Starting phenix.real_space_refine on Mon Apr 6 17:30:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.map" model { file = "/net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dfc_27404/04_2026/8dfc_27404.cif" } resolution = 2.48 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= 0.050 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: 10 Type Number sf(0) Gaussians Mo 2 10.26 5 Fe 36 7.16 5 Al 2 5.89 5 P 4 5.49 5 Mg 2 5.21 5 S 184 5.16 5 C 12770 2.51 5 N 3416 2.21 5 O 4289 1.98 5 F 8 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20713 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3795 Classifications: {'peptide': 478} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 456} Chain: "D" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 495} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2065 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 265} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "B" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Classifications: {'water': 146} Link IDs: {None: 145} Chain: "C" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Classifications: {'water': 152} Link IDs: {None: 151} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2089 SG CYS A 275 59.960 34.612 26.567 1.00 44.32 S ATOM 1170 SG CYS A 154 46.340 52.145 21.510 1.00 34.77 S ATOM 4554 SG CYS B 95 43.803 51.476 26.303 1.00 44.22 S ATOM 465 SG CYS A 62 49.106 47.637 25.314 1.00 37.18 S ATOM 652 SG CYS A 88 48.588 54.021 27.092 1.00 39.97 S ATOM 652 SG CYS A 88 48.588 54.021 27.092 1.00 39.97 S ATOM 5007 SG CYS B 153 44.366 56.249 24.068 1.00 54.18 S ATOM 4374 SG CYS B 70 43.576 55.750 31.074 1.00 60.52 S ATOM 4554 SG CYS B 95 43.803 51.476 26.303 1.00 44.22 S ATOM 10054 SG CYS C 275 62.680 70.133 95.323 1.00 48.24 S ATOM 9135 SG CYS C 154 51.855 51.047 101.815 1.00 39.02 S ATOM 12519 SG CYS D 95 48.670 51.483 97.345 1.00 42.50 S ATOM 8430 SG CYS C 62 53.797 55.884 97.765 1.00 30.44 S ATOM 8617 SG CYS C 88 53.495 49.532 96.088 1.00 48.51 S ATOM 8617 SG CYS C 88 53.495 49.532 96.088 1.00 48.51 S ATOM 12972 SG CYS D 153 50.220 46.950 99.588 1.00 39.79 S ATOM 12339 SG CYS D 70 48.429 47.123 92.696 1.00 45.85 S ATOM 12519 SG CYS D 95 48.670 51.483 97.345 1.00 42.50 S ATOM 16886 SG CYS E 132 47.006 40.659 113.776 1.00 21.13 S ATOM 16615 SG CYS E 97 50.621 39.823 109.096 1.00 25.40 S ATOM 18951 SG CYS F 132 53.612 41.056 114.761 1.00 20.58 S ATOM 18680 SG CYS F 97 50.712 45.727 112.318 1.00 12.88 S Time building chain proxies: 4.68, per 1000 atoms: 0.23 Number of scatterers: 20713 At special positions: 0 Unit cell: (100.672, 99.008, 163.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Mo 2 41.97 Fe 36 26.01 S 184 16.00 P 4 15.00 Al 2 13.00 Mg 2 11.99 F 8 9.00 O 4289 8.00 N 3416 7.00 C 12770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=17, symmetry=0 Number of additional bonds: simple=17, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 911.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 E 300 " pdb="FE3 SF4 E 300 " - pdb=" SG CYS F 132 " pdb="FE1 SF4 E 300 " - pdb=" SG CYS E 132 " pdb="FE4 SF4 E 300 " - pdb=" SG CYS F 97 " pdb="FE2 SF4 E 300 " - pdb=" SG CYS E 97 " Number of angles added : 12 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 14 sheets defined 57.9% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.933A pdb=" N LYS A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 127 through 142 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.591A pdb=" N GLY A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.967A pdb=" N VAL A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 4.197A pdb=" N GLY A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.417A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.698A pdb=" N LEU A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 275 through 290 removed outlier: 5.935A pdb=" N TYR A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.258A pdb=" N LYS A 304 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 347 removed outlier: 3.538A pdb=" N GLN A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Proline residue: A 333 - end of helix Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 383 through 394 removed outlier: 4.111A pdb=" N LYS A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 424 through 434 removed outlier: 4.323A pdb=" N PHE A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) removed outlier: 5.034A 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 Processing helix chain 'A' and resid 469 through 475 removed outlier: 3.969A pdb=" N LEU A 475 " --> pdb=" O TRP A 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 17 through 32 removed outlier: 3.573A pdb=" N GLU B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 49 through 58 Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.123A pdb=" N GLY B 74 " --> pdb=" O CYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 108 removed outlier: 3.934A pdb=" N VAL B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 127 through 143 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 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 233 through 247 removed outlier: 3.834A pdb=" N PHE B 237 " --> pdb=" O TYR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.210A pdb=" N THR B 263 " --> pdb=" O VAL B 260 " (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: 4.287A pdb=" N TRP B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 363 removed outlier: 5.027A pdb=" N THR B 360 " --> pdb=" O THR B 356 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 Processing helix chain 'B' and resid 399 through 412 Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.719A pdb=" N GLY B 416 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 