Starting phenix.real_space_refine on Mon Apr 6 05:59:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ut6_26756/04_2026/7ut6_26756.map" } resolution = 1.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 32 7.16 5 S 139 5.16 5 C 10170 2.51 5 N 2702 2.21 5 O 3397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 16442 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3793 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Conformer: "B" Number of residues, atoms: 477, 3790 Classifications: {'peptide': 477} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} bond proxies already assigned to first conformer: 3874 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "C" Number of atoms: 3790 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 477, 3787 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 455} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 3871 Chain: "D" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4174 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {'HCA': 1, 'ICS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {' FE': 1, 'CLF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Classifications: {'water': 126} Link IDs: {None: 125} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2092 SG CYS A 275 47.781 104.752 58.633 1.00 23.62 S ATOM 4552 SG CYS B 95 31.507 99.319 42.686 1.00 19.10 S ATOM 1170 SG CYS A 154 29.327 103.527 45.294 1.00 18.14 S ATOM 465 SG CYS A 62 34.754 101.543 48.190 1.00 15.85 S ATOM 652 SG CYS A 88 28.975 97.621 48.314 1.00 17.18 S ATOM 652 SG CYS A 88 28.975 97.621 48.314 1.00 17.18 S ATOM 5005 SG CYS B 153 26.040 99.849 43.955 1.00 19.41 S ATOM 4372 SG CYS B 70 28.447 93.339 43.009 1.00 16.63 S ATOM 4552 SG CYS B 95 31.507 99.319 42.686 1.00 19.10 S ATOM 10056 SG CYS C 275 34.252 27.956 63.734 1.00 24.05 S ATOM 12516 SG CYS D 95 52.299 31.045 49.128 1.00 19.28 S ATOM 9134 SG CYS C 154 54.145 27.316 52.603 1.00 17.76 S ATOM 8429 SG CYS C 62 48.362 29.629 54.543 1.00 13.97 S ATOM 8616 SG CYS C 88 54.169 33.585 54.676 1.00 13.41 S ATOM 8616 SG CYS C 88 54.169 33.585 54.676 1.00 13.41 S ATOM 12969 SG CYS D 153 57.575 30.764 51.077 1.00 19.66 S ATOM 12336 SG CYS D 70 55.352 37.030 48.883 1.00 16.19 S ATOM 12516 SG CYS D 95 52.299 31.045 49.128 1.00 19.28 S Time building chain proxies: 5.05, per 1000 atoms: 0.31 Number of scatterers: 16442 At special positions: 0 Unit cell: (84.76, 130.4, 101.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mo 2 41.97 Fe 32 26.01 S 139 16.00 O 3397 8.00 N 2702 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 773.7 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 59.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 18 Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.954A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.505A pdb=" N GLN A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.948A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.637A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.240A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 245 removed outlier: 4.147A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 291 removed outlier: 5.793A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 317 through 347 Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.930A 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 434 removed outlier: 4.476A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE A 430 " --> pdb=" O LYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 451 through 468 removed outlier: 3.627A pdb=" N ALA A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.070A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 4.072A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 127 through 143 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 161 through 172 Processing helix chain 'B' and resid 192 through 210 Processing helix chain 'B' and resid 211 through 216 removed outlier: 5.477A pdb=" N ASP B 214 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 215 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.832A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'B' and resid 320 through 337 removed outlier: 4.093A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.461A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 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 460 through 463 Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 30 removed outlier: 3.954A pdb=" N LYS C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 86 through 92 removed outlier: 3.507A pdb=" N GLN C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 removed outlier: 3.977A pdb=" N GLY C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.225A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 245 removed outlier: 4.113A 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: 