Starting phenix.real_space_refine on Mon Apr 6 18:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu0_45924/04_2026/9cu0_45924.map" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 38 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 193 5.16 5 C 13402 2.51 5 N 3589 2.21 5 O 4141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21371 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" 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: "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: 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: "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: "E" Number of atoms: 2077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2077 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 8, 'TRANS': 265} Chain: "F" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2145 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 8, 'TRANS': 274} Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'CLF': 1, 'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 2} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CLF': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "F" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 56.167 65.641 82.521 1.00 96.56 S ATOM 4549 SG CYS B 95 39.327 48.870 85.179 1.00 86.05 S ATOM 1167 SG CYS A 154 37.457 52.502 80.916 1.00 87.82 S ATOM 462 SG CYS A 62 42.795 54.848 84.040 1.00 93.13 S ATOM 649 SG CYS A 88 36.256 54.415 86.974 1.00 84.72 S ATOM 649 SG CYS A 88 36.256 54.415 86.974 1.00 84.72 S ATOM 5002 SG CYS B 153 34.409 50.379 83.866 1.00 90.27 S ATOM 4369 SG CYS B 70 35.801 49.402 90.890 1.00 83.78 S ATOM 4549 SG CYS B 95 39.327 48.870 85.179 1.00 86.05 S ATOM 10056 SG CYS C 275 35.206 65.324 157.926 1.00126.38 S ATOM 12516 SG CYS D 95 53.459 50.987 155.989 1.00 91.09 S ATOM 9134 SG CYS C 154 55.400 54.712 159.632 1.00 94.00 S ATOM 8429 SG CYS C 62 50.133 56.089 157.194 1.00 93.45 S ATOM 12969 SG CYS D 153 59.125 52.721 156.673 1.00 94.64 S ATOM 12336 SG CYS D 70 57.455 51.753 149.878 1.00 94.08 S ATOM 18693 SG CYS F 98 38.091 48.013 41.531 1.00192.28 S ATOM 18964 SG CYS F 133 39.378 41.833 42.584 1.00189.75 S ATOM 16615 SG CYS E 98 43.006 45.298 45.502 1.00175.42 S ATOM 16886 SG CYS E 133 42.646 45.232 38.854 1.00202.72 S ATOM 20463 SG CYS G 42 37.083 43.661 57.638 1.00154.01 S ATOM 20498 SG CYS G 47 37.503 45.076 54.373 1.00159.61 S ATOM 20514 SG CYS G 50 37.103 50.187 56.718 1.00151.91 S ATOM 20925 SG CYS G 102 36.867 48.471 59.985 1.00147.31 S Time building chain proxies: 6.26, per 1000 atoms: 0.29 Number of scatterers: 21371 At special positions: 0 Unit cell: (88.935, 103.635, 183.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mo 2 41.97 Fe 38 26.01 S 193 16.00 P 4 15.00 Mg 2 11.99 O 4141 8.00 N 3589 7.00 C 13402 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=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES G 201 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 42 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 102 " pdb="FE1 FES G 201 " - pdb=" SG CYS G 47 " pdb="FE2 FES G 201 " - pdb=" SG CYS G 50 " pdb=" SF4 F 301 " pdb="FE2 SF4 F 301 " - pdb=" SG CYS F 133 " pdb="FE4 SF4 F 301 " - pdb=" SG CYS E 133 " pdb="FE1 SF4 F 301 " - pdb=" SG CYS F 98 " pdb="FE3 SF4 F 301 " - pdb=" SG CYS E 98 " Number of angles added : 18 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 15 sheets defined 54.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 removed outlier: 3.555A pdb=" N GLU A 18 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.690A 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 160 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.601A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 205 removed outlier: 4.078A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.996A pdb=" N ARG A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.530A pdb=" N MET A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.492A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.550A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) 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: 3.552A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 392 removed outlier: 4.489A 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 433 removed outlier: 4.233A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 468 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 31 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 80 removed outlier: 4.071A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.984A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 removed outlier: 3.500A pdb=" N LYS B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 192 through 209 Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.626A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.531A pdb=" N MET B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 294 through 297 removed outlier: 3.553A pdb=" N HIS B 297 " --> pdb=" O GLN B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 294 through 297' Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 341 through 363 removed outlier: 3.531A pdb=" N THR B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.612A 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 426 through 437 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 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 removed outlier: 3.674A pdb=" N ASN B 518 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 20 removed outlier: 3.573A pdb=" N VAL C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 removed outlier: 4.269A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.620A pdb=" N LYS C 44 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 85 through 92 removed outlier: 4.266A pdb=" N GLY C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 92 " --> pdb=" O CYS C 88 " (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 Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.128A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.999A 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: 3.514A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 315 removed outlier: 3.791A pdb=" N LYS C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 343 removed outlier: 3.718A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 344 through 346 No H-bonds generated for 'chain 'C' and resid 344 through 346' Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.697A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.915A pdb=" N ARG C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 432 removed outlier: 4.580A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 451 through 468 removed outlier: 3.736A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 4.055A pdb=" N GLN C 476 " --> pdb=" O LYS C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 31 Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 71 through 80 removed outlier: 3.650A pdb=" N ALA D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.959A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.656A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 143 removed outlier: 3.525A pdb=" N LYS D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 209 Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.667A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 277 through 283 Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 3.582A pdb=" N THR D 345 " --> pdb=" O PRO D 341 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.527A 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 426 through 437 Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.511A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.811A pdb=" N GLU E 29 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 57 through 65 removed outlier: 3.614A pdb=" N MET E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 71 Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.787A pdb=" N VAL