417 " --> pdb=" O PRO B 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 413 through 417' Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 447 through 459 removed outlier: 4.461A pdb=" N ILE B 451 " --> pdb=" O TYR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 463 removed outlier: 3.663A pdb=" N GLU B 463 " --> pdb=" O LYS B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.646A pdb=" N ARG B 481 " --> pdb=" O HIS B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 509 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'C' and resid 5 through 18 Processing helix chain 'C' and resid 21 through 29 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 87 through 92 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 127 through 142 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 162 through 175 Processing helix chain 'C' and resid 190 through 206 removed outlier: 4.230A pdb=" N GLY C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 removed outlier: 4.292A pdb=" N ARG C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.712A 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 290 removed outlier: 3.514A pdb=" N MET C 279 " --> pdb=" O CYS C 275 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N TYR C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 6.100A 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 removed outlier: 3.564A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 383 through 392 removed outlier: 4.069A 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: 4.695A pdb=" N PHE C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 5.443A 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: 3.878A pdb=" N ILE C 458 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.662A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 36 through 48 Processing helix chain 'D' and resid 49 through 58 Processing helix chain 'D' and resid 70 through 80 removed outlier: 3.988A pdb=" N GLY D 74 " --> pdb=" O CYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 108 removed outlier: 3.991A 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 233 through 247 removed outlier: 3.888A 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 298 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 341 through 363 removed outlier: 5.145A pdb=" N THR D 360 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N TRP D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 412 Processing helix chain 'D' and resid 413 through 417 removed outlier: 3.813A pdb=" N LYS D 417 " --> pdb=" O PRO D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 437 Processing helix chain 'D' and resid 447 through 459 removed outlier: 4.319A pdb=" N ILE D 451 " --> pdb=" O TYR D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 463 removed outlier: 3.690A pdb=" N GLU D 463 " --> pdb=" O LYS D 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 460 through 463' Processing helix chain 'D' and resid 478 through 482 removed outlier: 3.742A pdb=" N ARG D 481 " --> pdb=" O HIS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 509 Processing helix chain 'D' and resid 515 through 519 Processing helix chain 'E' and resid 14 through 29 Processing helix chain 'E' and resid 45 through 50 Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 66 through 70 Processing helix chain 'E' and resid 71 through 75 Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.564A pdb=" N GLY E 101 " --> pdb=" O CYS E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 140 Proline residue: E 138 - end of helix Processing helix chain 'E' and resid 154 through 175 removed outlier: 4.335A pdb=" N LYS E 170 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 215 through 223 removed outlier: 3.504A pdb=" N ARG E 219 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 260 through 273 removed outlier: 4.265A pdb=" N ILE E 273 " --> pdb=" O MET E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 29 Processing helix chain 'F' and resid 45 through 50 Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 66 through 70 Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.777A pdb=" N VAL F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.547A pdb=" N GLY F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 140 removed outlier: 3.557A pdb=" N PHE F 135 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Proline residue: F 138 - end of helix Processing helix chain 'F' and resid 154 through 174 removed outlier: 4.076A pdb=" N LYS F 170 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR F 171 " --> pdb=" O GLY F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 214 through 223 removed outlier: 4.263A pdb=" N GLN F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 234 through 250 Processing helix chain 'F' and resid 260 through 272 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 3.564A pdb=" N LEU A 399 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A 353 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR A 377 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ARG A 350 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY A 422 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET A 352 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 6.177A 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: 6.150A pdb=" N ILE A 79 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN A 151 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A 81 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE A 114 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 254 removed outlier: 7.173A pdb=" N VAL A 223 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N TRP A 253 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.824A 