5.787A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 314 Processing helix chain 'C' and resid 317 through 347 Proline residue: C 333 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 358 through 363 Processing helix chain 'C' and resid 363 through 370 removed outlier: 3.571A pdb=" N LEU C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.268A pdb=" N LYS C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 424 through 434 removed outlier: 4.505A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.295A 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: 3.621A pdb=" N ALA C 457 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 removed outlier: 3.518A pdb=" N GLU D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 81 removed outlier: 4.068A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 4.022A pdb=" N VAL D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 127 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 192 through 210 Processing helix chain 'D' and resid 211 through 216 removed outlier: 5.475A pdb=" N ASP D 214 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 247 removed outlier: 3.829A pdb=" N PHE D 237 " --> pdb=" O TYR D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.318A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 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 460 through 463 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.384A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 421 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 178 through 181 removed outlier: 6.888A pdb=" N ILE A 148 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 181 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 150 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.252A 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: 6.992A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 225 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 251 through 253 removed outlier: 6.331A pdb=" N ASN B 225 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 423 removed outlier: 8.580A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE B 367 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE B 393 " --> pdb=" O PHE B 367 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 369 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS B 395 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.372A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.387A 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: 6.881A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 6.935A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE C 225 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 removed outlier: 6.330A pdb=" N ASN D 225 " --> pdb=" O VAL D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 420 through 423 removed outlier: 8.559A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE D 367 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE D 393 " --> pdb=" O PHE D 367 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU D 369 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS D 395 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 789 hydrogen bonds defined for protein. 2247 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: 3.04 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.85: 16347 1.85 - 2.48: 102 2.48 - 3.11: 20 3.11 - 3.74: 10 3.74 - 4.37: 4 Bond restraints: 16483 Sorted by residual: bond pdb="FE2 CLF D 602 " pdb="FE8 CLF D 602 " ideal model delta sigma weight residual 2.200 4.375 -2.175 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE2 CLF B 602 " pdb="FE8 CLF B 602 " ideal model delta sigma weight residual 2.200 4.369 -2.169 2.00e-02 2.50e+03 1.18e+04 bond pdb="FE5 CLF D 602 " pdb="FE6 CLF D 602 " ideal model delta sigma weight residual 2.200 3.929 -1.729 2.00e-02 2.50e+03 7.48e+03 bond pdb="FE5 CLF B 602 " pdb="FE6 CLF B 602 " ideal model delta sigma weight residual 2.200 3.922 -1.722 2.00e-02 2.50e+03 7.42e+03 bond pdb=" S1 CLF D 602 " pdb="FE5 CLF D 602 " ideal model delta sigma weight residual 2.200 3.688 -1.488 2.00e-02 2.50e+03 5.53e+03 ... (remaining 16478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.88: 22237 6.88 - 13.76: 0 13.76 - 20.64: 2 20.64 - 27.52: 0 27.52 - 34.40: 4 Bond angle restraints: 22243 Sorted by residual: angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE4 CLF B 602 " ideal model delta sigma weight residual 90.00 55.60 34.40 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE4 CLF D 602 " ideal model delta sigma weight residual 90.00 55.62 34.38 3.00e+00 1.11e-01 1.31e+02 angle pdb=" S1 CLF B 602 " pdb="FE2 CLF B 602 " pdb="FE1 CLF B 602 " ideal model delta sigma weight residual 90.00 60.62 29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE1 CLF D 602 " ideal model delta sigma weight residual 90.00 60.