (tp30) cc_final: 0.6313 (mm-30) REVERT: A 322 LYS cc_start: 0.7601 (ttmt) cc_final: 0.7241 (ttpt) REVERT: A 362 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6011 (t70) REVERT: A 391 MET cc_start: 0.5139 (mtt) cc_final: 0.4838 (mmm) REVERT: B 4 GLN cc_start: 0.7355 (mt0) cc_final: 0.6956 (mm-40) REVERT: B 120 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7712 (mm-30) REVERT: B 214 ASP cc_start: 0.7950 (m-30) cc_final: 0.7070 (p0) REVERT: B 417 LYS cc_start: 0.8529 (tttt) cc_final: 0.8196 (ttmm) REVERT: B 503 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 15 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6547 (mt-10) REVERT: C 23 LYS cc_start: 0.7773 (tttt) cc_final: 0.6477 (ttpt) REVERT: C 43 LYS cc_start: 0.6892 (mtpt) cc_final: 0.6431 (pttp) REVERT: C 51 LYS cc_start: 0.8404 (ptpt) cc_final: 0.7776 (pttm) REVERT: C 120 GLU cc_start: 0.8179 (tp30) cc_final: 0.7267 (mp0) REVERT: C 129 LYS cc_start: 0.8170 (mttm) cc_final: 0.7897 (mtmt) REVERT: C 212 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6179 (pm20) REVERT: C 218 SER cc_start: 0.8349 (p) cc_final: 0.8032 (m) REVERT: C 415 ARG cc_start: 0.7075 (tpp80) cc_final: 0.6440 (mmp80) REVERT: D 26 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8254 (mtmm) REVERT: D 50 LYS cc_start: 0.8304 (mttm) cc_final: 0.7780 (tmtt) REVERT: D 171 LYS cc_start: 0.7799 (tttm) cc_final: 0.7578 (ttmm) REVERT: D 178 GLU cc_start: 0.7805 (mp0) cc_final: 0.7528 (pm20) REVERT: D 303 LYS cc_start: 0.8417 (mtpp) cc_final: 0.8165 (mtmm) REVERT: D 404 LYS cc_start: 0.8255 (mttp) cc_final: 0.8044 (mtpt) REVERT: D 417 LYS cc_start: 0.8136 (tptt) cc_final: 0.7553 (mmpt) outliers start: 10 outliers final: 2 residues processed: 292 average time/residue: 0.8874 time to fit residues: 282.0977 Evaluate side-chains 198 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 195 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 92 SER 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: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 145 ASN A 442 HIS A 451 HIS C 98 ASN C 199 ASN C 384 ASN C 469 ASN C 476 GLN D 45 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109276 restraints weight = 14861.966| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.09 r_work: 0.3184 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.398 16499 Z= 0.253 Angle : 0.775 30.815 22243 Z= 0.379 Chirality : 0.049 0.347 2336 Planarity : 0.005 0.054 2858 Dihedral : 6.097 57.719 2521 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.04 % Allowed : 7.31 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.53 (0.18), residues: 1992 helix: 1.21 (0.16), residues: 994 sheet: -0.54 (0.37), residues: 178 loop : -0.41 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 310 TYR 0.022 0.002 TYR D 102 PHE 0.021 0.002 PHE A 118 TRP 0.022 0.002 TRP A 253 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00486 (16483) covalent geometry : angle 0.77546 (22243) hydrogen bonds : bond 0.06252 ( 797) hydrogen bonds : angle 5.66899 ( 2283) Misc. bond : bond 0.16675 ( 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 216 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 198 time to evaluate : 0.593 Fit side-chains REVERT: A 218 SER cc_start: 0.8661 (p) cc_final: 0.8151 (m) REVERT: A 318 GLU cc_start: 0.6239 (tp30) cc_final: 0.5928 (mm-30) REVERT: A 322 LYS cc_start: 0.7382 (ttmt) cc_final: 0.6816 (ttpt) REVERT: A 362 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.5995 (t70) REVERT: A 373 GLU cc_start: 0.7225 (pm20) cc_final: 0.7011 (pm20) REVERT: A 391 MET cc_start: 0.5091 (mtt) cc_final: 0.4729 (mmm) REVERT: B 4 GLN cc_start: 0.7355 (mt0) cc_final: 0.7025 (mm-40) REVERT: B 120 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7522 (mm-30) REVERT: B 214 ASP cc_start: 0.7891 (m-30) cc_final: 0.6938 (p0) REVERT: B 417 LYS cc_start: 0.8550 (tttt) cc_final: 0.8137 (ttmm) REVERT: B 503 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7913 (tm-30) REVERT: C 23 LYS cc_start: 0.7800 (tttt) cc_final: 0.6394 (ttpt) REVERT: C 43 LYS cc_start: 0.6899 (mtpt) cc_final: 0.6678 (pttp) REVERT: C 51 LYS cc_start: 