E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 114 removed outlier: 3.512A pdb=" N ILE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 155 through 172 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.692A pdb=" N ARG E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 235 through 250 Processing helix chain 'E' and resid 261 through 272 removed outlier: 3.579A pdb=" N LEU E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 31 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.517A pdb=" N MET F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 77 removed outlier: 3.880A pdb=" N VAL F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 114 removed outlier: 3.508A pdb=" N ILE F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 Processing helix chain 'F' and resid 155 through 172 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.618A pdb=" N ARG F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG F 224 " --> pdb=" O ARG F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 235 through 250 Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.775A pdb=" N ILE F 282 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL F 283 " --> pdb=" O GLU F 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 279 through 283' Processing helix chain 'G' and resid 26 through 34 removed outlier: 3.576A pdb=" N ASN G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 79 Processing helix chain 'G' and resid 82 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 9.988A pdb=" N LEU A 399 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 375 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N TYR A 401 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 351 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 376 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 378 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.411A 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 182 removed outlier: 7.003A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 79 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLN A 151 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 81 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.077A 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: 7.001A pdb=" N ILE A 225 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN A 252 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 227 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 254 " --> pdb=" O GLY A 227 " (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: 6.563A pdb=" N ILE B 224 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.586A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.498A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 351 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY C 378 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 353 " --> pdb=" O GLY C 378 " (cutoff:3.500A) removed outlier: 6.583A 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: 6.519A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 79 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN C 151 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 81 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 63 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.414A pdb=" N VAL C 223 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA C 251 " --> pdb=" O VAL C 223 " (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 250 through 253 removed outlier: 6.533A pdb=" N ILE D 224 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N VAL D 291 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.741A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LEU D 369 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE D 393 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.958A pdb=" N VAL E 34 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N VAL E 87 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE E 36 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET E 35 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASP E 126 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL E 37 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LEU E 128 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY E 10 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN E 5 " --> pdb=" O GLU E 147 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N TYR E 149 " --> pdb=" O GLN E 5 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ALA E 7 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 151 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR E 9 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE E 148 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 183 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 150 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS E 185 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS E 152 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE E 209 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU E 183 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE E 211 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N CYS E 185 " --> pdb=" O PHE E 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 78 through 80 removed outlier: 6.519A pdb=" N VAL F 34 " --> pdb=" O LYS F 85 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL F 87 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE F 36 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N MET F 35 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ASP F 126 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 37 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN F 5 " --> pdb=" O GLU F 147 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N TYR F 149 " --> pdb=" O GLN F 5 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA F 7 " --> pdb=" O TYR F 149 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL F 151 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR F 9 " --> pdb=" O VAL F 151 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE F 148 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE F 184 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 150 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASN F 186 " --> pdb=" O ILE F 150 " (cutoff:3.500A) removed outlier: 13.247A pdb=" N MET F 208 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N GLY F 181 " --> pdb=" O MET F 208 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N HIS F 210 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU F 183 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL F 212 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS F 185 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 15 through 18 956 hydrogen bonds defined for protein. 2784 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: 3.74 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.84: 21606 1.84 - 2.48: 119 2.48 - 3.12: 22 3.12 - 3.76: 7 3.76 - 4.40: 4 Bond restraints: 21758 Sorted by residual: bond pdb="FE2 CLF A 503 " pdb="FE8 CLF A 503 " ideal model delta sigma weight residual 2.200 4.395 -2.195 2.00e-02 2.50e+03 1.20e+04 bond pdb="FE2 CLF D 601 " pdb="FE8 CLF D 601 " ideal model delta sigma weight residual 2.200 4.372 -2.172 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 601 " pdb="FE6 CLF D 601 " ideal model delta sigma weight residual 2.200 3.934 -1.734 2.00e-02 2.50e+03 7.52e+03 bond pdb="FE5 CLF A 503 " pdb="FE6 CLF A 503 " ideal model delta sigma weight residual 2.200 3.931 -1.731 2.00e-02 2.50e+03 7.49e+03 bond pdb="FE4 CLF A 503 " pdb="FE5 CLF A 503 " ideal model delta sigma weight residual 2.200 3.416 -1.216 2.00e-02 2.50e+03 3.69e+03 ... (remaining 21753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.85: 29345 6.85 - 13.70: 16 13.70 - 20.55: 2 20.55 - 27.40: 0 27.40 - 34.24: 4 Bond angle restraints: 29367 Sorted by residual: angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE4 CLF D 601 " ideal model delta sigma weight residual 