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" S1 CLF D 602 " pdb="FE2 CLF D 602 " pdb="FE3 CLF D 602 " ideal model delta sigma weight residual 90.00 108.24 -18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 22238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9029 17.99 - 35.99: 786 35.99 - 53.98: 200 53.98 - 71.98: 50 71.98 - 89.97: 36 Dihedral angle restraints: 10101 sinusoidal: 4359 harmonic: 5742 Sorted by residual: dihedral pdb=" CA ILE C 75 " pdb=" C ILE C 75 " pdb=" N LYS C 76 " pdb=" CA LYS C 76 " ideal model delta harmonic sigma weight residual -180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA SER D 11 " pdb=" C SER D 11 " pdb=" N TYR D 12 " pdb=" CA TYR D 12 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA SER B 11 " pdb=" C SER B 11 " pdb=" N TYR B 12 " pdb=" CA TYR B 12 " ideal model delta harmonic sigma weight residual 180.00 161.21 18.79 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 10098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1596 0.043 - 0.086: 553 0.086 - 0.129: 175 0.129 - 0.173: 11 0.173 - 0.216: 1 Chirality restraints: 2336 Sorted by residual: chirality pdb=" CA GLU D 109 " pdb=" N GLU D 109 " pdb=" C GLU D 109 " pdb=" CB GLU D 109 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA PHE A 431 " pdb=" N PHE A 431 " pdb=" C PHE A 431 " pdb=" CB PHE A 431 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA PHE C 431 " pdb=" N PHE C 431 " pdb=" C PHE C 431 " pdb=" CB PHE C 431 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 2333 not shown) Planarity restraints: 2858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 359 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 360 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 73 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO A 74 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 73 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 74 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " -0.022 5.00e-02 4.00e+02 ... (remaining 2855 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 532 2.69 - 3.24: 17112 3.24 - 3.80: 30875 3.80 - 4.35: 41719 4.35 - 4.90: 65108 Nonbonded interactions: 155346 Sorted by model distance: nonbonded pdb=" O2 HCA C 501 " pdb=" O7 HCA C 501 " model vdw 2.140 3.040 nonbonded pdb=" O2 HCA A 501 " pdb=" O7 HCA A 501 " model vdw 2.155 3.040 nonbonded pdb=" OD2 ASP D 353 " pdb="FE FE D 601 " model vdw 2.204 2.260 nonbonded pdb=" OD2 ASP D 357 " pdb="FE FE D 601 " model vdw 2.205 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH D 812 " model vdw 2.213 2.260 ... (remaining 155341 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 4 and (name N or name CA or name C or name O or name CB ) \ ) or resid 5 through 248 or resid 250 through 502)) selection = (chain 'C' and (resid 4 through 248 or resid 250 through 502)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.530 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.300 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:8.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 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 : 0.048 2.175 16499 Z= 2.413 Angle : 0.806 34.404 22243 Z= 0.400 Chirality : 0.047 0.216 2336 Planarity : 0.005 0.061 2858 Dihedral : 15.909 89.973 6433 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.93 % Allowed : 12.36 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.18), residues: 1992 helix: 0.98 (0.16), residues: 992 sheet: -0.89 (0.32), residues: 202 loop : -0.44 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 359 TYR 0.024 0.003 TYR C 229 PHE 0.023 0.003 PHE A 431 TRP 0.015 0.002 TRP C 444 HIS 0.010 0.002 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.04789 (16483) covalent geometry : angle 0.80589 (22243) hydrogen bonds : bond 0.14345 ( 789) hydrogen bonds : angle 6.74082 ( 2247) Misc. bond : bond 0.10369 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 268 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8061 (mm) cc_final: 0.7754 (tp) REVERT: A 295 MET cc_start: 0.8861 (ptm) cc_final: 0.8629 (ptm) REVERT: A 389 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7672 (mtt90) REVERT: A 415 ARG cc_start: 0.6539 (tpp80) cc_final: 0.6165 (tpt-90) REVERT: B 7 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7542 (tttt) REVERT: B 18 GLN cc_start: 0.8362 (tp-100) cc_final: 0.8145 (tp-100) REVERT: B 93 GLN cc_start: 0.8756 (pt0) cc_final: 0.7770 (tp-100) REVERT: B 146 MET cc_start: 0.8995 (ttp) cc_final: 0.8659 (ttp) REVERT: B 206 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.8038 (ttm-80) REVERT: B 211 LYS cc_start: 0.8100 (mtpm) cc_final: 0.7452 (mptt) REVERT: B 355 MET cc_start: 0.9188 (mtp) cc_final: 0.8963 (mtp) REVERT: C 22 GLU cc_start: 0.6665 (tp30) cc_final: 