0.8400 (ptpt) cc_final: 0.7711 (pttm) REVERT: C 129 LYS cc_start: 0.8240 (mttm) cc_final: 0.7913 (mtmt) REVERT: C 212 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6148 (pm20) REVERT: C 218 SER cc_start: 0.8404 (p) cc_final: 0.8051 (m) REVERT: C 287 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: C 288 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: C 388 ASP cc_start: 0.7797 (m-30) cc_final: 0.7524 (m-30) REVERT: C 393 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 26 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8117 (mtmm) REVERT: D 50 LYS cc_start: 0.8445 (mttm) cc_final: 0.7921 (mmmt) REVERT: D 171 LYS cc_start: 0.8029 (tttm) cc_final: 0.7754 (ttmm) REVERT: D 172 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: D 404 LYS cc_start: 0.8310 (mttp) cc_final: 0.8097 (mtpt) REVERT: D 417 LYS cc_start: 0.8198 (tptt) cc_final: 0.7552 (mmpt) REVERT: D 461 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7848 (pt0) outliers start: 18 outliers final: 4 residues processed: 211 average time/residue: 0.8361 time to fit residues: 193.4792 Evaluate side-chains 191 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 138 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 451 HIS B 268 GLN C 35 ASN C 476 GLN D 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107869 restraints weight = 18325.979| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.20 r_work: 0.3161 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.364 16499 Z= 0.243 Angle : 0.757 30.819 22243 Z= 0.367 Chirality : 0.048 0.286 2336 Planarity : 0.005 0.049 2858 Dihedral : 5.976 58.708 2520 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.04 % Allowed : 8.30 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.56 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1006 sheet: -0.59 (0.36), residues: 176 loop : -0.42 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 310 TYR 0.018 0.002 TYR D 102 PHE 0.019 0.002 PHE A 118 TRP 0.022 0.002 TRP A 253 HIS 0.009 0.002 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00474 (16483) covalent geometry : angle 0.75722 (22243) hydrogen bonds : bond 0.06018 ( 797) hydrogen bonds : angle 5.53231 ( 2283) Misc. bond : bond 0.15083 ( 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 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.722 Fit side-chains REVERT: A 121 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8137 (ptmt) REVERT: A 218 SER cc_start: 0.8686 (p) cc_final: 0.8151 (m) REVERT: A 318 GLU cc_start: 0.6405 (tp30) cc_final: 0.6043 (mm-30) REVERT: A 322 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6874 (ttpt) REVERT: A 373 GLU cc_start: 0.7332 (pm20) cc_final: 0.7113 (pm20) REVERT: A 391 MET cc_start: 0.5250 (mtt) cc_final: 0.4831 (mmm) REVERT: A 442 HIS cc_start: 0.7594 (m90) cc_final: 0.7197 (m-70) REVERT: B 4 GLN cc_start: 0.7385 (mt0) cc_final: 0.7022 (mm-40) REVERT: B 120 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7504 (mm-30) REVERT: B 214 ASP cc_start: 0.7940 (m-30) cc_final: 0.6942 (p0) REVERT: B 417 LYS cc_start: 0.8585 (tttt) cc_final: 0.8128 (ttmm) REVERT: B 503 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7956 (tm-30) REVERT: C 15 GLU cc_start: 0.6661 (mt-10) cc_final: 0.6455 (mt-10) REVERT: C 22 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: C 43 LYS cc_start: 0.6992 (mtpt) cc_final: 0.6754 (pttp) REVERT: C 51 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7759 (pttm) REVERT: C 129 LYS cc_start: 0.8283 (mttm) cc_final: 0.7946 (mtmt) REVERT: C 287 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: C 288 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: C 388 ASP cc_start: 0.7798 (m-30) cc_final: 0.7562 (m-30) REVERT: C 393 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7208 (mm-30) REVERT: C 415 ARG cc_start: 0.7425 (mmm160) cc_final: 0.6163 (mmp80) REVERT: D 4 GLN cc_start: 0.7914 (mt0) cc_final: 0.7653 (mt0) REVERT: D 26 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8180 (mtmm) REVERT: D 50 LYS cc_start: 0.8486 (mttm) cc_final: 0.7956 (mmmt) REVERT: D 171 LYS cc_start: 0.8050 (tttm) cc_final: 0.7757 (ttmm) REVERT: D 214 ASP cc_start: 0.7431 (m-30) cc_final: 0.7045 (p0) REVERT: D 404 LYS cc_start: 0.8353 (mttp) cc_final: 0.8085 (ttpt) REVERT: D 417 LYS cc_start: 0.8257 (tptt) cc_final: 0.7725 (mptt) REVERT: D 461 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7890 (pt0) outliers start: 18 outliers final: 8 residues processed: 198 average time/residue: 0.8218 time to fit residues: 178.4626 Evaluate side-chains 190 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 288 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 0.7980 chunk 193 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN A 451 HIS C 476 GLN D 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106473 restraints weight = 21041.761| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.28 r_work: 0.3126 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.352 16499 Z= 0.242 Angle : 0.754 30.803 22243 Z= 0.365 Chirality : 0.048 0.272 2336 Planarity : 0.005 0.053 2858 Dihedral : 5.880 59.444 2520 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.16 % Allowed : 8.65 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.55 (0.18), residues: 1992 helix: 1.25 (0.16), residues: 1006 sheet: -0.62 (0.36), residues: 176 loop : -0.45 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 310 TYR 0.019 0.002 TYR A 229 PHE 0.016 0.002 PHE A 118 TRP 0.018 0.002 TRP A 253 HIS 0.008 0.002 HIS A 383 Details of bonding type rmsd covalent geometry : bond 0.00473 (16483) covalent geometry : angle 0.75372 (22243) hydrogen bonds : bond 0.05996 ( 797) hydrogen bonds : angle 5.49263 ( 2283) Misc. bond : bond 0.14719 ( 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 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.728 Fit side-chains REVERT: A 121 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8148 (ptmt) REVERT: A 165 SER cc_start: 0.8493 (p) cc_final: 0.8290 (p) REVERT: A 218 SER cc_start: 0.8733 (p) cc_final: 0.8183 (m) REVERT: A 318 GLU cc_start: 0.6461 (tp30) cc_final: 0.6094 (mm-30) REVERT: A 322 LYS cc_start: 0.7483 (ttmt) cc_final: 0.6787 (ttpt) REVERT: A 373 GLU cc_start: 0.7315 (pm20) cc_final: 0.7076 (pm20) REVERT: A 391 MET cc_start: 0.5174 (mtt) cc_final: 0.4184 (mmm) REVERT: A 476 GLN cc_start: 0.8562 (tp-100) cc_final: 0.8304 (tp-100) REVERT: B 4 GLN cc_start: 0.7416 (mt0) cc_final: 0.7033 (mm-40) REVERT: B 120 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7477 (mm-30) REVERT: B 171 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7938 (ttpp) REVERT: B 172 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 214 ASP cc_start: 0.7937 (m-30) cc_final: 0.6920 (p0) REVERT: B 279 GLU cc_start: 0.7988 (mp0) cc_final: 0.7764 (mp0) REVERT: B 417 LYS cc_start: 0.8591 (tttt) cc_final: 0.8151 (ttmm) REVERT: B 503 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 22 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: C 51 LYS cc_start: 0.8438 (ptpt) cc_final: 0.7762 (pttm) REVERT: C 129 LYS cc_start: 0.8296 (mttm) cc_final: 0.7954 (mtmt) REVERT: C 388 ASP cc_start: 0.7824 (m-30) cc_final: 0.7567 (m-30) REVERT: C 393 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7190 (mm-30) REVERT: C 415 ARG cc_start: 0.7483 (mmm160) cc_final: 0.6922 (tpt-90) REVERT: D 4 GLN cc_start: 0.7921 (mt0) cc_final: 0.7650 (mt0) REVERT: D 26 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8250 (mtmm) REVERT: D 50 LYS cc_start: 0.8521 (mttm) cc_final: 0.7969 (mmmt) REVERT: D 171 LYS cc_start: 0.8059 (tttm) cc_final: 0.7765 (ttmm) REVERT: D 172 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: D 214 ASP cc_start: 0.7444 (m-30) cc_final: 0.7039 (p0) REVERT: D 404 LYS cc_start: 0.8390 (mttp) cc_final: 0.8095 (ttpt) REVERT: D 417 LYS cc_start: 0.8284 (tptt) cc_final: 0.7743 (mptt) REVERT: D 461 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7769 (pt0) outliers start: 20 outliers final: 7 residues processed: 198 average time/residue: 0.8268 time to fit residues: 179.9356 Evaluate side-chains 191 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 252 GLN A 321 GLN A 451 HIS C 35 ASN C 476 GLN D 104 ASN D 418 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106892 