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: 6.333A 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: 8.424A pdb=" N THR B 420 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 391 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N TYR B 422 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE B 393 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE B 367 " --> pdb=" O PRO B 390 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG B 366 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ILE B 443 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA B 368 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N MET B 442 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.710A pdb=" N LEU C 399 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU C 353 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR C 377 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 350 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLY C 422 " --> pdb=" O ARG C 350 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET C 352 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 6.115A 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: 6.897A pdb=" N ILE C 148 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL C 181 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 150 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE C 114 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 248 through 254 removed outlier: 7.302A pdb=" N VAL C 223 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N TRP C 253 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 6.742A 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: 6.450A 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: 8.480A pdb=" N THR D 420 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 391 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TYR D 422 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE D 393 " --> pdb=" O TYR D 422 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU D 369 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE D 393 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG D 366 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE D 443 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 368 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET D 442 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 78 removed outlier: 6.662A pdb=" N VAL E 33 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N VAL E 86 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE E 35 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N MET E 34 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP E 125 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL E 36 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY E 9 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN E 4 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR E 148 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA E 6 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL E 150 " --> pdb=" O ALA E 6 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N TYR E 8 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE E 147 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY E 181 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 12.646A pdb=" N MET E 207 " --> pdb=" O ARG E 178 " (cutoff:3.500A) removed outlier: 10.573A pdb=" N GLY E 180 " --> pdb=" O MET E 207 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N HIS E 209 " --> pdb=" O GLY E 180 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU E 182 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL E 211 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N CYS E 184 " --> pdb=" O VAL E 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.553A pdb=" N MET F 34 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP F 125 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL F 36 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLY F 9 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN F 4 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR F 148 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA F 6 " --> pdb=" O TYR F 148 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL F 150 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TYR F 8 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE F 147 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE F 183 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ILE F 149 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN F 185 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N CYS F 151 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 13.031A pdb=" N MET F 207 " --> pdb=" O ARG F 178 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N GLY F 180 " --> pdb=" O MET F 207 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N HIS F 209 " --> pdb=" O GLY F 180 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU F 182 " --> pdb=" O HIS F 209 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL F 211 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS F 184 " --> pdb=" O VAL F 211 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2823 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: 3.80 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.57: 20326 1.57 - 1.92: 262 1.92 - 2.27: 46 2.27 - 2.61: 84 2.61 - 2.96: 18 Bond restraints: 20736 Sorted by residual: bond pdb="FE2 CLF B 600 " pdb="FE8 CLF B 600 " ideal model delta sigma weight residual 2.200 2.963 -0.763 2.00e-02 2.50e+03 1.46e+03 bond pdb="FE2 CLF D 600 " pdb="FE8 CLF D 600 " ideal model delta sigma weight residual 2.200 2.960 -0.760 2.00e-02 2.50e+03 1.44e+03 bond pdb="FE4 CLF D 600 " pdb="FE5 CLF D 600 " ideal model delta