0.6435 (tm-30) REVERT: C 26 LYS cc_start: 0.7369 (tttt) cc_final: 0.7060 (ttmt) REVERT: C 373 GLU cc_start: 0.7149 (tt0) cc_final: 0.6923 (tm-30) REVERT: C 476 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: D 303 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8221 (tptp) REVERT: D 377 MET cc_start: 0.9110 (ptm) cc_final: 0.8826 (ptm) outliers start: 16 outliers final: 6 residues processed: 279 average time/residue: 0.9282 time to fit residues: 278.5675 Evaluate side-chains 223 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 175 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 362 HIS A 432 GLN B 4 GLN B 93 GLN C 53 GLN C 98 ASN C 321 GLN C 432 GLN D 4 GLN D 168 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.139401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121074 restraints weight = 10713.459| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 0.69 r_work: 0.3278 rms_B_bonded: 0.98 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 1.66 restraints_weight: 0.2500 r_work: 0.3017 rms_B_bonded: 4.45 restraints_weight: 0.1250 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.381 16499 Z= 0.320 Angle : 0.807 30.795 22243 Z= 0.397 Chirality : 0.048 0.170 2336 Planarity : 0.005 0.078 2858 Dihedral : 5.680 78.645 2530 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.45 % Allowed : 11.09 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 1992 helix: 1.15 (0.16), residues: 1014 sheet: -0.74 (0.34), residues: 192 loop : -0.38 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 284 TYR 0.026 0.003 TYR C 446 PHE 0.019 0.002 PHE A 429 TRP 0.019 0.002 TRP A 253 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00617 (16483) covalent geometry : angle 0.80666 (22243) hydrogen bonds : bond 0.06631 ( 789) hydrogen bonds : angle 5.87048 ( 2247) Misc. bond : bond 0.19042 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7987 (mm) cc_final: 0.7581 (tp) REVERT: A 176 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7571 (mtpt) REVERT: A 322 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8069 (tmmt) REVERT: A 415 ARG cc_start: 0.6644 (tpp80) cc_final: 0.5670 (tpt-90) REVERT: A 445 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: B 7 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7673 (tttt) REVERT: B 18 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8431 (tp-100) REVERT: B 146 MET cc_start: 0.9014 (ttp) cc_final: 0.8703 (ttp) REVERT: B 160 ASP cc_start: 0.8512 (m-30) cc_final: 0.8242 (m-30) REVERT: B 211 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7392 (mmpt) REVERT: C 22 GLU cc_start: 0.7028 (tp30) cc_final: 0.6713 (tp30) REVERT: C 26 LYS cc_start: 0.7633 (tttt) cc_final: 0.7219 (ttmt) REVERT: C 389 ARG cc_start: 0.7798 (mtt90) cc_final: 0.7461 (mtt180) REVERT: C 476 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7745 (tt0) REVERT: D 303 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8496 (tptp) REVERT: D 377 MET cc_start: 0.9194 (ptm) cc_final: 0.8905 (ptm) outliers start: 25 outliers final: 12 residues processed: 243 average time/residue: 0.9004 time to fit residues: 235.9854 Evaluate side-chains 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 476 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN A 285 HIS C 53 GLN C 98 ASN C 321 GLN C 384 ASN D 4 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122401 restraints weight = 16248.378| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 0.87 r_work: 0.3292 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.341 16499 Z= 0.259 Angle : 0.736 30.830 22243 Z= 0.352 Chirality : 0.045 0.153 2336 Planarity : 0.004 0.058 2858 Dihedral : 5.444 74.506 2527 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.63 % Allowed : 10.80 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1992 helix: 1.32 (0.16), residues: 1016 sheet: -0.76 (0.36), residues: 176 loop : -0.41 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 284 TYR 0.020 0.002 TYR C 446 PHE 0.015 0.002 PHE C 431 TRP 0.015 0.002 TRP A 253 HIS 0.016 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00493 (16483) covalent geometry : angle 0.73564 (22243) hydrogen bonds : bond 0.05509 ( 789) hydrogen bonds : angle 5.61608 ( 2247) Misc. bond : bond 0.16007 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 47 ILE cc_start: 0.7968 (mm) cc_final: 0.7573 (tp) REVERT: A 176 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7658 (mtpt) REVERT: A 322 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7774 (tmmt) REVERT: A 415 ARG cc_start: 0.6551 (tpp80) cc_final: 0.5752 (tpt-90) REVERT: A 445 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: B 7 LYS cc_start: 0.7930 (ttpp) cc_final: 0.7634 (tttt) REVERT: B 18 GLN cc_start: 0.8530 (tp-100) cc_final: 0.8257 (tp-100) REVERT: B 146 MET cc_start: 0.8908 (ttp) cc_final: 