restraints weight = 23724.301| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.36 r_work: 0.3126 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 16499 Z= 0.228 Angle : 0.734 30.871 22243 Z= 0.353 Chirality : 0.047 0.256 2336 Planarity : 0.005 0.050 2858 Dihedral : 5.753 59.781 2520 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.10 % Allowed : 9.29 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.59 (0.18), residues: 1992 helix: 1.31 (0.16), residues: 1006 sheet: -0.64 (0.36), residues: 176 loop : -0.47 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.018 0.002 TYR A 229 PHE 0.015 0.002 PHE C 431 TRP 0.017 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00443 (16483) covalent geometry : angle 0.73438 (22243) hydrogen bonds : bond 0.05650 ( 797) hydrogen bonds : angle 5.42668 ( 2283) Misc. bond : bond 0.13917 ( 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 204 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.686 Fit side-chains REVERT: A 218 SER cc_start: 0.8752 (p) cc_final: 0.8194 (m) REVERT: A 318 GLU cc_start: 0.6399 (tp30) cc_final: 0.6043 (mm-30) REVERT: A 322 LYS cc_start: 0.7452 (ttmt) cc_final: 0.6766 (ttpt) REVERT: A 373 GLU cc_start: 0.7338 (pm20) cc_final: 0.7096 (pm20) REVERT: A 391 MET cc_start: 0.5171 (mtt) cc_final: 0.4206 (mmm) REVERT: A 476 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8045 (tp-100) REVERT: B 4 GLN cc_start: 0.7396 (mt0) cc_final: 0.6996 (mm-40) REVERT: B 120 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7448 (mm-30) REVERT: B 214 ASP cc_start: 0.7933 (m-30) cc_final: 0.6901 (p0) REVERT: B 279 GLU cc_start: 0.8011 (mp0) cc_final: 0.7776 (mp0) REVERT: B 417 LYS cc_start: 0.8613 (tttt) cc_final: 0.8150 (ttmm) REVERT: B 503 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 11 SER cc_start: 0.7334 (m) cc_final: 0.6639 (p) REVERT: C 51 LYS cc_start: 0.8393 (ptpt) cc_final: 0.7725 (pttm) REVERT: C 129 LYS cc_start: 0.8287 (mttm) cc_final: 0.7944 (mtmt) REVERT: C 287 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: C 388 ASP cc_start: 0.7834 (m-30) cc_final: 0.7589 (m-30) REVERT: C 393 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7125 (mm-30) REVERT: C 415 ARG cc_start: 0.7451 (mmm160) cc_final: 0.6932 (tpt-90) REVERT: D 4 GLN cc_start: 0.7905 (mt0) cc_final: 0.7610 (mt0) REVERT: D 26 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8243 (mtmm) REVERT: D 50 LYS cc_start: 0.8520 (mttm) cc_final: 0.7963 (mmmt) REVERT: D 171 LYS cc_start: 0.8046 (tttm) cc_final: 0.7751 (ttmm) REVERT: D 172 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 214 ASP cc_start: 0.7439 (m-30) cc_final: 0.7005 (p0) REVERT: D 404 LYS cc_start: 0.8376 (mttp) cc_final: 0.8096 (ttpt) REVERT: D 417 LYS cc_start: 0.8299 (tptt) cc_final: 0.7741 (mptt) REVERT: D 461 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7777 (pt0) outliers start: 19 outliers final: 9 residues processed: 199 average time/residue: 0.8132 time to fit residues: 178.0186 Evaluate side-chains 193 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 178 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 195 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN C 35 ASN C 476 GLN D 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109288 restraints weight = 21856.707| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.30 r_work: 0.3154 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.324 16499 Z= 0.201 Angle : 0.704 30.791 22243 Z= 0.333 Chirality : 0.045 0.225 2336 Planarity : 0.004 0.043 2858 Dihedral : 5.585 59.960 2520 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.87 % Allowed : 10.16 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.67 (0.18), residues: 1992 helix: 1.42 (0.16), residues: 1008 sheet: -0.66 (0.36), residues: 176 loop : -0.48 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 284 TYR 0.016 0.001 TYR A 229 PHE 0.016 0.001 PHE C 431 TRP 0.015 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00382 (16483) covalent geometry : angle 0.70424 (22243) hydrogen bonds : bond 0.05016 ( 797) hydrogen bonds : angle 5.33681 ( 2283) Misc. bond : bond 0.12561 ( 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 205 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.745 Fit side-chains REVERT: A 218 SER cc_start: 0.8747 (p) cc_final: 0.8201 (m) REVERT: A 318 GLU cc_start: 0.6429 (tp30) cc_final: 0.6134 (mm-30) REVERT: A 322 LYS cc_start: 0.7398 (ttmt) cc_final: 0.6725 (ttpt) REVERT: A 373 GLU cc_start: 0.7286 (pm20) cc_final: 0.7046 (pm20) REVERT: A 391 MET cc_start: 0.5071 (mtt) cc_final: 0.4153 (mmm) REVERT: A 476 GLN cc_start: 0.8573 (tp-100) cc_final: 0.8032 (tp-100) REVERT: B 4 GLN cc_start: 0.7337 (mt0) cc_final: 0.6973 (mm-40) REVERT: B 120 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7438 (mm-30) REVERT: B 214 ASP cc_start: 0.7946 (m-30) cc_final: 0.6918 (p0) REVERT: B 279 GLU cc_start: 0.7987 (mp0) cc_final: 0.7752 (mp0) REVERT: B 417 LYS cc_start: 0.8599 (tttt) cc_final: 0.8155 (ttmm) REVERT: B 503 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8069 (tm-30) REVERT: C 11 SER cc_start: 0.7284 (m) cc_final: 0.6638 (p) REVERT: C 51 LYS cc_start: 0.8359 (ptpt) cc_final: 0.7706 (pttm) REVERT: C 129 LYS cc_start: 0.8250 (mttm) cc_final: 0.7915 (mtmt) REVERT: C 287 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: C 388 ASP cc_start: 0.7785 (m-30) cc_final: 0.7564 (m-30) REVERT: C 393 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7067 (mm-30) REVERT: C 415 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6928 (tpt-90) REVERT: D 4 GLN cc_start: 0.7866 (mt0) cc_final: 0.7554 (mt0) REVERT: D 26 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8230 (mtmm) REVERT: D 50 LYS cc_start: 0.8477 (mttm) cc_final: 0.7927 (mmmt) REVERT: D 171 LYS cc_start: 0.8038 (tttm) cc_final: 0.7760 (ttmm) REVERT: D 172 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: D 214 ASP cc_start: 0.7393 (m-30) cc_final: 0.7017 (p0) REVERT: D 404 LYS cc_start: 0.8363 (mttp) cc_final: 0.8104 (ttpt) REVERT: D 417 LYS cc_start: 0.8290 (tptt) cc_final: 0.7749 (mptt) REVERT: D 461 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7741 (pt0) outliers start: 15 outliers final: 8 residues processed: 201 average time/residue: 0.8118 time to fit residues: 179.5011 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 143 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 134 optimal weight: 0.2980 chunk 121 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN A 321 GLN A 442 HIS C 476 GLN D 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106692 restraints weight = 18543.844| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.20 r_work: 0.3138 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.348 16499 Z= 0.260 Angle : 0.769 30.892 22243 Z= 0.373 Chirality : 0.049 0.275 2336 Planarity : 0.005 0.058 2858 Dihedral : 5.772 59.875 2520 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.99 % Allowed : 9.92 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.53 (0.18), residues: 1992 helix: 1.26 (0.16), residues: 1008 sheet: -0.62 (0.36), residues: 176 loop : -0.49 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 25 TYR 0.018 0.002 TYR D 88 PHE 0.017 0.002 PHE C 431 TRP 0.017 0.002 TRP A 253 HIS 0.009 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00516 (16483) covalent geometry : angle 0.76916 (22243) hydrogen bonds : bond 0.06313 ( 797) hydrogen bonds : angle 5.48042 ( 2283) Misc. bond : bond 0.15151 ( 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 201 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.684 Fit side-chains REVERT: A 218 SER cc_start: 0.8726 (p) cc_final: 0.8167 (m) REVERT: A 318 GLU cc_start: 0.6456 (tp30) cc_final: 0.6144 (mm-30) REVERT: A 322 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6796 (ttpt) REVERT: A 373 GLU cc_start: 0.7322 (pm20) cc_final: 0.7092 (pm20) REVERT: A 391 MET cc_start: 0.5191 (mtt) cc_final: 0.4438 (mmm) REVERT: A 476 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8234 (tp-100) REVERT: B 4 GLN cc_start: 0.7428 (mt0) cc_final: 0.7039 (mm-40) REVERT: B 120 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7465 (mm-30) REVERT: B 214 ASP cc_start: 0.7913 (m-30) cc_final: 0.6906 (p0) REVERT: B 279 GLU cc_start: 