90.00 55.76 34.24 3.00e+00 1.11e-01 1.30e+02 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE4 CLF A 503 " ideal model delta sigma weight residual 90.00 55.89 34.11 3.00e+00 1.11e-01 1.29e+02 angle pdb=" S1 CLF D 601 " pdb="FE2 CLF D 601 " pdb="FE1 CLF D 601 " ideal model delta sigma weight residual 90.00 60.64 29.36 3.00e+00 1.11e-01 9.58e+01 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE1 CLF A 503 " ideal model delta sigma weight residual 90.00 61.06 28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" S1 CLF A 503 " pdb="FE2 CLF A 503 " pdb="FE3 CLF A 503 " ideal model delta sigma weight residual 90.00 108.84 -18.84 3.00e+00 1.11e-01 3.95e+01 ... (remaining 29362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11123 17.91 - 35.82: 1606 35.82 - 53.73: 454 53.73 - 71.64: 113 71.64 - 89.55: 40 Dihedral angle restraints: 13336 sinusoidal: 5673 harmonic: 7663 Sorted by residual: dihedral pdb=" CA GLU E 117 " pdb=" C GLU E 117 " pdb=" N ASP E 118 " pdb=" CA ASP E 118 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" C5' ADP F 302 " pdb=" O5' ADP F 302 " pdb=" PA ADP F 302 " pdb=" O2A ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 17.32 -77.32 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" C ILE F 14 " pdb=" N ILE F 14 " pdb=" CA ILE F 14 " pdb=" CB ILE F 14 " ideal model delta harmonic sigma weight residual -122.00 -131.45 9.45 0 2.50e+00 1.60e-01 1.43e+01 ... (remaining 13333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2679 0.068 - 0.137: 424 0.137 - 0.205: 39 0.205 - 0.273: 8 0.273 - 0.341: 2 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ILE G 38 " pdb=" N ILE G 38 " pdb=" C ILE G 38 " pdb=" CB ILE G 38 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL D 260 " pdb=" CA VAL D 260 " pdb=" CG1 VAL D 260 " pdb=" CG2 VAL D 260 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL B 464 " pdb=" CA VAL B 464 " pdb=" CG1 VAL B 464 " pdb=" CG2 VAL B 464 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3149 not shown) Planarity restraints: 3780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 131 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C VAL F 131 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL F 131 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL F 132 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 231 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR E 231 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR E 231 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR E 231 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR E 231 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR E 231 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 231 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 231 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 145 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C ASN A 145 " -0.050 2.00e-02 2.50e+03 pdb=" O ASN A 145 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 146 " 0.017 2.00e-02 2.50e+03 ... (remaining 3777 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 275 2.58 - 3.16: 18041 3.16 - 3.74: 36183 3.74 - 4.32: 49102 4.32 - 4.90: 79810 Nonbonded interactions: 183411 Sorted by model distance: nonbonded pdb=" OE1 GLU E 147 " pdb=" O HOH E 401 " model vdw 2.005 3.040 nonbonded pdb=" OD2 ASP C 136 " pdb=" O HOH C 601 " model vdw 2.023 3.040 nonbonded pdb=" OE2 GLU C 22 " pdb=" O HOH C 602 " model vdw 2.026 3.040 nonbonded pdb=" OE1 GLN B 58 " pdb=" O HOH B 701 " model vdw 2.047 3.040 nonbonded pdb=" CA ALA E 235 " pdb=" O HOH E 409 " model vdw 2.054 3.470 ... (remaining 183406 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 through 248 or resid 250 through 502)) selection = (chain 'C' 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)) } ncs_group { reference = (chain 'B' and resid 2 through 523) selection = (chain 'D' and resid 2 through 523) } ncs_group { reference = (chain 'E' and (resid 3 through 82 or resid 84 through 302)) selection = (chain 'F' and (resid 3 through 276 or resid 302 through 303)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.340 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.038 2.195 21783 Z= 1.932 Angle : 0.932 34.244 29385 Z= 0.513 Chirality : 0.051 0.341 3152 Planarity : 0.005 0.055 3780 Dihedral : 18.729 89.547 8442 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.35 % Allowed : 29.23 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: -0.01 (0.16), residues: 2664 helix: 0.92 (0.15), residues: 1237 sheet: -0.21 (0.29), residues: 297 loop : -0.95 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 28 TYR 0.056 0.002 TYR E 231 PHE 0.020 0.002 PHE F 272 TRP 0.017 0.002 TRP C 236 HIS 0.005 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.03773 (21758) covalent geometry : angle 0.91150 (29367) hydrogen bonds : bond 0.15086 ( 956) hydrogen bonds : angle 6.61402 ( 2784) metal coordination : bond 0.07117 ( 8) metal coordination : angle 7.98909 ( 18) Misc. bond : bond 0.25911 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 328 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 117 ASP cc_start: 0.8125 (t0) cc_final: 0.7901 (m-30) REVERT: A 427 GLU cc_start: 0.8713 (mp0) cc_final: 0.8513 (mp0) REVERT: A 441 MET cc_start: 0.8999 (mmm) cc_final: 0.8754 (mmm) REVERT: A 465 MET cc_start: 0.8939 (ttt) cc_final: 0.8250 (ttt) REVERT: B 131 MET cc_start: 0.8613 (tpp) cc_final: 0.8032 (tpp) REVERT: B 133 ASP cc_start: 0.7992 (m-30) cc_final: 0.7772 (m-30) REVERT: B 395 CYS cc_start: 0.8647 (t) cc_final: 0.8238 (t) REVERT: B 467 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8794 (pt) REVERT: C 4 MET cc_start: 0.5491 (pp-130) cc_final: 0.2520 (tpp) REVERT: C 57 MET cc_start: 0.9000 (ttt) cc_final: 0.8664 (tmm) REVERT: C 98 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8731 (p0) REVERT: C 234 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7903 (t0) REVERT: C 256 ASP cc_start: 0.8440 (t0) cc_final: 0.7521 (t0) REVERT: C 277 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7356 (tpp-160) REVERT: C 362 HIS cc_start: 0.8006 (OUTLIER) cc_final: 0.7742 (t70) REVERT: C 401 TYR cc_start: 0.7606 (OUTLIER) cc_final: 0.6265 (p90) REVERT: D 95 CYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8534 (m) REVERT: D 131 MET cc_start: 0.9207 (tpp) cc_final: 0.8830 (tpp) REVERT: D 320 MET cc_start: 0.8354 (ttm) cc_final: 0.7758 (ttm) REVERT: D 453 ARG cc_start: 0.9151 (tmm-80) cc_final: 0.8912 (tmm-80) REVERT: E 60 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6490 (tt0) REVERT: E 237 GLN cc_start: 0.5493 (tp40) cc_final: 0.4949 (tp-100) REVERT: F 33 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.6492 (tttt) REVERT: F 45 SER cc_start: 0.7645 (OUTLIER) cc_final: 0.7421 (p) REVERT: F 156 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.4841 (tpp) REVERT: G 65 MET cc_start: 0.8049 (ppp) cc_final: 0.7785 (pmm) outliers start: 98 outliers final: 34 residues processed: 389 average time/residue: 0.1379 time to fit residues: 85.7053 Evaluate side-chains 316 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 95 CYS Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 TYR Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN B 317 ASN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 237 GLN ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.093520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073363 restraints weight = 102726.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076268 restraints weight = 45866.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.078186 restraints weight = 25604.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079451 restraints weight = 16411.