0.8522 (ttp) REVERT: B 211 LYS cc_start: 0.8139 (mtpm) cc_final: 0.7483 (mmpt) REVERT: C 22 GLU cc_start: 0.6923 (tp30) cc_final: 0.6698 (tm-30) REVERT: C 26 LYS cc_start: 0.7469 (tttt) cc_final: 0.7118 (ttmt) REVERT: C 476 GLN cc_start: 0.7972 (tp-100) cc_final: 0.7569 (tt0) REVERT: D 299 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: D 303 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8408 (tptp) REVERT: D 377 MET cc_start: 0.9038 (ptm) cc_final: 0.8719 (ptm) outliers start: 28 outliers final: 10 residues processed: 246 average time/residue: 0.8917 time to fit residues: 236.9946 Evaluate side-chains 229 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 216 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 155 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 98 ASN C 321 GLN D 4 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.119042 restraints weight = 19433.043| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 0.97 r_work: 0.3243 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.420 16499 Z= 0.301 Angle : 0.783 30.661 22243 Z= 0.380 Chirality : 0.047 0.160 2336 Planarity : 0.005 0.072 2858 Dihedral : 5.270 50.085 2523 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 11.14 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 1992 helix: 1.24 (0.16), residues: 1016 sheet: -0.72 (0.36), residues: 176 loop : -0.45 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 284 TYR 0.025 0.002 TYR C 446 PHE 0.020 0.002 PHE C 431 TRP 0.015 0.002 TRP B 296 HIS 0.009 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00581 (16483) covalent geometry : angle 0.78265 (22243) hydrogen bonds : bond 0.06329 ( 789) hydrogen bonds : angle 5.72950 ( 2247) Misc. bond : bond 0.18401 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7512 (mtpt) REVERT: A 322 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7806 (tmmt) REVERT: A 415 ARG cc_start: 0.6584 (tpp80) cc_final: 0.5661 (tpt-90) REVERT: A 445 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: B 7 LYS cc_start: 0.7965 (ttpp) cc_final: 0.7660 (tttt) REVERT: B 18 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8309 (tp-100) REVERT: B 146 MET cc_start: 0.8939 (ttp) cc_final: 0.8613 (ttp) REVERT: B 211 LYS cc_start: 0.8187 (mtpm) cc_final: 0.7501 (mmpt) REVERT: C 22 GLU cc_start: 0.6976 (tp30) cc_final: 0.6755 (tm-30) REVERT: C 23 LYS cc_start: 0.7841 (ttmt) cc_final: 0.6994 (ttpp) REVERT: C 26 LYS cc_start: 0.7480 (tttt) cc_final: 0.7122 (ttmt) REVERT: C 182 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8053 (mtt-85) REVERT: D 299 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: D 303 LYS cc_start: 0.8884 (mtmt) cc_final: 0.8550 (mppt) outliers start: 25 outliers final: 14 residues processed: 232 average time/residue: 0.8855 time to fit residues: 221.8166 Evaluate side-chains 227 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 161 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 4 GLN ** D 104 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 = 0.3635 r_free = 0.3635 target = 0.142754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122730 restraints weight = 16613.395| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.89 r_work: 0.3299 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.328 16499 Z= 0.252 Angle : 0.726 30.726 22243 Z= 0.345 Chirality : 0.045 0.147 2336 Planarity : 0.004 0.057 2858 Dihedral : 5.011 50.382 2520 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.33 % Allowed : 11.55 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 1992 helix: 1.40 (0.16), residues: 1014 sheet: -0.68 (0.36), residues: 176 loop : -0.37 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 284 TYR 0.018 0.002 TYR C 446 PHE 0.017 0.002 PHE C 431 TRP 0.013 0.002 TRP A 253 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00482 (16483) covalent geometry : angle 0.72563 (22243) hydrogen bonds : bond 0.05270 ( 789) hydrogen bonds : angle 5.53569 ( 2247) Misc. bond : bond 0.15231 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7638 (mtpt) REVERT: A 322 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7768 (tmmt) REVERT: A 352 MET cc_start: 0.8375 (mtp) cc_final: 0.8165 (mtp) REVERT: A 415 ARG cc_start: 0.6655 (tpp80) cc_final: 0.5765 (tpt-90) REVERT: A 445 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: B 7 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7638 (tttt) REVERT: B 18 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8326 (tp-100) REVERT: B 26 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8366 (mtmm) REVERT: B 146 MET cc_start: 0.8914 (ttp) cc_final: 0.8548 (ttp) REVERT: B 211 LYS cc_start: 0.8131 (mtpm) cc_final: 0.7495 (mmpt) REVERT: B 238 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7716 (mtt180) REVERT: C 22 GLU cc_start: 0.6952 (tp30) cc_final: 