Starting phenix.real_space_refine on Tue Jul 7 01:53:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rkh_24497/07_2026/7rkh_24497.map" } resolution = 2.8 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= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8096 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 80 5.16 5 C 11176 2.51 5 N 3056 2.21 5 O 3444 1.98 5 H 17564 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35352 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8776 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "A" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8776 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "B" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8776 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "C" Number of atoms: 8776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 8776 Classifications: {'peptide': 559} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 534} Chain breaks: 1 Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' MG': 2, 'ATP': 1, 'UTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.70, per 1000 atoms: 0.16 Number of scatterers: 35352 At special positions: 0 Unit cell: (120.75, 103.95, 131.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 80 16.00 P 24 15.00 Mg 8 11.99 O 3444 8.00 N 3056 7.00 C 11176 6.00 H 17564 1.00 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=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 969.4 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 16 sheets defined 50.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.646A pdb=" N LEU D 30 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 115 through 130 removed outlier: 3.692A pdb=" N LYS D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.992A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 221 through 232 Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 259 through 268 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 276 through 300 Processing helix chain 'D' and resid 315 through 318 Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 348 through 355 removed outlier: 4.000A pdb=" N GLN D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU D 353 " --> pdb=" O PRO D 349 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.688A pdb=" N PHE D 359 " --> pdb=" O ASP D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 397 Processing helix chain 'D' and resid 404 through 418 Processing helix chain 'D' and resid 469 through 472 removed outlier: 4.322A pdb=" N TRP D 472 " --> pdb=" O ASN D 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 469 through 472' Processing helix chain 'D' and resid 473 through 480 Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.677A pdb=" N TYR D 540 " --> pdb=" O HIS D 537 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 561 through 571 Processing helix chain 'A' and resid 15 through 30 removed outlier: 3.646A pdb=" N LEU A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 79 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.692A pdb=" N LYS A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 removed outlier: 3.992A pdb=" N PHE A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 276 through 300 Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 348 through 355 removed outlier: 4.000A pdb=" N GLN A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.688A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 404 through 418 Processing helix chain 'A' and resid 469 through 472 removed outlier: 4.322A pdb=" N TRP A 472 " --> pdb=" O ASN A 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 469 through 472' Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.678A pdb=" N TYR A 540 " --> pdb=" O HIS A 537 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 561 through 571 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.646A pdb=" N LEU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.692A pdb=" N LYS B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.991A pdb=" N PHE B 168 " --> pdb=" O ARG B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 192 through 205 Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 259 through 268 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 276 through 300 Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 333 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 348 through 355 removed outlier: 3.999A pdb=" N GLN B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 368 removed outlier: 3.688A pdb=" N PHE B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 469 through 472 removed outlier: 4.321A pdb=" N TRP B 472 " --> pdb=" O ASN B 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 473 through 480 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.677A pdb=" N TYR B 540 " --> pdb=" O HIS B 537 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'C' and resid 15 through 30 removed outlier: 3.646A pdb=" N LEU C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 115 through 130 removed outlier: 3.692A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.992A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 221 through 232 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 259 through 268 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 276 through 300 Processing helix chain 'C' and resid 315 through 318 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 348 through 355 removed outlier: 4.000A pdb=" N GLN C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 368 removed outlier: 3.688A pdb=" N PHE C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'C' and resid 469 through 472 removed outlier: 4.322A pdb=" N TRP C 472 " --> pdb=" O ASN C 469 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 469 through 472' Processing helix chain 'C' and resid 473 through 480 Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.677A pdb=" N TYR C 540 " --> pdb=" O HIS C 537 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 541 " --> pdb=" O PRO C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 561 through 571 Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 89 removed outlier: 8.194A pdb=" N ILE D 88 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS D 38 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR D 3 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL D 180 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU D 182 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N MET D 211 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU D 177 " --> pdb=" O MET D 211 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA D 213 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS D 179 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG D 215 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER D 181 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE D 212 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 242 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS D 214 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'D' and resid 336 through 343 removed outlier: 6.748A pdb=" N ILE D 372 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 403 " --> pdb=" O ILE D 372 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 374 " --> pdb=" O VAL D 403 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR D 531 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY D 512 " --> pdb=" O GLU D 521 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE D 523 " --> pdb=" O PHE D 510 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE D 510 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU D 525 " --> pdb=" O PHE D 508 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE D 508 " --> pdb=" O LEU D 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG D 492 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 443 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER D 425 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL D 441 " --> pdb=" O SER D 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 8.195A pdb=" N ILE A 88 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS A 38 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR A 3 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL A 180 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LEU A 182 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N MET A 211 