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080304 restraints weight = 11746.915| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.616 21783 Z= 0.255 Angle : 0.832 30.096 29385 Z= 0.378 Chirality : 0.047 0.201 3152 Planarity : 0.005 0.042 3780 Dihedral : 7.126 76.846 3353 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.31 % Allowed : 27.16 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.04 (0.16), residues: 2664 helix: 1.09 (0.15), residues: 1243 sheet: -0.56 (0.29), residues: 305 loop : -0.98 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 224 TYR 0.021 0.002 TYR D 88 PHE 0.020 0.002 PHE B 382 TRP 0.025 0.002 TRP A 253 HIS 0.006 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00540 (21758) covalent geometry : angle 0.79322 (29367) hydrogen bonds : bond 0.04344 ( 956) hydrogen bonds : angle 5.42682 ( 2784) metal coordination : bond 0.01913 ( 8) metal coordination : angle 10.18705 ( 18) Misc. bond : bond 0.19304 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 290 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.7845 (tp40) REVERT: A 98 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.7670 (p0) REVERT: A 151 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7399 (mt0) REVERT: A 465 MET cc_start: 0.9043 (ttt) cc_final: 0.8515 (ttt) REVERT: B 62 LEU cc_start: 0.8825 (tp) cc_final: 0.8614 (tt) REVERT: B 395 CYS cc_start: 0.8452 (t) cc_final: 0.8068 (t) REVERT: B 467 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8841 (pt) REVERT: C 4 MET cc_start: 0.5527 (pp-130) cc_final: 0.2689 (tpp) REVERT: C 98 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.8821 (p0) REVERT: C 152 SER cc_start: 0.9483 (m) cc_final: 0.9193 (t) REVERT: C 234 ASP cc_start: 0.8459 (m-30) cc_final: 0.8197 (m-30) REVERT: C 256 ASP cc_start: 0.8557 (t0) cc_final: 0.7510 (t0) REVERT: C 277 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7678 (tpp-160) REVERT: C 394 MET cc_start: 0.5388 (tpp) cc_final: 0.5144 (tpp) REVERT: C 401 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6638 (p90) REVERT: C 441 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7816 (mpp) REVERT: D 131 MET cc_start: 0.9208 (tpp) cc_final: 0.8999 (tpp) REVERT: D 200 MET cc_start: 0.8925 (tpt) cc_final: 0.8700 (tpt) REVERT: D 362 LEU cc_start: 0.9176 (mt) cc_final: 0.8906 (mt) REVERT: E 125 TYR cc_start: 0.8214 (m-80) cc_final: 0.7606 (m-80) REVERT: E 138 MET cc_start: 0.7964 (ttt) cc_final: 0.7702 (ttp) REVERT: E 237 GLN cc_start: 0.5364 (tp40) cc_final: 0.4958 (tp-100) REVERT: F 33 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.6323 (tttt) REVERT: F 125 TYR cc_start: 0.6690 (m-80) cc_final: 0.6392 (m-80) REVERT: F 138 MET cc_start: 0.8805 (tmm) cc_final: 0.8598 (tmm) REVERT: F 156 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5179 (tpp) REVERT: F 200 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7700 (mp) REVERT: F 226 MET cc_start: 0.6947 (tpt) cc_final: 0.6744 (tpt) REVERT: G 41 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: G 65 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7524 (ppp) outliers start: 97 outliers final: 55 residues processed: 356 average time/residue: 0.1402 time to fit residues: 80.3031 Evaluate side-chains 334 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 65 MET Chi-restraints excluded: chain G residue 93 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 114 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 ASN ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN D 199 ASN ** D 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.092940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072552 restraints weight = 108146.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075741 restraints weight = 51098.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077573 restraints weight = 29234.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078490 restraints weight = 17026.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079054 restraints weight = 14111.288| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.558 21783 Z= 0.219 Angle : 0.793 30.673 29385 Z= 0.352 Chirality : 0.045 0.232 3152 Planarity : 0.004 0.044 3780 Dihedral : 6.347 72.662 3321 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.66 % Allowed : 26.77 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.12 (0.16), residues: 2664 helix: 1.17 (0.15), residues: 1238 sheet: -0.46 (0.28), residues: 333 loop : -0.98 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 210 TYR 0.018 0.001 TYR C 401 PHE 0.019 0.001 PHE A 459 TRP 0.021 0.001 TRP A 253 HIS 0.011 0.001 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00464 (21758) covalent geometry : angle 0.75013 (29367) hydrogen bonds : bond 0.03915 ( 956) hydrogen bonds : angle 5.22397 ( 2784) metal coordination : bond 0.01679 ( 8) metal coordination : angle 10.36005 ( 18) Misc. bond : bond 0.16108 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 285 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.7908 (tp40) REVERT: A 98 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.7651 (p0) REVERT: A 465 MET cc_start: 0.9024 (ttt) cc_final: 0.8396 (ttt) REVERT: B 131 MET cc_start: 0.8490 (tpp) cc_final: 0.8147 (tpp) REVERT: B 133 ASP cc_start: 0.8054 (m-30) cc_final: 0.7472 (m-30) REVERT: B 352 VAL cc_start: 0.9712 (t) cc_final: 0.9410 (p) REVERT: B 354 MET cc_start: 0.8609 (tpp) cc_final: 0.8059 (mmt) REVERT: B 355 MET cc_start: 0.9270 (mtm) cc_final: 0.8957 (mtm) REVERT: B 395 CYS cc_start: 0.8436 (t) cc_final: 0.8011 (t) REVERT: B 409 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8869 (tp) REVERT: B 467 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8815 (pt) REVERT: C 4 MET cc_start: 0.5654 (pp-130) cc_final: 0.2776 (tpp) REVERT: C 152 SER cc_start: 0.9541 (m) cc_final: 0.9286 (t) REVERT: C 256 ASP cc_start: 0.8417 (t0) cc_final: 0.7321 (t0) REVERT: C 394 MET cc_start: 0.5599 (tpp) cc_final: 0.5364 (tpp) REVERT: C 401 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6727 (p90) REVERT: C 439 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7975 (mmm-85) REVERT: C 467 LEU cc_start: 0.9048 (tt) cc_final: 0.8593 (mm) REVERT: D 131 MET cc_start: 0.9251 (tpp) cc_final: 0.9046 (tpp) REVERT: D 504 ARG cc_start: 0.8971 (tpp80) cc_final: 0.8367 (tpt170) REVERT: E 9 TYR cc_start: 0.7109 (m-10) cc_final: 0.6675 (m-10) REVERT: E 60 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6658 (tt0) REVERT: E 138 MET cc_start: 0.8006 (ttt) cc_final: 0.7754 (ttp) REVERT: E 237 GLN cc_start: 0.5349 (tp40) cc_final: 0.4950 (tp-100) REVERT: E 269 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8051 (tp) REVERT: F 33 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6237 (tttt) REVERT: F 125 TYR cc_start: 0.6595 (m-80) cc_final: 0.6246 (m-80) REVERT: F 138 MET cc_start: 0.8832 (tmm) cc_final: 0.8589 (tmm) REVERT: F 149 TYR cc_start: 0.8313 (m-80) cc_final: 0.8004 (m-80) REVERT: F 156 MET cc_start: 0.5959 (OUTLIER) cc_final: 0.5155 (tpp) REVERT: F 226 MET cc_start: 0.7015 (tpt) cc_final: 0.6235 (tpt) REVERT: F 264 GLU cc_start: 0.8238 (tm-30) cc_final: 0.8011 (tm-30) REVERT: F 270 MET cc_start: 0.6677 (tpt) cc_final: 0.6353 (tpt) REVERT: G 41 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: G 65 MET cc_start: 0.8135 (ppp) cc_final: 0.7927 (pmm) outliers start: 105 outliers final: 58 residues processed: 357 average time/residue: 0.1282 time to fit residues: 74.8139 Evaluate side-chains 331 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 263 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 243 optimal weight: 30.0000 chunk 224 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 418 ASN E 146 GLN ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.093299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073362 restraints weight = 95477.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076583 restraints weight = 45833.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078255 restraints weight = 25844.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.080059 restraints weight = 15568.