sigma weight residual 2.200 2.924 -0.724 2.00e-02 2.50e+03 1.31e+03 bond pdb="FE4 CLF B 600 " pdb="FE5 CLF B 600 " ideal model delta sigma weight residual 2.200 2.924 -0.724 2.00e-02 2.50e+03 1.31e+03 bond pdb="FE6 CLF D 600 " pdb="FE7 CLF D 600 " ideal model delta sigma weight residual 2.200 2.858 -0.658 2.00e-02 2.50e+03 1.08e+03 ... (remaining 20731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.17: 27976 14.17 - 28.33: 10 28.33 - 42.50: 4 42.50 - 56.67: 0 56.67 - 70.83: 4 Bond angle restraints: 27994 Sorted by residual: angle pdb=" F1 ALF F 303 " pdb="AL ALF F 303 " pdb=" F2 ALF F 303 " ideal model delta sigma weight residual 108.68 179.51 -70.83 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F1 ALF E 302 " pdb="AL ALF E 302 " pdb=" F2 ALF E 302 " ideal model delta sigma weight residual 108.68 179.39 -70.71 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F3 ALF E 302 " pdb="AL ALF E 302 " pdb=" F4 ALF E 302 " ideal model delta sigma weight residual 109.63 179.60 -69.97 3.00e+00 1.11e-01 5.44e+02 angle pdb=" F3 ALF F 303 " pdb="AL ALF F 303 " pdb=" F4 ALF F 303 " ideal model delta sigma weight residual 109.63 179.42 -69.79 3.00e+00 1.11e-01 5.41e+02 angle pdb=" S1 CLF B 600 " pdb="FE2 CLF B 600 " pdb="FE4 CLF B 600 " ideal model delta sigma weight residual 90.00 55.81 34.19 3.00e+00 1.11e-01 1.30e+02 ... (remaining 27989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 12085 33.72 - 67.45: 548 67.45 - 101.17: 43 101.17 - 134.89: 2 134.89 - 168.62: 2 Dihedral angle restraints: 12680 sinusoidal: 5388 harmonic: 7292 Sorted by residual: dihedral pdb=" O1B ADP F 302 " pdb=" O3A ADP F 302 " pdb=" PB ADP F 302 " pdb=" PA ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 108.61 -168.62 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP F 302 " pdb=" O3A ADP F 302 " pdb=" PA ADP F 302 " pdb=" PB ADP F 302 " ideal model delta sinusoidal sigma weight residual -60.00 82.65 -142.65 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" O2A ADP E 301 " pdb=" O3A ADP E 301 " pdb=" PA ADP E 301 " pdb=" PB ADP E 301 " ideal model delta sinusoidal sigma weight residual -60.00 53.15 -113.15 1 2.00e+01 2.50e-03 3.34e+01 ... (remaining 12677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1930 0.035 - 0.069: 727 0.069 - 0.104: 232 0.104 - 0.139: 101 0.139 - 0.173: 4 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CA LEU F 268 " pdb=" N LEU F 268 " pdb=" C LEU F 268 " pdb=" CB LEU F 268 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CB ILE C 355 " pdb=" CA ILE C 355 " pdb=" CG1 ILE C 355 " pdb=" CG2 ILE C 355 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE F 255 " pdb=" N ILE F 255 " pdb=" C ILE F 255 " pdb=" CB ILE F 255 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 2991 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 359 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO C 360 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 360 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 360 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 372 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 373 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 373 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 373 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 284 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO D 285 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 285 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 285 " 0.023 5.00e-02 4.00e+02 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 268 2.54 - 3.13: 15560 3.13 - 3.72: 35539 3.72 - 4.31: 53581 4.31 - 4.90: 85713 Nonbonded interactions: 190661 Sorted by model distance: nonbonded pdb="MG MG F 301 " pdb=" F4 ALF F 303 " model vdw 1.946 2.120 nonbonded pdb="MG MG E 303 " pdb=" O HOH E 414 " model vdw 1.986 2.170 nonbonded pdb="FE FE D 601 " pdb=" O HOH D 731 " model vdw 2.032 2.260 nonbonded pdb="FE FE D 601 " pdb=" O HOH D 786 " model vdw 2.037 2.260 nonbonded pdb="FE FE B 601 " pdb=" O HOH B 719 " model vdw 2.041 2.260 ... (remaining 190656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 274 or resid 301 through 302)) selection = (chain 'F' and (resid 1 through 274 or resid 302 through 303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 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 : 0.022 0.763 20757 Z= 1.061 Angle : 1.164 70.834 28006 Z= 0.449 Chirality : 0.043 0.173 2994 Planarity : 0.004 0.051 3600 Dihedral : 17.689 168.615 8024 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.78 % Allowed : 21.66 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2536 helix: 1.18 (0.15), residues: 1246 sheet: -0.22 (0.30), residues: 278 loop : -1.12 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.014 0.001 TYR A 229 PHE 0.015 0.001 PHE C 429 TRP 0.015 0.001 TRP C 335 HIS 0.008 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.02114 (20736) covalent geometry : angle 1.15702 (27994) hydrogen bonds : bond 0.14139 ( 981) hydrogen bonds : angle 6.34414 ( 2823) metal coordination : bond 0.00944 ( 4) metal coordination : angle 6.43012 ( 12) Misc. bond : bond 0.13934 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 190 time to evaluate : 0.845 Fit side-chains REVERT: F 32 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7180 (pttm) outliers start: 60 outliers final: 54 residues processed: 243 average time/residue: 0.6620 time to fit residues: 182.4053 Evaluate side-chains 239 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 184 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 397 ASN Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 5 CYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 151 CYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 132 