0.6703 (tm-30) REVERT: C 23 LYS cc_start: 0.7817 (ttmt) cc_final: 0.6947 (ttpp) REVERT: C 26 LYS cc_start: 0.7468 (tttt) cc_final: 0.7134 (ttmt) REVERT: C 389 ARG cc_start: 0.7746 (mtt90) cc_final: 0.7474 (mtt180) REVERT: D 299 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: D 303 LYS cc_start: 0.8863 (mtmt) cc_final: 0.8523 (mppt) outliers start: 23 outliers final: 11 residues processed: 237 average time/residue: 0.8935 time to fit residues: 228.6640 Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 185 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 196 optimal weight: 0.3980 chunk 146 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3648 r_free = 0.3648 target = 0.143698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124544 restraints weight = 14201.776| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 0.80 r_work: 0.3325 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.310 16499 Z= 0.244 Angle : 0.714 30.703 22243 Z= 0.337 Chirality : 0.044 0.148 2336 Planarity : 0.004 0.054 2858 Dihedral : 4.914 49.835 2520 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.45 % Allowed : 11.43 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1992 helix: 1.46 (0.16), residues: 1014 sheet: -0.66 (0.37), residues: 176 loop : -0.34 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 284 TYR 0.017 0.002 TYR C 446 PHE 0.017 0.001 PHE C 431 TRP 0.013 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00465 (16483) covalent geometry : angle 0.71382 (22243) hydrogen bonds : bond 0.05032 ( 789) hydrogen bonds : angle 5.47433 ( 2247) Misc. bond : bond 0.14595 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6438 (mt-10) cc_final: 0.6210 (mt-10) REVERT: A 176 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7604 (mtpt) REVERT: A 322 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7745 (tmmt) REVERT: A 352 MET cc_start: 0.8334 (mtp) cc_final: 0.8060 (mtp) REVERT: A 415 ARG cc_start: 0.6681 (tpp80) cc_final: 0.5816 (tpt-90) REVERT: A 445 ASP cc_start: 0.7574 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: B 7 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7645 (tttt) REVERT: B 26 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (mtmm) REVERT: B 146 MET cc_start: 0.8889 (ttp) cc_final: 0.8546 (ttp) REVERT: B 211 LYS cc_start: 0.8142 (mtpm) cc_final: 0.7525 (mmpt) REVERT: B 238 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7668 (mtt180) REVERT: C 22 GLU cc_start: 0.6854 (tp30) cc_final: 0.6618 (tm-30) REVERT: C 23 LYS cc_start: 0.7812 (ttmt) cc_final: 0.6935 (ttpp) REVERT: C 26 LYS cc_start: 0.7442 (tttt) cc_final: 0.7122 (ttmt) REVERT: C 389 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7529 (mtt90) REVERT: C 394 MET cc_start: 0.7808 (mmm) cc_final: 0.7465 (mmm) REVERT: D 299 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: D 303 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8520 (mppt) outliers start: 25 outliers final: 12 residues processed: 236 average time/residue: 0.9019 time to fit residues: 229.4954 Evaluate side-chains 234 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 369 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 26 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3622 r_free = 0.3622 target = 0.141633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121857 restraints weight = 15850.688| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 0.86 r_work: 0.3287 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.374 16499 Z= 0.270 Angle : 0.745 30.665 22243 Z= 0.356 Chirality : 0.046 0.152 2336 Planarity : 0.004 0.062 2858 Dihedral : 4.999 50.405 2520 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.57 % Allowed : 11.43 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 1992 helix: 1.39 (0.16), residues: 1014 sheet: -0.66 (0.36), residues: 176 loop : -0.36 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 284 TYR 0.021 0.002 TYR C 446 PHE 0.020 0.002 PHE C 431 TRP 0.014 0.002 TRP B 296 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00518 (16483) covalent geometry : angle 0.74524 (22243) hydrogen bonds : bond 0.05625 ( 789) hydrogen bonds : angle 5.57186 ( 2247) Misc. bond : bond 0.16381 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7603 (mtpt) REVERT: A 322 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7778 (tmmt) REVERT: A 415 ARG cc_start: 0.6714 (tpp80) cc_final: 0.5765 (tpt-90) REVERT: A 445 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: B 7 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7647 (tttt) REVERT: B 26 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8348 (mtmm) REVERT: B 146 MET cc_start: 0.8923 (ttp) cc_final: 0.8559 (ttp) REVERT: B 211 LYS cc_start: 0.8130 (mtpm) cc_final: 0.7513 (mmpt) REVERT: B 238 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7730 (mtt180) REVERT: C 22 GLU cc_start: 0.6935 (tp30) cc_final: 0.6706 (tm-30) REVERT: C 23 LYS cc_start: 0.7795 (ttmt) cc_final: 0.6906 (ttpp) REVERT: C 26 LYS cc_start: 0.7427 (tttt) cc_final: 0.7098 (ttmt) REVERT: C 176 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.6856 (mttm) REVERT: C 389 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7551 (mtt90) REVERT: C 394 MET cc_start: 0.7829 (mmm) cc_final: 0.7428 (mmm) REVERT: D 299 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: D 303 LYS cc_start: 0.8857 (mtmt) cc_final: 0.8521 (mppt) outliers start: 27 outliers final: 15 residues processed: 235 average time/residue: 0.8895 time to fit residues: 225.6255 Evaluate side-chains 236 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 chunk 11 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.6644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3597 r_free = 0.3597 target = 0.139662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.120371 restraints weight = 14392.854| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.81 r_work: 0.3267 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.439 16499 Z= 0.303 Angle : 0.789 30.520 22243 Z= 0.383 Chirality : 0.047 0.169 2336 Planarity : 0.005 0.071 2858 Dihedral : 5.170 51.474 2520 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.45 % Allowed : 11.78 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 1992 helix: 1.27 (0.16), residues: 1016 sheet: -0.61 (0.35), residues: 192 loop : -0.40 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 284 TYR 0.024 0.003 TYR C 446 PHE 0.023 0.002 PHE C 431 TRP 0.016 0.002 TRP B 296 HIS 0.010 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00590 (16483) covalent geometry : angle 0.78921 (22243) hydrogen bonds : bond 0.06352 ( 789) hydrogen bonds : angle 5.71318 ( 2247) Misc. bond : bond 0.18298 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6638 (mt-10) cc_final: 0.6410 (mt-10) REVERT: A 176 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: A 322 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7789 (tmmt) REVERT: A 415 ARG cc_start: 0.6665 (tpp80) cc_final: 0.5792 (tmt170) REVERT: A 445 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: B 7 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7649 (tttt) REVERT: B 26 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8342 (mtmm) REVERT: B 146 MET cc_start: 0.8930 (ttp) cc_final: 0.8610 (ttp) REVERT: B 211 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7548 (mmpt) REVERT: B 238 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7749 (mtt180) REVERT: C 22 GLU cc_start: 0.6938 (tp30) cc_final: 0.6717 (tm-30) REVERT: C 23 LYS cc_start: 0.7808 (ttmt) cc_final: 0.6926 (ttpp) REVERT: C 26 LYS cc_start: 0.7402 (tttt) cc_final: 0.7099 (ttmt) REVERT: C 176 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.6874 (mttm) REVERT: D 299 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: D 303 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8522 (mppt) REVERT: D 417 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8231 (ptpp) outliers start: 25 outliers final: 14 residues processed: 232 average time/residue: 0.8874 time to fit residues: 221.9841 Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 238 ARG Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3586 r_free = 0.3586 target = 0.138803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117991 restraints weight = 21953.744| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.02 r_work: 0.3227 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 2.30 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.481 16499 Z= 0.321 Angle : 0.818 30.458 22243 Z= 0.401 Chirality : 0.049 0.180 2336 Planarity : 0.005 0.077 2858 Dihedral : 5.265 51.702 2520 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 11.61 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 1992 helix: 1.16 (0.16), residues: 1016 sheet: -0.64 (0.34), residues: 192 loop : -0.45 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 284 TYR 0.025 0.003 TYR C 446 PHE 0.024 0.002 PHE C 431 TRP 0.015 0.002 TRP B 296 HIS 0.010 0.002 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00629 (16483) covalent geometry : angle 0.81770 (22243) hydrogen bonds : bond 0.06707 ( 789) hydrogen bonds : angle 5.80211 ( 2247) Misc. bond : bond 0.19309 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 176 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7657 (mtpt) REVERT: A 322 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7815 (tmmt) REVERT: A 386 ASP cc_start: 0.7455 (m-30) cc_final: 0.7206 (m-30) REVERT: A 415 ARG cc_start: 0.6704 (tpp80) cc_final: 0.5767 (tmt170) REVERT: A 445 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: B 7 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7659 (tttt) REVERT: B 