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.080493 restraints weight = 9190.888| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.575 21783 Z= 0.192 Angle : 0.772 30.645 29385 Z= 0.340 Chirality : 0.045 0.223 3152 Planarity : 0.004 0.046 3780 Dihedral : 6.141 70.207 3309 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.53 % Allowed : 27.25 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.15 (0.16), residues: 2664 helix: 1.27 (0.15), residues: 1234 sheet: -0.49 (0.28), residues: 333 loop : -1.03 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 224 TYR 0.030 0.001 TYR F 231 PHE 0.018 0.001 PHE A 459 TRP 0.018 0.001 TRP A 253 HIS 0.013 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00406 (21758) covalent geometry : angle 0.73313 (29367) hydrogen bonds : bond 0.03609 ( 956) hydrogen bonds : angle 5.10543 ( 2784) metal coordination : bond 0.01309 ( 8) metal coordination : angle 9.78013 ( 18) Misc. bond : bond 0.15804 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 289 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.7616 (p0) REVERT: A 462 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: A 465 MET cc_start: 0.8971 (ttt) cc_final: 0.8429 (ttt) REVERT: B 121 ASP cc_start: 0.8456 (t0) cc_final: 0.8090 (t0) REVERT: B 131 MET cc_start: 0.8375 (tpp) cc_final: 0.8086 (tpp) REVERT: B 133 ASP cc_start: 0.7891 (m-30) cc_final: 0.7589 (m-30) REVERT: B 181 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8615 (m) REVERT: B 352 VAL cc_start: 0.9709 (t) cc_final: 0.9476 (p) REVERT: B 354 MET cc_start: 0.8529 (tpp) cc_final: 0.8069 (mmt) REVERT: B 395 CYS cc_start: 0.8385 (t) cc_final: 0.7923 (t) REVERT: B 409 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 467 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8848 (pt) REVERT: C 4 MET cc_start: 0.5595 (pp-130) cc_final: 0.2834 (tpp) REVERT: C 152 SER cc_start: 0.9495 (m) cc_final: 0.9274 (t) REVERT: C 256 ASP cc_start: 0.8303 (t0) cc_final: 0.7208 (t0) REVERT: C 394 MET cc_start: 0.5885 (tpp) cc_final: 0.5625 (tpp) REVERT: C 401 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6401 (p90) REVERT: C 439 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7827 (mmm-85) REVERT: C 441 MET cc_start: 0.7891 (mpp) cc_final: 0.7597 (mtm) REVERT: C 467 LEU cc_start: 0.9025 (tt) cc_final: 0.8620 (mm) REVERT: D 117 SER cc_start: 0.8819 (m) cc_final: 0.8548 (p) REVERT: D 186 THR cc_start: 0.9415 (OUTLIER) cc_final: 0.9138 (p) REVERT: D 362 LEU cc_start: 0.9156 (mt) cc_final: 0.8821 (mt) REVERT: D 504 ARG cc_start: 0.8794 (tpp80) cc_final: 0.8279 (tpt170) REVERT: E 9 TYR cc_start: 0.7193 (m-10) cc_final: 0.6683 (m-10) REVERT: E 60 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6660 (tt0) REVERT: E 138 MET cc_start: 0.8080 (ttt) cc_final: 0.7833 (ttp) REVERT: E 269 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8007 (tp) REVERT: F 5 GLN cc_start: 0.3849 (OUTLIER) cc_final: 0.3130 (mt0) REVERT: F 33 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6179 (tttt) REVERT: F 138 MET cc_start: 0.8837 (tmm) cc_final: 0.8609 (tmm) REVERT: F 149 TYR cc_start: 0.8315 (m-80) cc_final: 0.7997 (m-80) REVERT: F 156 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5285 (tpp) REVERT: F 226 MET cc_start: 0.6588 (tpt) cc_final: 0.6289 (tpt) REVERT: F 270 MET cc_start: 0.6921 (tpt) cc_final: 0.6581 (tpt) REVERT: G 41 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: G 65 MET cc_start: 0.8230 (ppp) cc_final: 0.8026 (pmm) outliers start: 102 outliers final: 59 residues processed: 362 average time/residue: 0.1372 time to fit residues: 80.2447 Evaluate side-chains 342 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 270 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 126 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 251 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 HIS ** A 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 GLN F 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.089556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069520 restraints weight = 101785.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.072999 restraints weight = 48575.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.074251 restraints weight = 24849.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.076249 restraints weight = 16609.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076349 restraints weight = 10095.083| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.500 21783 Z= 0.302 Angle : 0.876 35.290 29385 Z= 0.394 Chirality : 0.048 0.229 3152 Planarity : 0.005 0.051 3780 Dihedral : 6.206 73.636 3304 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.54 % Allowed : 26.64 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2664 helix: 0.94 (0.15), residues: 1274 sheet: -0.68 (0.29), residues: 314 loop : -1.09 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 72 TYR 0.022 0.002 TYR F 231 PHE 0.026 0.002 PHE A 459 TRP 0.031 0.002 TRP A 253 HIS 0.011 0.002 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00660 (21758) covalent geometry : angle 0.82598 (29367) hydrogen bonds : bond 0.04313 ( 956) hydrogen bonds : angle 5.33513 ( 2784) metal coordination : bond 0.02499 ( 8) metal coordination : angle 11.84111 ( 18) Misc. bond : bond 0.14023 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 260 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: A 90 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8715 (tp40) REVERT: A 98 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 462 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: A 465 MET cc_start: 0.9061 (ttt) cc_final: 0.8551 (ttt) REVERT: B 121 ASP cc_start: 0.8423 (t0) cc_final: 0.8145 (t0) REVERT: B 131 MET cc_start: 0.8374 (tpp) cc_final: 0.8061 (tpp) REVERT: B 133 ASP cc_start: 0.8004 (m-30) cc_final: 0.7771 (m-30) REVERT: B 395 CYS cc_start: 0.8413 (t) cc_final: 0.8030 (t) REVERT: B 409 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8866 (tp) REVERT: B 467 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8820 (pt) REVERT: C 4 MET cc_start: 0.6014 (pp-130) cc_final: 0.3171 (tpp) REVERT: C 161 ASP cc_start: 0.4812 (OUTLIER) cc_final: 0.4374 (m-30) REVERT: C 252 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: C 256 ASP cc_start: 0.8381 (t0) cc_final: 0.7312 (t0) REVERT: C 401 TYR cc_start: 0.7836 (OUTLIER) cc_final: 0.6834 (p90) REVERT: C 467 LEU cc_start: 0.9082 (tt) cc_final: 0.8746 (mm) REVERT: D 186 THR cc_start: 0.9450 (OUTLIER) cc_final: 0.9191 (p) REVERT: D 322 LEU cc_start: 0.9454 (tp) cc_final: 0.9244 (tp) REVERT: E 9 TYR cc_start: 0.7305 (m-10) cc_final: 0.6816 (m-10) REVERT: E 78 LYS cc_start: 0.6922 (mttp) cc_final: 0.6523 (ptpp) REVERT: E 237 GLN cc_start: 0.5172 (tp40) cc_final: 0.4864 (tp40) REVERT: E 269 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8090 (tp) REVERT: F 5 GLN cc_start: 0.3983 (OUTLIER) cc_final: 0.3354 (mt0) REVERT: F 33 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6247 (tttt) REVERT: F 138 MET cc_start: 0.8805 (tmm) cc_final: 0.8600 (tmm) REVERT: F 149 TYR cc_start: 0.8322 (m-80) cc_final: 0.8079 (m-80) REVERT: F 156 MET cc_start: 0.6000 (OUTLIER) cc_final: 0.5430 (tpp) REVERT: F 226 MET cc_start: 0.6789 (tpt) cc_final: 0.6464 (tpt) REVERT: F 231 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.6224 (m-80) outliers start: 125 outliers final: 77 residues processed: 353 average time/residue: 0.1325 time to fit residues: 75.8889 Evaluate side-chains 338 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 246 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 478 HIS Chi-restraints excluded: chain D residue 491 MET Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 93 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 202 optimal weight: 4.9990 chunk 167 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 90 optimal weight: 0.4980 chunk 174 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 244 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.093281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074130 restraints weight = 80149.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076689 restraints weight = 38683.