CYS Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 193 ASP Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.2980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 513 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 37 GLN D 513 GLN D 518 ASN E 20 GLN E 50 HIS E 206 GLN E 218 GLN F 201 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100264 restraints weight = 25904.846| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.50 r_work: 0.3196 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 20757 Z= 0.150 Angle : 0.797 30.449 28006 Z= 0.342 Chirality : 0.043 0.148 2994 Planarity : 0.004 0.061 3600 Dihedral : 7.911 155.225 3216 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.66 % Allowed : 20.41 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2536 helix: 1.37 (0.15), residues: 1254 sheet: -0.28 (0.29), residues: 288 loop : -0.92 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 46 TYR 0.015 0.001 TYR A 229 PHE 0.010 0.001 PHE C 431 TRP 0.014 0.001 TRP A 335 HIS 0.007 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00312 (20736) covalent geometry : angle 0.78206 (27994) hydrogen bonds : bond 0.04512 ( 981) hydrogen bonds : angle 5.23588 ( 2823) metal coordination : bond 0.00887 ( 4) metal coordination : angle 7.42909 ( 12) Misc. bond : bond 0.08375 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 200 time to evaluate : 0.844 Fit side-chains REVERT: A 476 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: C 210 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7905 (mtt180) REVERT: C 334 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: E 223 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6781 (mpp-170) REVERT: F 119 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7529 (mt) REVERT: F 146 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: F 187 ARG cc_start: 0.7459 (tpp80) cc_final: 0.6675 (tpp-160) REVERT: F 207 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6357 (tpt) REVERT: F 214 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6597 (m-30) outliers start: 79 outliers final: 35 residues processed: 259 average time/residue: 0.7089 time to fit residues: 206.0081 Evaluate side-chains 228 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 469 ASN Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 214 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 230 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 518 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 513 GLN E 50 HIS F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.100309 restraints weight = 26113.156| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.50 r_work: 0.3199 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 20757 Z= 0.147 Angle : 0.790 29.917 28006 Z= 0.336 Chirality : 0.043 0.152 2994 Planarity : 0.004 0.048 3600 Dihedral : 7.195 156.662 3158 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.66 % Allowed : 20.27 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.17), residues: 2536 helix: 1.42 (0.15), residues: 1256 sheet: -0.25 (0.29), residues: 288 loop : -0.92 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 359 TYR 0.015 0.001 TYR C 379 PHE 0.012 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00319 (20736) covalent geometry : angle 0.77490 (27994) hydrogen bonds : bond 0.04235 ( 981) hydrogen bonds : angle 5.03929 ( 2823) metal coordination : bond 0.00941 ( 4) metal coordination : angle 7.45295 ( 12) Misc. bond : bond 0.07611 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 200 time to evaluate : 0.816 Fit side-chains REVERT: A 192 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7742 (p) REVERT: A 476 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: C 120 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: C 334 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7003 (mt-10) REVERT: E 223 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6656 (mpp-170) REVERT: F 119 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7548 (mt) REVERT: F 146 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: F 187 ARG cc_start: 0.7487 (tpp80) cc_final: 0.6654 (ttm170) REVERT: F 191 ARG cc_start: 0.5527 (OUTLIER) cc_final: 0.5145 (ttp80) REVERT: F 207 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6506 (tpt) outliers start: 79 outliers final: 41 residues processed: 252 average time/residue: 0.6956 time to fit residues: 196.7612 Evaluate side-chains 238 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 207 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 12 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 150 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 18 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS C 476 GLN D 513 GLN E 50 HIS F 20 GLN F 21 ASN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099615 restraints weight = 26103.449| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.51 r_work: 0.3203 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.143 20757 Z= 0.155 Angle : 0.790 30.000 28006 Z= 0.336 Chirality : 0.044 0.148 2994 Planarity : 0.004 0.042 3600 Dihedral : 7.006 158.827 3149 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.17 % Allowed : 20.22 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2536 helix: 1.43 (0.15), residues: 1256 sheet: -0.24 (0.29), residues: 286 loop : -0.94 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 359 TYR 0.014 0.001 TYR C 379 PHE 0.011 0.001 PHE C 429 TRP 0.014 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00343 (20736) covalent geometry : angle 0.77606 (27994) hydrogen bonds : bond 0.04222 ( 981) hydrogen bonds : angle 4.97908 ( 2823) metal coordination : bond 0.01038 ( 4) metal coordination : angle 7.26617 ( 12) Misc. bond : bond 0.07226 