0.7944 (mp0) cc_final: 0.7715 (mp0) REVERT: B 417 LYS cc_start: 0.8543 (tttt) cc_final: 0.8102 (ttmm) REVERT: B 503 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8052 (tm-30) REVERT: C 11 SER cc_start: 0.7398 (m) cc_final: 0.6793 (p) REVERT: C 51 LYS cc_start: 0.8358 (ptpt) cc_final: 0.7686 (pttm) REVERT: C 129 LYS cc_start: 0.8296 (mttm) cc_final: 0.7958 (mtmt) REVERT: C 212 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: C 287 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7314 (tm-30) REVERT: C 388 ASP cc_start: 0.7803 (m-30) cc_final: 0.7548 (m-30) REVERT: C 393 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7140 (mm-30) REVERT: C 415 ARG cc_start: 0.7399 (mmm160) cc_final: 0.6889 (tpt-90) REVERT: D 4 GLN cc_start: 0.7917 (mt0) cc_final: 0.7609 (mt0) REVERT: D 26 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8253 (mtmm) REVERT: D 50 LYS cc_start: 0.8520 (mttm) cc_final: 0.7971 (mmmt) REVERT: D 171 LYS cc_start: 0.8074 (tttm) cc_final: 0.7784 (ttmm) REVERT: D 172 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: D 214 ASP cc_start: 0.7481 (m-30) cc_final: 0.7070 (p0) REVERT: D 404 LYS cc_start: 0.8354 (mttp) cc_final: 0.8099 (mtpt) REVERT: D 417 LYS cc_start: 0.8294 (tptt) cc_final: 0.7742 (mptt) REVERT: D 461 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7774 (pt0) outliers start: 17 outliers final: 8 residues processed: 197 average time/residue: 0.8155 time to fit residues: 176.4235 Evaluate side-chains 190 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 252 GLN A 321 GLN A 469 ASN C 476 GLN D 418 ASN D 457 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109071 restraints weight = 19736.120| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.25 r_work: 0.3162 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.323 16499 Z= 0.204 Angle : 0.709 30.860 22243 Z= 0.336 Chirality : 0.045 0.229 2336 Planarity : 0.004 0.046 2858 Dihedral : 5.583 59.779 2520 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.75 % Allowed : 10.21 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.65 (0.18), residues: 1992 helix: 1.40 (0.16), residues: 1008 sheet: -0.63 (0.36), residues: 176 loop : -0.48 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 284 TYR 0.017 0.001 TYR A 229 PHE 0.016 0.001 PHE C 431 TRP 0.015 0.001 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00389 (16483) covalent geometry : angle 0.70897 (22243) hydrogen bonds : bond 0.05110 ( 797) hydrogen bonds : angle 5.33998 ( 2283) Misc. bond : bond 0.12820 ( 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 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.643 Fit side-chains REVERT: A 218 SER cc_start: 0.8746 (p) cc_final: 0.8186 (m) REVERT: A 318 GLU cc_start: 0.6388 (tp30) cc_final: 0.6110 (mm-30) REVERT: A 322 LYS cc_start: 0.7429 (ttmt) cc_final: 0.6742 (ttpt) REVERT: A 373 GLU cc_start: 0.7282 (pm20) cc_final: 0.7067 (pm20) REVERT: A 391 MET cc_start: 0.5034 (mtt) cc_final: 0.4269 (mmm) REVERT: A 476 GLN cc_start: 0.8550 (tp-100) cc_final: 0.8259 (tp-100) REVERT: B 4 GLN cc_start: 0.7366 (mt0) cc_final: 0.6982 (mm-40) REVERT: B 120 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7423 (mm-30) REVERT: B 214 ASP cc_start: 0.7921 (m-30) cc_final: 0.6907 (p0) REVERT: B 279 GLU cc_start: 0.7964 (mp0) cc_final: 0.7724 (mp0) REVERT: B 315 LYS cc_start: 0.8625 (tppt) cc_final: 0.7994 (tttp) REVERT: B 417 LYS cc_start: 0.8611 (tttt) cc_final: 0.8170 (ttmm) REVERT: B 503 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 11 SER cc_start: 0.7208 (m) cc_final: 0.6603 (p) REVERT: C 51 LYS cc_start: 0.8323 (ptpt) cc_final: 0.7666 (pttm) REVERT: C 129 LYS cc_start: 0.8245 (mttm) cc_final: 0.7897 (mtmt) REVERT: C 287 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: C 388 ASP cc_start: 0.7764 (m-30) cc_final: 0.7528 (m-30) REVERT: C 393 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 415 ARG cc_start: 0.7363 (mmm160) cc_final: 0.6884 (tpt-90) REVERT: D 4 GLN cc_start: 0.7881 (mt0) cc_final: 0.7557 (mt0) REVERT: D 26 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8216 (mtmm) REVERT: D 50 LYS cc_start: 0.8473 (mttm) cc_final: 0.7911 (mmmt) REVERT: D 171 LYS cc_start: 0.8048 (tttm) cc_final: 0.7784 (ttmm) REVERT: D 172 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: D 214 ASP cc_start: 0.7441 (m-30) cc_final: 0.7045 (p0) REVERT: D 404 LYS cc_start: 0.8349 (mttp) cc_final: 0.8081 (ttpt) REVERT: D 417 LYS cc_start: 0.8310 (tptt) cc_final: 0.7756 (mptt) REVERT: D 461 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7730 (pt0) outliers start: 13 outliers final: 8 residues processed: 192 average time/residue: 0.8352 time to fit residues: 176.1532 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN A 321 GLN A 432 GLN C 35 ASN D 418 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106760 restraints weight = 20982.450| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.29 r_work: 0.3147 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 16499 Z= 0.233 Angle : 0.739 30.865 22243 Z= 0.354 Chirality : 0.047 0.253 2336 Planarity : 0.005 0.052 2858 Dihedral : 5.657 59.906 2520 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.75 % Allowed : 10.16 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.59 (0.18), residues: 1992 helix: 1.33 (0.16), residues: 1008 sheet: -0.64 (0.36), residues: 176 loop : -0.49 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.016 0.002 TYR A 229 PHE 0.016 0.002 PHE C 431 TRP 0.015 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00454 (16483) covalent geometry : angle 0.73889 (22243) hydrogen bonds : bond 0.05742 ( 797) hydrogen bonds : angle 5.39450 ( 2283) Misc. bond : bond 0.14046 ( 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 196 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.734 Fit side-chains REVERT: A 218 SER cc_start: 0.8729 (p) cc_final: 0.8167 (m) REVERT: A 318 GLU cc_start: 0.6414 (tp30) cc_final: 0.6130 (mm-30) REVERT: A 322 LYS cc_start: 0.7460 (ttmt) cc_final: 0.6777 (ttpt) REVERT: A 373 GLU cc_start: 0.7302 (pm20) cc_final: 0.7083 (pm20) REVERT: A 391 MET cc_start: 0.5046 (mtt) cc_final: 0.4312 (mmm) REVERT: A 476 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8256 (tp-100) REVERT: B 4 GLN cc_start: 0.7411 (mt0) cc_final: 0.7010 (mm-40) REVERT: B 120 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7456 (mm-30) REVERT: B 214 ASP cc_start: 0.7904 (m-30) cc_final: 0.6898 (p0) REVERT: B 279 GLU cc_start: 0.7970 (mp0) cc_final: 0.7727 (mp0) REVERT: B 417 LYS cc_start: 0.8599 (tttt) cc_final: 0.8130 (ttmm) REVERT: B 503 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8112 (tm-30) REVERT: C 11 SER cc_start: 0.7288 (m) cc_final: 0.6689 (p) REVERT: C 51 LYS cc_start: 0.8351 (ptpt) cc_final: 0.7690 (pttm) REVERT: C 129 LYS cc_start: 0.8302 (mttm) cc_final: 0.7964 (mtmt) REVERT: C 287 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: C 388 ASP cc_start: 0.7775 (m-30) cc_final: 0.7529 (m-30) REVERT: C 393 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7094 (mm-30) REVERT: C 415 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6902 (tpt-90) REVERT: C 476 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: D 4 GLN cc_start: 0.7926 (mt0) cc_final: 0.7604 (mt0) REVERT: D 26 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8267 (mtmm) REVERT: D 50 LYS cc_start: 0.8510 (mttm) cc_final: 0.7966 (mmmt) REVERT: D 171 LYS cc_start: 0.8069 (tttm) cc_final: 0.7802 (ttmm) REVERT: D 172 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: D 214 ASP cc_start: 0.7462 (m-30) cc_final: 0.7073 (p0) REVERT: D 404 LYS cc_start: 0.8368 (mttp) cc_final: 0.8111 (mtpt) REVERT: D 417 LYS cc_start: 0.8336 (tptt) cc_final: 0.7775 (mptt) REVERT: D 461 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7775 (pt0) outliers start: 13 outliers final: 8 residues processed: 191 average time/residue: 0.8237 time to fit residues: 172.7797 Evaluate side-chains 195 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 172 GLU Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 192 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN A 321 GLN C 35 ASN D 418 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108791 restraints weight = 21899.924| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.32 