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078380 restraints weight = 22551.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.079504 restraints weight = 14938.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.080259 restraints weight = 10958.534| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.542 21783 Z= 0.179 Angle : 0.782 30.666 29385 Z= 0.344 Chirality : 0.045 0.218 3152 Planarity : 0.004 0.046 3780 Dihedral : 6.029 69.104 3302 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.18 % Allowed : 28.22 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.10 (0.16), residues: 2664 helix: 1.19 (0.15), residues: 1252 sheet: -0.52 (0.29), residues: 322 loop : -1.03 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 361 TYR 0.016 0.001 TYR C 401 PHE 0.040 0.001 PHE A 412 TRP 0.025 0.001 TRP C 253 HIS 0.010 0.001 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00371 (21758) covalent geometry : angle 0.74065 (29367) hydrogen bonds : bond 0.03576 ( 956) hydrogen bonds : angle 5.06549 ( 2784) metal coordination : bond 0.00919 ( 8) metal coordination : angle 10.17334 ( 18) Misc. bond : bond 0.14990 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 282 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: A 90 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8707 (tp40) REVERT: A 98 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.7704 (p0) REVERT: A 462 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: A 465 MET cc_start: 0.9010 (ttt) cc_final: 0.8420 (ttt) REVERT: B 131 MET cc_start: 0.8382 (tpp) cc_final: 0.8116 (tpp) REVERT: B 133 ASP cc_start: 0.7916 (m-30) cc_final: 0.7448 (m-30) REVERT: B 271 MET cc_start: 0.8478 (ttm) cc_final: 0.7543 (tpp) REVERT: B 395 CYS cc_start: 0.8278 (t) cc_final: 0.7738 (t) REVERT: B 409 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8896 (tp) REVERT: B 467 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8824 (pt) REVERT: B 479 LEU cc_start: 0.8891 (tp) cc_final: 0.8680 (tp) REVERT: C 4 MET cc_start: 0.5572 (pp-130) cc_final: 0.2878 (tpp) REVERT: C 161 ASP cc_start: 0.4842 (OUTLIER) cc_final: 0.4514 (m-30) REVERT: C 256 ASP cc_start: 0.8151 (t0) cc_final: 0.7130 (t0) REVERT: C 380 GLU cc_start: 0.7698 (tt0) cc_final: 0.7498 (tm-30) REVERT: C 401 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.4973 (p90) REVERT: C 439 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7847 (mmm-85) REVERT: C 467 LEU cc_start: 0.9047 (tt) cc_final: 0.8682 (mm) REVERT: E 9 TYR cc_start: 0.7135 (m-10) cc_final: 0.6904 (m-80) REVERT: E 35 MET cc_start: 0.7959 (mmm) cc_final: 0.7726 (tpp) REVERT: E 61 MET cc_start: 0.5995 (ppp) cc_final: 0.5724 (ppp) REVERT: E 78 LYS cc_start: 0.6799 (mttp) cc_final: 0.6400 (ptpp) REVERT: E 155 GLU cc_start: 0.7450 (tt0) cc_final: 0.6971 (tt0) REVERT: E 159 MET cc_start: 0.8825 (mmt) cc_final: 0.8480 (mtm) REVERT: F 5 GLN cc_start: 0.3877 (OUTLIER) cc_final: 0.3176 (mt0) REVERT: F 33 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6218 (tttt) REVERT: F 48 LEU cc_start: 0.8057 (mp) cc_final: 0.7598 (mt) REVERT: F 138 MET cc_start: 0.8872 (tmm) cc_final: 0.8639 (tmm) REVERT: F 149 TYR cc_start: 0.8234 (m-80) cc_final: 0.7997 (m-80) REVERT: F 156 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5631 (tpp) REVERT: F 226 MET cc_start: 0.6788 (tpt) cc_final: 0.6188 (tpt) REVERT: F 231 TYR cc_start: 0.6534 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: F 270 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.6355 (mmm) outliers start: 94 outliers final: 57 residues processed: 350 average time/residue: 0.1373 time to fit residues: 77.5227 Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 235 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 202 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 256 optimal weight: 0.0980 chunk 239 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS E 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073186 restraints weight = 76377.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.076366 restraints weight = 40579.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077392 restraints weight = 21167.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078238 restraints weight = 14898.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078964 restraints weight = 10841.739| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.532 21783 Z= 0.208 Angle : 0.806 31.062 29385 Z= 0.355 Chirality : 0.045 0.187 3152 Planarity : 0.004 0.050 3780 Dihedral : 5.979 67.509 3302 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.22 % Allowed : 28.09 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2664 helix: 1.24 (0.15), residues: 1237 sheet: -0.51 (0.30), residues: 315 loop : -1.11 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 468 TYR 0.016 0.001 TYR B 88 PHE 0.021 0.001 PHE A 459 TRP 0.020 0.001 TRP A 253 HIS 0.010 0.001 HIS D 478 Details of bonding type rmsd covalent geometry : bond 0.00452 (21758) covalent geometry : angle 0.76383 (29367) hydrogen bonds : bond 0.03684 ( 956) hydrogen bonds : angle 5.08591 ( 2784) metal coordination : bond 0.01400 ( 8) metal coordination : angle 10.36765 ( 18) Misc. bond : bond 0.14421 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 270 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8408 (pm20) REVERT: A 90 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8740 (tp40) REVERT: A 98 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 465 MET cc_start: 0.9013 (ttt) cc_final: 0.8441 (ttt) REVERT: B 98 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: B 120 GLU cc_start: 0.8633 (mp0) cc_final: 0.8265 (mp0) REVERT: B 131 MET cc_start: 0.8350 (tpp) cc_final: 0.8065 (tpp) REVERT: B 133 ASP cc_start: 0.8019 (m-30) cc_final: 0.7711 (m-30) REVERT: B 271 MET cc_start: 0.8540 (ttm) cc_final: 0.7580 (tpp) REVERT: B 354 MET cc_start: 0.8626 (tpp) cc_final: 0.8406 (tpp) REVERT: B 395 CYS cc_start: 0.8306 (t) cc_final: 0.7756 (t) REVERT: B 409 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8906 (tp) REVERT: B 467 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8810 (pt) REVERT: B 517 TYR cc_start: 0.8448 (p90) cc_final: 0.8219 (p90) REVERT: C 4 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.2966 (tpp) REVERT: C 161 ASP cc_start: 0.4981 (OUTLIER) cc_final: 0.4536 (m-30) REVERT: C 256 ASP cc_start: 0.8166 (t0) cc_final: 0.7103 (t0) REVERT: C 380 GLU cc_start: 0.7967 (tt0) cc_final: 0.7680 (tm-30) REVERT: C 401 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.5084 (p90) REVERT: C 467 LEU cc_start: 0.9075 (tt) cc_final: 0.8732 (mm) REVERT: D 186 THR cc_start: 0.9479 (OUTLIER) cc_final: 0.9235 (p) REVERT: E 9 TYR cc_start: 0.7278 (m-10) cc_final: 0.6730 (m-10) REVERT: E 35 MET cc_start: 0.7943 (mmm) cc_final: 0.7682 (tpp) REVERT: E 61 MET cc_start: 0.5997 (ppp) cc_final: 0.5614 (ppp) REVERT: E 155 GLU cc_start: 0.7464 (tt0) cc_final: 0.7171 (tt0) REVERT: E 156 MET cc_start: 0.7872 (ppp) cc_final: 0.7593 (ppp) REVERT: E 159 MET cc_start: 0.8836 (mmt) cc_final: 0.8554 (mtm) REVERT: E 237 GLN cc_start: 0.4957 (tp40) cc_final: 0.4614 (tp40) REVERT: E 275 MET cc_start: 0.6482 (OUTLIER) cc_final: 0.5077 (ttm) REVERT: F 5 GLN cc_start: 0.3840 (OUTLIER) cc_final: 0.3159 (mt0) REVERT: F 30 MET cc_start: 0.7235 (ttm) cc_final: 0.6924 (ttt) REVERT: F 33 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.6268 (ttmt) REVERT: F 48 LEU cc_start: 0.8095 (mp) cc_final: 0.7672 (mt) REVERT: F 138 MET cc_start: 0.8843 (tmm) cc_final: 0.8611 (tmm) REVERT: F 156 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5612 (tpp) REVERT: F 226 MET cc_start: 0.6792 (tpt) cc_final: 0.6119 (tpt) REVERT: F 231 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: F 270 MET cc_start: 0.6699 (tpt) cc_final: 0.6376 (mmm) REVERT: G 115 PHE cc_start: 0.8818 (p90) cc_final: 0.8589 (p90) outliers start: 95 outliers final: 66 residues processed: 338 average time/residue: 0.1335 time to fit residues: 73.1047 Evaluate side-chains 339 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 258 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 118 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 228 optimal weight: 30.0000 chunk 198 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 97 optimal weight: 0.0980 chunk 204 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.091428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072456 restraints weight = 79239.