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 0.804 Fit side-chains REVERT: A 192 SER cc_start: 0.8003 (OUTLIER) cc_final: 0.7741 (p) REVERT: A 476 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: C 120 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 334 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: C 480 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5291 (mt-10) REVERT: E 223 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.6597 (mpp-170) REVERT: F 119 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7556 (mt) REVERT: F 156 MET cc_start: 0.6051 (mmp) cc_final: 0.5704 (mmp) REVERT: F 187 ARG cc_start: 0.7439 (tpp80) cc_final: 0.6651 (ttm170) REVERT: F 191 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4733 (ttp80) REVERT: F 207 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6562 (tpt) outliers start: 90 outliers final: 50 residues processed: 254 average time/residue: 0.6861 time to fit residues: 196.4144 Evaluate side-chains 245 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.5980 chunk 207 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 198 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 513 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.128444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100686 restraints weight = 26090.449| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.51 r_work: 0.3207 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 20757 Z= 0.134 Angle : 0.779 29.892 28006 Z= 0.329 Chirality : 0.043 0.178 2994 Planarity : 0.004 0.040 3600 Dihedral : 6.795 159.062 3146 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.76 % Allowed : 20.64 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2536 helix: 1.49 (0.15), residues: 1256 sheet: -0.22 (0.29), residues: 286 loop : -0.91 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 97 TYR 0.013 0.001 TYR C 379 PHE 0.011 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00289 (20736) covalent geometry : angle 0.76394 (27994) hydrogen bonds : bond 0.03939 ( 981) hydrogen bonds : angle 4.91947 ( 2823) metal coordination : bond 0.00847 ( 4) metal coordination : angle 7.29434 ( 12) Misc. bond : bond 0.06560 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 198 time to evaluate : 0.795 Fit side-chains REVERT: A 192 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7701 (p) REVERT: A 476 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: C 120 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: C 334 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: C 480 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5276 (mt-10) REVERT: E 223 ARG cc_start: 0.6868 (OUTLIER) cc_final: 0.6571 (mpp-170) REVERT: F 74 ASP cc_start: 0.7966 (t0) cc_final: 0.7610 (m-30) REVERT: F 119 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7514 (mt) REVERT: F 146 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: F 187 ARG cc_start: 0.7447 (tpp80) cc_final: 0.6624 (ttm170) REVERT: F 207 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6489 (tpt) REVERT: F 224 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6718 (mtp85) outliers start: 81 outliers final: 48 residues processed: 253 average time/residue: 0.7056 time to fit residues: 200.4979 Evaluate side-chains 248 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 228 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 184 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 18 GLN B 513 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 HIS C 476 GLN D 513 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100075 restraints weight = 26009.160| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.51 r_work: 0.3199 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 20757 Z= 0.148 Angle : 0.786 29.899 28006 Z= 0.334 Chirality : 0.043 0.169 2994 Planarity : 0.004 0.042 3600 Dihedral : 6.637 160.907 3141 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.45 % Allowed : 20.18 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2536 helix: 1.43 (0.15), residues: 1268 sheet: -0.20 (0.29), residues: 286 loop : -0.90 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.014 0.001 TYR C 379 PHE 0.012 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00329 (20736) covalent geometry : angle 0.77140 (27994) hydrogen bonds : bond 0.04083 ( 981) hydrogen bonds : angle 4.91416 ( 2823) metal coordination : bond 0.00987 ( 4) metal coordination : angle 7.22340 ( 12) Misc. bond : bond 0.06774 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 192 time to evaluate : 0.831 Fit side-chains REVERT: A 192 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 245 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7979 (mtp) REVERT: A 476 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: C 120 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 334 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: C 480 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5322 (mt-10) REVERT: D 171 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7995 (ttmt) REVERT: D 222 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8298 (mmtp) REVERT: E 223 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6588 (mpp-170) REVERT: F 74 ASP cc_start: 0.7966 (t0) cc_final: 0.7683 (m-30) REVERT: F 146 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: F 187 ARG cc_start: 0.7414 (tpp80) cc_final: 0.6570 (ttm170) REVERT: F 206 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6559 (pp30) REVERT: F 207 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6479 (tpt) outliers start: 96 outliers final: 56 residues processed: 261 average time/residue: 0.7069 time to fit residues: 207.1781 Evaluate side-chains 257 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 222 LYS Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 315 LYS Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 117 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 223 optimal weight: 6.