r_work: 0.3162 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 16499 Z= 0.199 Angle : 0.702 30.766 22243 Z= 0.331 Chirality : 0.045 0.224 2336 Planarity : 0.004 0.045 2858 Dihedral : 5.498 59.822 2520 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.87 % Allowed : 10.21 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.71 (0.19), residues: 1992 helix: 1.46 (0.16), residues: 1008 sheet: -0.65 (0.36), residues: 176 loop : -0.45 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.016 0.001 TYR A 229 PHE 0.015 0.001 PHE C 431 TRP 0.015 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00381 (16483) covalent geometry : angle 0.70162 (22243) hydrogen bonds : bond 0.04914 ( 797) hydrogen bonds : angle 5.29073 ( 2283) Misc. bond : bond 0.12246 ( 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 202 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 0.720 Fit side-chains REVERT: A 218 SER cc_start: 0.8724 (p) cc_final: 0.8171 (m) REVERT: A 318 GLU cc_start: 0.6363 (tp30) cc_final: 0.6091 (mm-30) REVERT: A 322 LYS cc_start: 0.7436 (ttmt) cc_final: 0.6742 (ttpt) REVERT: A 391 MET cc_start: 0.5132 (mtt) cc_final: 0.4429 (mmm) REVERT: A 476 GLN cc_start: 0.8549 (tp-100) cc_final: 0.8261 (tp-100) REVERT: B 4 GLN cc_start: 0.7369 (mt0) cc_final: 0.6964 (mm-40) REVERT: B 120 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 214 ASP cc_start: 0.7914 (m-30) cc_final: 0.6864 (p0) REVERT: B 315 LYS cc_start: 0.8606 (tppt) cc_final: 0.7983 (tttp) REVERT: B 417 LYS cc_start: 0.8622 (tttt) cc_final: 0.8174 (ttmm) REVERT: B 503 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8109 (tm-30) REVERT: C 11 SER cc_start: 0.7268 (m) cc_final: 0.6690 (p) REVERT: C 51 LYS cc_start: 0.8334 (ptpt) cc_final: 0.7675 (pttm) REVERT: C 129 LYS cc_start: 0.8248 (mttm) cc_final: 0.7894 (mtmt) REVERT: C 287 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: C 362 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.6822 (m90) REVERT: C 388 ASP cc_start: 0.7771 (m-30) cc_final: 0.7544 (m-30) REVERT: C 393 GLU cc_start: 0.7277 (mm-30) cc_final: 0.7033 (mm-30) REVERT: C 415 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6894 (tpt-90) REVERT: C 476 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: D 4 GLN cc_start: 0.7885 (mt0) cc_final: 0.7546 (mt0) REVERT: D 26 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8241 (mtmm) REVERT: D 50 LYS cc_start: 0.8473 (mttm) cc_final: 0.7904 (mmmt) REVERT: D 171 LYS cc_start: 0.8046 (tttm) cc_final: 0.7780 (ttmm) REVERT: D 404 LYS cc_start: 0.8359 (mttp) cc_final: 0.8092 (ttpt) REVERT: D 417 LYS cc_start: 0.8313 (tptt) cc_final: 0.7720 (mptt) REVERT: D 461 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7726 (pt0) outliers start: 15 outliers final: 7 residues processed: 197 average time/residue: 0.8015 time to fit residues: 173.5911 Evaluate side-chains 194 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 461 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 252 GLN A 321 GLN A 432 GLN A 442 HIS C 35 ASN D 418 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108554 restraints weight = 16455.436| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.15 r_work: 0.3178 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.330 16499 Z= 0.222 Angle : 0.728 30.830 22243 Z= 0.347 Chirality : 0.046 0.243 2336 Planarity : 0.004 0.050 2858 Dihedral : 5.554 59.757 2520 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.81 % Allowed : 10.33 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 0.67 (0.18), residues: 1992 helix: 1.39 (0.16), residues: 1008 sheet: -0.61 (0.36), residues: 176 loop : -0.45 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 25 TYR 0.015 0.002 TYR D 88 PHE 0.016 0.002 PHE C 431 TRP 0.015 0.002 TRP A 253 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00430 (16483) covalent geometry : angle 0.72773 (22243) hydrogen bonds : bond 0.05466 ( 797) hydrogen bonds : angle 5.33926 ( 2283) Misc. bond : bond 0.13464 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9208.99 seconds wall clock time: 157 minutes 13.87 seconds (9433.87 seconds total)