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074863 restraints weight = 38946.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076455 restraints weight = 23043.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077538 restraints weight = 15423.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078261 restraints weight = 11401.203| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.494 21783 Z= 0.235 Angle : 0.825 33.573 29385 Z= 0.367 Chirality : 0.046 0.201 3152 Planarity : 0.005 0.054 3780 Dihedral : 6.058 67.446 3302 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.31 % Allowed : 28.26 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.05 (0.16), residues: 2664 helix: 1.21 (0.15), residues: 1237 sheet: -0.52 (0.29), residues: 315 loop : -1.13 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 468 TYR 0.042 0.002 TYR E 241 PHE 0.047 0.002 PHE A 412 TRP 0.022 0.002 TRP A 253 HIS 0.025 0.002 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00510 (21758) covalent geometry : angle 0.77875 (29367) hydrogen bonds : bond 0.03840 ( 956) hydrogen bonds : angle 5.12006 ( 2784) metal coordination : bond 0.01614 ( 8) metal coordination : angle 10.98988 ( 18) Misc. bond : bond 0.13555 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 253 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: A 98 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.7659 (p0) REVERT: A 465 MET cc_start: 0.9008 (ttt) cc_final: 0.8554 (ttt) REVERT: B 120 GLU cc_start: 0.8643 (mp0) cc_final: 0.8288 (mp0) REVERT: B 131 MET cc_start: 0.8345 (tpp) cc_final: 0.8051 (tpp) REVERT: B 133 ASP cc_start: 0.7939 (m-30) cc_final: 0.7598 (m-30) REVERT: B 271 MET cc_start: 0.8517 (ttm) cc_final: 0.7578 (tpp) REVERT: B 354 MET cc_start: 0.8679 (tpp) cc_final: 0.8395 (tpp) REVERT: B 355 MET cc_start: 0.9323 (mtm) cc_final: 0.9009 (mtm) REVERT: B 395 CYS cc_start: 0.8339 (t) cc_final: 0.7832 (t) REVERT: B 409 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8892 (tp) REVERT: C 4 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.3071 (tpp) REVERT: C 161 ASP cc_start: 0.5048 (OUTLIER) cc_final: 0.4625 (m-30) REVERT: C 256 ASP cc_start: 0.8171 (t0) cc_final: 0.7066 (t0) REVERT: C 380 GLU cc_start: 0.7868 (tt0) cc_final: 0.7655 (tm-30) REVERT: C 401 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.6644 (p90) REVERT: D 186 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9214 (p) REVERT: D 396 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.8303 (t-90) REVERT: D 518 ASN cc_start: 0.8781 (t0) cc_final: 0.8527 (t0) REVERT: E 9 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: E 35 MET cc_start: 0.8068 (mmm) cc_final: 0.7793 (tpp) REVERT: E 61 MET cc_start: 0.5923 (ppp) cc_final: 0.5635 (ppp) REVERT: E 78 LYS cc_start: 0.6940 (mttp) cc_final: 0.6533 (ptpp) REVERT: E 155 GLU cc_start: 0.7508 (tt0) cc_final: 0.7225 (tt0) REVERT: E 156 MET cc_start: 0.7944 (ppp) cc_final: 0.7686 (ppp) REVERT: E 159 MET cc_start: 0.8826 (mmt) cc_final: 0.8523 (mtm) REVERT: E 275 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.5298 (ttm) REVERT: F 5 GLN cc_start: 0.3970 (OUTLIER) cc_final: 0.3262 (mt0) REVERT: F 30 MET cc_start: 0.7147 (ttm) cc_final: 0.6805 (ttt) REVERT: F 33 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6239 (ttmt) REVERT: F 48 LEU cc_start: 0.8102 (mp) cc_final: 0.7693 (mt) REVERT: F 138 MET cc_start: 0.8840 (tmm) cc_final: 0.8586 (tmm) REVERT: F 156 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5670 (tpp) REVERT: F 157 MET cc_start: 0.6774 (ttp) cc_final: 0.6479 (ttm) REVERT: F 226 MET cc_start: 0.7023 (tpt) cc_final: 0.6290 (tpt) REVERT: F 231 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: G 53 LYS cc_start: 0.8492 (tppt) cc_final: 0.8205 (mmmt) REVERT: G 115 PHE cc_start: 0.8851 (p90) cc_final: 0.8603 (p90) outliers start: 97 outliers final: 69 residues processed: 321 average time/residue: 0.1342 time to fit residues: 70.1898 Evaluate side-chains 329 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 246 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 9 TYR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 156 MET Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 39 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 134 optimal weight: 50.0000 chunk 148 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.091753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072736 restraints weight = 80032.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.075159 restraints weight = 39365.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076762 restraints weight = 23274.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077826 restraints weight = 15605.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078576 restraints weight = 11562.879| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.477 21783 Z= 0.215 Angle : 0.814 33.924 29385 Z= 0.361 Chirality : 0.045 0.252 3152 Planarity : 0.004 0.051 3780 Dihedral : 6.033 66.634 3302 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.00 % Allowed : 28.31 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % 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: 0.05 (0.16), residues: 2664 helix: 1.20 (0.15), residues: 1237 sheet: -0.49 (0.30), residues: 315 loop : -1.13 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 468 TYR 0.038 0.002 TYR E 241 PHE 0.020 0.001 PHE A 459 TRP 0.020 0.002 TRP A 253 HIS 0.019 0.001 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00464 (21758) covalent geometry : angle 0.76680 (29367) hydrogen bonds : bond 0.03761 ( 956) hydrogen bonds : angle 5.09414 ( 2784) metal coordination : bond 0.01381 ( 8) metal coordination : angle 11.06970 ( 18) Misc. bond : bond 0.13215 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 251 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8446 (pm20) REVERT: A 98 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.7637 (p0) REVERT: A 372 MET cc_start: 0.8128 (mpp) cc_final: 0.7459 (mtt) REVERT: A 465 MET cc_start: 0.8997 (ttt) cc_final: 0.8434 (ttt) REVERT: B 120 GLU cc_start: 0.8620 (mp0) cc_final: 0.8283 (mp0) REVERT: B 131 MET cc_start: 0.8333 (tpp) cc_final: 0.8031 (tpp) REVERT: B 133 ASP cc_start: 0.7902 (m-30) cc_final: 0.7645 (m-30) REVERT: B 271 MET cc_start: 0.8531 (ttm) cc_final: 0.7597 (tpp) REVERT: B 354 MET cc_start: 0.8709 (tpp) cc_final: 0.8418 (tpp) REVERT: B 355 MET cc_start: 0.9317 (mtm) cc_final: 0.8996 (mtm) REVERT: B 395 CYS cc_start: 0.8320 (t) cc_final: 0.7780 (t) REVERT: B 409 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8896 (tp) REVERT: C 4 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.3082 (tpp) REVERT: C 161 ASP cc_start: 0.4982 (OUTLIER) cc_final: 0.4574 (m-30) REVERT: C 256 ASP cc_start: 0.8147 (t0) cc_final: 0.7021 (t0) REVERT: C 372 MET cc_start: 0.8070 (mmt) cc_final: 0.7780 (mmt) REVERT: C 380 GLU cc_start: 0.7844 (tt0) cc_final: 0.7636 (tm-30) REVERT: C 401 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.6681 (p90) REVERT: D 186 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9219 (p) REVERT: D 247 MET cc_start: 0.7291 (tpp) cc_final: 0.6736 (mtt) REVERT: D 396 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.8195 (t-90) REVERT: D 518 ASN cc_start: 0.8826 (t0) cc_final: 0.8558 (t0) REVERT: E 35 MET cc_start: 0.8157 (mmm) cc_final: 0.7868 (tpp) REVERT: E 61 MET cc_start: 0.6022 (ppp) cc_final: 0.5800 (ppp) REVERT: E 78 LYS cc_start: 0.6932 (mttp) cc_final: 0.6518 (ptpp) REVERT: E 122 PHE cc_start: 0.6304 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: E 155 GLU cc_start: 0.7484 (tt0) cc_final: 0.7217 (tt0) REVERT: E 156 MET cc_start: 0.8010 (ppp) cc_final: 0.7773 (ppp) REVERT: E 159 MET cc_start: 0.8794 (mmt) cc_final: 0.8519 (mtm) REVERT: E 275 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5805 (mtp) REVERT: F 5 GLN cc_start: 0.3963 (OUTLIER) cc_final: 0.3262 (mt0) REVERT: F 30 MET cc_start: 0.7128 (ttm) cc_final: 0.6832 (ttt) REVERT: F 33 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6349 (ttmt) REVERT: F 48 LEU cc_start: 0.8096 (mp) cc_final: 0.7691 (mt) REVERT: F 138 MET cc_start: 0.8860 (tmm) cc_final: 0.8588 (tmm) REVERT: F 157 MET cc_start: 0.6774 (ttp) cc_final: 0.6492 (ttm) REVERT: F 226 MET cc_start: 0.7077 (tpt) cc_final: 0.6343 (tpt) REVERT: F 231 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6416 (m-80) REVERT: G 53 LYS cc_start: 0.8482 (tppt) cc_final: 0.8219 (mmmt) REVERT: G 115 PHE cc_start: 0.8832 (p90) cc_final: 0.8594 (p90) outliers start: 90 outliers final: 70 residues processed: 313 average time/residue: 0.1350 time to fit residues: 68.9530 Evaluate side-chains 332 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 249 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 MET Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 171 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.091711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072112 restraints weight = 92616.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.075128 restraints weight = 45730.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076730 restraints weight = 26618.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.078055 restraints weight = 15658.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.078661 restraints weight = 10252.814| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.463 21783 Z= 0.211 Angle : 0.834 40.508 29385 Z= 0.360 Chirality : 0.045 0.201 3152 Planarity : 0.004 0.050 3780 Dihedral : 5.808 65.981 3297 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.00 % Allowed : 28.40 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2664 helix: 1.18 (0.15), residues: 1237 sheet: -0.48 (0.30), residues: 315 loop : -1.14 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 468 TYR 0.024 0.002 TYR F 241 PHE 0.021 0.001 PHE C 412 TRP 0.019 0.002 TRP A 253 HIS 0.016 0.001 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00456 (21758) covalent geometry : angle 0.76793 (29367) hydrogen bonds : bond 0.03717 ( 956) hydrogen bonds : angle 5.08267 ( 2784) metal coordination : bond 0.01563 ( 8) metal coordination : angle 13.18228 ( 18) Misc. bond : bond 0.12882 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 256 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8473 (pm20) REVERT: A 98 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8092 (p0) REVERT: A 372 MET cc_start: 0.8125 (mpp) cc_final: 0.7652 (mtt) REVERT: A 465 MET cc_start: 0.8991 (ttt) cc_final: 0.8424 (ttt) REVERT: B 98 TYR cc_start: 0.9229 (OUTLIER) cc_final: 0.8671 (m-10) REVERT: B 107 PHE cc_start: 0.9408 (m-80) cc_final: 0.8992 (m-10) REVERT: B 116 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (p0) REVERT: B 120 GLU cc_start: 0.8624 (mp0) cc_final: 0.8284 (mp0) REVERT: B 131 MET cc_start: 0.8338 (tpp) cc_final: 0.8046 (tpp) REVERT: B 133 ASP cc_start: 0.7968 (m-30) cc_final: 0.7736 (m-30) REVERT: B 271 MET cc_start: 0.8530 (ttm) cc_final: 0.7622 (tpp) REVERT: B 395 CYS cc_start: 0.8309 (t) cc_final: 0.7769 (t) REVERT: B 409 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8897 (tp) REVERT: C 4 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.3043 (tpp) REVERT: C 161 ASP cc_start: 0.4965 (OUTLIER) cc_final: 0.4553 (m-30) REVERT: C 256 ASP cc_start: 0.8137 (t0) cc_final: 0.7003 (t0) REVERT: C 380 GLU cc_start: 0.7930 (tt0) cc_final: 0.7680 (tm-30) REVERT: C 401 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.6644 (p90) REVERT: D 154 MET cc_start: 0.8517 (ppp) cc_final: 0.8274 (ppp) REVERT: D 186 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9223 (p) REVERT: D 247 MET cc_start: 0.7200 (tpp) cc_final: 0.6724 (mtt) REVERT: D 396 HIS cc_start: 0.8656 (OUTLIER) cc_final: 0.8096 (t-90) REVERT: D 518 ASN cc_start: 0.8825 (t0) cc_final: 0.8516 (t0) REVERT: E 35 MET cc_start: 0.8175 (mmm) cc_final: 0.7883 (tpp) REVERT: E 61 MET cc_start: 0.6025 (ppp) cc_final: 0.5711 (ppp) REVERT: E 78 LYS cc_start: 0.6905 (mttp) cc_final: 0.6496 (ptpp) REVERT: E 122 PHE cc_start: 0.6321 (OUTLIER) cc_final: 0.5406 (m-80) REVERT: E 155 GLU cc_start: 0.7489 (tt0) cc_final: 0.7244 (tt0) REVERT: E 156 MET cc_start: 0.8055 (ppp) cc_final: 0.7808 (ppp) REVERT: E 159 MET cc_start: 0.8807 (mmt) cc_final: 0.8535 (mtm) REVERT: E 241 TYR cc_start: 0.6184 (m-80) cc_final: 0.5972 (m-80) REVERT: E 275 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.5720 (mtp) REVERT: F 5 GLN cc_start: 0.3934 (OUTLIER) cc_final: 0.3229 (mt0) REVERT: F 30 MET cc_start: 0.7222 (ttm) cc_final: 0.6963 (ttt) REVERT: F 33 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6443 (ttmt) REVERT: F 48 LEU cc_start: 0.8105 (mp) cc_final: 0.7704 (mt) REVERT: F 138 MET cc_start: 0.8880 (tmm) cc_final: 0.8572 (tmm) REVERT: F 226 MET cc_start: 0.6986 (tpt) cc_final: 0.6206 (tpt) REVERT: F 231 TYR cc_start: 0.6892 (OUTLIER) cc_final: 0.6419 (m-80) REVERT: G 53 LYS cc_start: 0.8459 (tppt) cc_final: 0.8196 (mmmt) REVERT: G 115 PHE cc_start: 0.8838 (p90) cc_final: 0.8603 (p90) outliers start: 90 outliers final: 71 residues processed: 317 average time/residue: 0.1319 time to fit residues: 68.4114 Evaluate side-chains 334 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 248 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 116 ASP Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 409 ILE Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain C residue 4 MET Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 300 LYS Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain D residue 396 HIS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 262 MET Chi-restraints excluded: chain E residue 275 MET Chi-restraints excluded: chain F residue 5 GLN Chi-restraints excluded: chain F residue 33 LYS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 231 TYR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 105 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 0.4980 chunk 253 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** F 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.092055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073445 restraints weight = 69587.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076344 restraints weight = 37012.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077320 restraints weight = 21085.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.078182 restraints weight = 15072.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.078775 restraints weight = 10780.139| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.457 21783 Z= 0.202 Angle : 0.835 41.119 29385 Z= 0.357 Chirality : 0.045 0.195 3152 Planarity : 0.004 0.049 3780 Dihedral : 5.786 64.739 3297 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.96 % Allowed : 28.35 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.22 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2664 helix: 1.17 (0.15), residues: 1237 sheet: -0.49 (0.29), residues: 315 loop : -1.15 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 468 TYR 0.020 0.002 TYR E 125 PHE 0.022 0.001 PHE C 412 TRP 0.018 0.001 TRP A 253 HIS 0.010 0.001 HIS D 396 Details of bonding type rmsd covalent geometry : bond 0.00437 (21758) covalent geometry : angle 0.76774 (29367) hydrogen bonds : bond 0.03679 ( 956) hydrogen bonds : angle 5.07087 ( 2784) metal coordination : bond 0.01469 ( 8) metal coordination : angle 13.24491 ( 18) Misc. bond : bond 0.12728 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.26 seconds wall clock time: 65 minutes 53.83 seconds (3953.83 seconds total)