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 98 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 513 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.128359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100422 restraints weight = 25988.244| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.53 r_work: 0.3211 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.122 20757 Z= 0.126 Angle : 0.774 29.916 28006 Z= 0.326 Chirality : 0.043 0.155 2994 Planarity : 0.004 0.041 3600 Dihedral : 6.518 161.243 3139 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.80 % Allowed : 20.87 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2536 helix: 1.48 (0.15), residues: 1268 sheet: -0.19 (0.30), residues: 286 loop : -0.89 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 46 TYR 0.014 0.001 TYR A 229 PHE 0.010 0.001 PHE A 459 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00273 (20736) covalent geometry : angle 0.75945 (27994) hydrogen bonds : bond 0.03764 ( 981) hydrogen bonds : angle 4.85610 ( 2823) metal coordination : bond 0.00786 ( 4) metal coordination : angle 7.23056 ( 12) Misc. bond : bond 0.06089 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.877 Fit side-chains REVERT: A 476 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: C 120 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: C 334 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: C 480 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5366 (mt-10) REVERT: D 171 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8020 (ttmt) REVERT: E 170 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7635 (ttpp) REVERT: E 215 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6912 (t0) REVERT: E 218 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.5642 (mp-120) REVERT: E 223 ARG cc_start: 0.6879 (OUTLIER) cc_final: 0.6537 (mpp-170) REVERT: F 146 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: F 187 ARG cc_start: 0.7418 (tpp80) cc_final: 0.6604 (ttm170) REVERT: F 206 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.6594 (pp30) REVERT: F 207 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6442 (tpt) outliers start: 82 outliers final: 49 residues processed: 255 average time/residue: 0.6870 time to fit residues: 197.1482 Evaluate side-chains 255 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 194 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 401 TYR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 16 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 175 optimal weight: 0.0170 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 513 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.100165 restraints weight = 25901.220| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.51 r_work: 0.3200 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 20757 Z= 0.152 Angle : 0.796 29.912 28006 Z= 0.340 Chirality : 0.044 0.148 2994 Planarity : 0.004 0.043 3600 Dihedral : 6.545 164.448 3136 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.80 % Allowed : 21.06 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2536 helix: 1.46 (0.15), residues: 1266 sheet: -0.32 (0.29), residues: 300 loop : -0.85 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 219 TYR 0.015 0.001 TYR A 401 PHE 0.034 0.001 PHE A 409 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00340 (20736) covalent geometry : angle 0.78182 (27994) hydrogen bonds : bond 0.04097 ( 981) hydrogen bonds : angle 4.92303 ( 2823) metal coordination : bond 0.01039 ( 4) metal coordination : angle 7.17198 ( 12) Misc. bond : bond 0.06687 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 192 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 476 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: C 120 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 334 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: C 480 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5367 (mt-10) REVERT: D 171 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7997 (ttmt) REVERT: E 110 GLU cc_start: 0.7614 (tp30) cc_final: 0.7252 (pt0) REVERT: E 170 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7617 (ttpp) REVERT: F 146 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: F 187 ARG cc_start: 0.7401 (tpp80) cc_final: 0.6594 (ttm170) REVERT: F 206 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.6554 (pp30) REVERT: F 207 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6503 (tpt) outliers start: 82 outliers final: 54 residues processed: 251 average time/residue: 0.7096 time to fit residues: 200.2148 Evaluate side-chains 251 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 229 optimal weight: 1.9990 chunk 239 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 192 optimal weight: 0.0980 chunk 178 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 98 ASN B 18 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN D 513 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.128556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100782 restraints weight = 25901.561| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.50 r_work: 0.3211 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 20757 Z= 0.133 Angle : 0.783 29.917 28006 Z= 0.332 Chirality : 0.043 0.148 2994 Planarity : 0.004 0.042 3600 Dihedral : 6.486 165.717 3136 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.62 % Allowed : 21.29 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2536 helix: 1.48 (0.15), residues: 1268 sheet: -0.21 (0.29), residues: 286 loop : -0.88 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.013 0.001 TYR A 229 PHE 0.011 0.001 PHE A 409 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00290 (20736) covalent geometry : angle 0.76919 (27994) hydrogen bonds : bond 0.03843 ( 981) hydrogen bonds : angle 4.87975 ( 2823) metal coordination : bond 0.00846 ( 4) metal coordination : angle 7.18667 ( 12) Misc. bond : bond 0.06171 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 0.847 Fit side-chains REVERT: A 476 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7559 (tm-30) REVERT: B 241 LYS cc_start: 0.9026 (mtpm) cc_final: 0.8726 (mtmt) REVERT: C 120 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: C 334 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: D 171 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7984 (ttmt) REVERT: E 110 GLU cc_start: 0.7631 (tp30) cc_final: 0.7248 (pt0) REVERT: E 170 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7599 (ttpp) REVERT: E 223 ARG cc_start: 0.6874 (OUTLIER) cc_final: 0.6280 (mpp80) REVERT: F 146 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: F 187 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6598 (ttm170) REVERT: F 206 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6555 (pp30) REVERT: F 207 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6450 (tpt) outliers start: 78 outliers final: 50 residues processed: 252 average time/residue: 0.6820 time to fit residues: 193.5883 Evaluate side-chains 252 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 245 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 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 14 GLN A 98 ASN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101030 restraints weight = 25955.607| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.50 r_work: 0.3214 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 20757 Z= 0.134 Angle : 0.787 29.830 28006 Z= 0.335 Chirality : 0.043 0.148 2994 Planarity : 0.004 0.042 3600 Dihedral : 6.484 169.053 3136 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.39 % Allowed : 21.71 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.17), residues: 2536 helix: 1.46 (0.15), residues: 1268 sheet: -0.21 (0.29), residues: 286 loop : -0.88 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.013 0.001 TYR A 229 PHE 0.011 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.007 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00293 (20736) covalent geometry : angle 0.77319 (27994) hydrogen bonds : bond 0.03843 ( 981) hydrogen bonds : angle 4.88090 ( 2823) metal coordination : bond 0.00879 ( 4) metal coordination : angle 7.17826 ( 12) Misc. bond : bond 0.06217 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5072 Ramachandran restraints generated. 2536 Oldfield, 0 Emsley, 2536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 192 time to evaluate : 0.858 Fit side-chains REVERT: A 476 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: B 241 LYS cc_start: 0.9033 (mtpm) cc_final: 0.8737 (mtmt) REVERT: C 120 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: C 334 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: D 171 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7985 (ttmt) REVERT: E 110 GLU cc_start: 0.7708 (tp30) cc_final: 0.7380 (pt0) REVERT: E 170 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7587 (ttpp) REVERT: E 223 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.5709 (mpp80) REVERT: F 146 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: F 187 ARG cc_start: 0.7438 (tpp80) cc_final: 0.6637 (ttm170) REVERT: F 206 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6550 (pp30) REVERT: F 207 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6456 (tpt) outliers start: 73 outliers final: 53 residues processed: 241 average time/residue: 0.6915 time to fit residues: 187.4681 Evaluate side-chains 252 residues out of total 2162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 88 CYS Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 432 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 HIS Chi-restraints excluded: chain C residue 401 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 171 LYS Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 394 LEU Chi-restraints excluded: chain D residue 484 THR Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 191 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 207 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 39 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 98 ASN C 252 GLN C 476 GLN E 50 HIS E 218 GLN F 20 GLN ** F 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100265 restraints weight = 26020.466| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.50 r_work: 0.3201 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 20757 Z= 0.147 Angle : 0.799 29.842 28006 Z= 0.341 Chirality : 0.043 0.149 2994 Planarity : 0.004 0.042 3600 Dihedral : 6.533 173.719 3136 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.29 % Allowed : 21.75 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2536 helix: 1.42 (0.15), residues: 1268 sheet: -0.22 (0.29), residues: 286 loop : -0.88 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 359 TYR 0.013 0.001 TYR A 229 PHE 0.012 0.001 PHE C 429 TRP 0.013 0.001 TRP A 335 HIS 0.008 0.001 HIS B 297 Details of bonding type rmsd covalent geometry : bond 0.00328 (20736) covalent geometry : angle 0.78481 (27994) hydrogen bonds : bond 0.04015 ( 981) hydrogen bonds : angle 4.90251 ( 2823) metal coordination : bond 0.00981 ( 4) metal coordination : angle 7.23423 ( 12) Misc. bond : bond 0.06533 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7813.53 seconds wall clock time: 134 minutes 6.44 seconds (8046.44 seconds total)