146 MET cc_start: 0.8961 (ttp) cc_final: 0.8586 (ttp) REVERT: B 211 LYS cc_start: 0.8187 (mtpm) cc_final: 0.7498 (mmpt) REVERT: C 22 GLU cc_start: 0.6943 (tp30) cc_final: 0.6709 (tm-30) REVERT: C 23 LYS cc_start: 0.7864 (ttmt) cc_final: 0.6990 (ttpp) REVERT: C 26 LYS cc_start: 0.7414 (tttt) cc_final: 0.7088 (ttmt) REVERT: C 176 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.6907 (mttm) REVERT: C 182 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8013 (mtt-85) REVERT: D 299 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: D 303 LYS cc_start: 0.8895 (mtmt) cc_final: 0.8552 (mppt) REVERT: D 417 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8288 (ptpp) outliers start: 25 outliers final: 15 residues processed: 230 average time/residue: 0.9172 time to fit residues: 228.6032 Evaluate side-chains 235 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 130 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 4 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 75 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3646 r_free = 0.3646 target = 0.143560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124793 restraints weight = 13301.137| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.77 r_work: 0.3330 rms_B_bonded: 1.10 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.305 16499 Z= 0.242 Angle : 0.724 30.649 22243 Z= 0.343 Chirality : 0.045 0.160 2336 Planarity : 0.004 0.057 2858 Dihedral : 5.006 51.169 2520 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.33 % Allowed : 11.96 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 1992 helix: 1.44 (0.16), residues: 1014 sheet: -0.67 (0.36), residues: 176 loop : -0.35 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 284 TYR 0.017 0.002 TYR C 229 PHE 0.018 0.001 PHE C 431 TRP 0.014 0.001 TRP C 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00463 (16483) covalent geometry : angle 0.72382 (22243) hydrogen bonds : bond 0.05010 ( 789) hydrogen bonds : angle 5.50166 ( 2247) Misc. bond : bond 0.14349 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.665 Fit side-chains REVERT: A 15 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6389 (mt-10) REVERT: A 176 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7610 (mtpt) REVERT: A 322 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7748 (tmmt) REVERT: A 415 ARG cc_start: 0.6695 (tpp80) cc_final: 0.5738 (tpt-90) REVERT: A 445 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: B 7 LYS cc_start: 0.7924 (ttpp) cc_final: 0.7649 (tttt) REVERT: B 146 MET cc_start: 0.8885 (ttp) cc_final: 0.8538 (ttp) REVERT: B 211 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7542 (mmpt) REVERT: C 22 GLU cc_start: 0.6927 (tp30) cc_final: 0.6699 (tm-30) REVERT: C 23 LYS cc_start: 0.7803 (ttmt) cc_final: 0.6892 (ttpp) REVERT: C 26 LYS cc_start: 0.7405 (tttt) cc_final: 0.7154 (ttmt) REVERT: C 176 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.6804 (mttm) REVERT: D 299 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: D 303 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8509 (mppt) REVERT: D 417 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8202 (ptpp) outliers start: 23 outliers final: 13 residues processed: 234 average time/residue: 0.8864 time to fit residues: 224.0636 Evaluate side-chains 230 residues out of total 1720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 322 LYS Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 176 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 507 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 139 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 321 GLN D 4 GLN ** D 104 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 = 0.3617 r_free = 0.3617 target = 0.141317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121495 restraints weight = 16729.162| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 0.89 r_work: 0.3281 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.376 16499 Z= 0.274 Angle : 0.768 30.597 22243 Z= 0.367 Chirality : 0.046 0.171 2336 Planarity : 0.005 0.065 2858 Dihedral : 5.051 50.962 2520 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.28 % Allowed : 12.07 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 1992 helix: 1.36 (0.16), residues: 1014 sheet: -0.66 (0.36), residues: 176 loop : -0.37 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 284 TYR 0.021 0.002 TYR C 446 PHE 0.020 0.002 PHE C 431 TRP 0.014 0.002 TRP B 296 HIS 0.009 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00529 (16483) covalent geometry : angle 0.76841 (22243) hydrogen bonds : bond 0.05688 ( 789) hydrogen bonds : angle 5.58979 ( 2247) Misc. bond : bond 0.16332 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9206.48 seconds wall clock time: 157 minutes 8.07 seconds (9428.07 seconds total)