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A 177 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA A 213 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N HIS A 179 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A 215 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 181 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 212 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 242 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS A 214 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 343 removed outlier: 6.747A pdb=" N ILE A 372 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 403 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL A 374 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TYR A 531 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY A 512 " --> pdb=" O GLU A 521 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE A 523 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 510 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 525 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE A 508 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ARG A 492 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 443 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER A 425 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 441 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89 removed outlier: 8.194A pdb=" N ILE B 88 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS B 38 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR B 3 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE B 178 " --> pdb=" O TYR B 3 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 5 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL B 180 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N SER B 7 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N LEU B 182 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N MET B 211 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 177 " --> pdb=" O MET B 211 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA B 213 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS B 179 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG B 215 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 181 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 212 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL B 242 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS B 214 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 58 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 185 through 186 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 343 removed outlier: 6.747A pdb=" N ILE B 372 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL B 403 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 374 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR B 531 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY B 512 " --> pdb=" O GLU B 521 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 523 " --> pdb=" O PHE B 510 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE B 510 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 525 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE B 508 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 492 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 443 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER B 425 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 441 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 89 removed outlier: 8.195A pdb=" N ILE C 88 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LYS C 38 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR C 3 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL C 180 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N LEU C 182 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N MET C 211 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU C 177 " --> pdb=" O MET C 211 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ALA C 213 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS C 179 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG C 215 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER C 181 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 212 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 242 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS C 214 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 58 through 60 Processing sheet with id=AB6, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 343 removed outlier: 6.747A pdb=" N ILE C 372 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 403 " --> pdb=" O ILE C 372 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C 374 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TYR C 531 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLY C 512 " --> pdb=" O GLU C 521 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE C 523 " --> pdb=" O PHE C 510 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N PHE C 510 " --> pdb=" O PHE C 523 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 525 " --> pdb=" O PHE C 508 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE C 508 " --> pdb=" O LEU C 525 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 492 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 443 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N SER C 425 " --> pdb=" O ASP C 439 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 441 " --> pdb=" O SER C 425 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2472 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: 11.18 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.10: 17532 1.10 - 1.28: 3012 1.28 - 1.46: 5638 1.46 - 1.64: 9390 1.64 - 1.82: 128 Bond restraints: 35700 Sorted by residual: bond pdb=" CH2 TRP A 341 " pdb=" HH2 TRP A 341 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" CE1 HIS C 259 " pdb=" HE1 HIS C 259 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" NE1 TRP C 472 " pdb=" HE1 TRP C 472 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CZ PHE A 414 " pdb=" HZ PHE A 414 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" CE1 HIS A 250 " pdb=" HE1 HIS A 250 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 35695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.38: 63479 6.38 - 12.76: 1153 12.76 - 19.14: 8 19.14 - 25.52: 0 25.52 - 31.90: 12 Bond angle restraints: 64652 Sorted by residual: angle pdb=" N SER A 217 " pdb=" CA SER A 217 " pdb=" HA SER A 217 " ideal model delta sigma weight residual 110.00 78.10 31.90 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N SER C 217 " pdb=" CA SER C 217 " pdb=" HA SER C 217 " ideal model delta sigma weight residual 110.00 78.13 31.87 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N SER B 217 " pdb=" CA SER B 217 " pdb=" HA SER B 217 " ideal model delta sigma weight residual 110.00 78.14 31.86 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N SER D 217 " pdb=" CA SER D 217 " pdb=" HA SER D 217 " ideal model delta sigma weight residual 110.00 78.14 31.86 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C SER A 217 " pdb=" CA SER A 217 " pdb=" HA SER A 217 " ideal model delta sigma weight residual 109.00 77.84 31.16 3.00e+00 1.11e-01 1.08e+02 ... (remaining 64647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.76: 14951 18.76 - 37.52: 1077 37.52 - 56.28: 452 56.28 - 75.03: 276 75.03 - 93.79: 56 Dihedral angle restraints: 16812 sinusoidal: 9464 harmonic: 7348 Sorted by residual: dihedral pdb=" C SER C 217 " pdb=" N SER C 217 " pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta harmonic sigma weight residual -122.60 -144.12 21.52 0 2.50e+00 1.60e-01 7.41e+01 dihedral pdb=" C SER B 217 " pdb=" N SER B 217 " pdb=" CA SER B 217 " pdb=" CB SER B 217 " ideal model delta harmonic sigma weight residual -122.60 -144.12 21.52 0 2.50e+00 1.60e-01 7.41e+01 dihedral pdb=" C SER D 217 " pdb=" N SER D 217 " pdb=" CA SER D 217 " pdb=" CB SER D 217 " ideal model delta harmonic sigma weight residual -122.60 -144.07 21.47 0 2.50e+00 1.60e-01 7.37e+01 ... (remaining 16809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 2588 0.188 - 0.375: 188 0.375 - 0.563: 4 0.563 - 0.750: 0 0.750 - 0.938: 4 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA SER C 217 " pdb=" N SER C 217 " pdb=" C SER C 217 " pdb=" CB SER C 217 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA SER B 217 " pdb=" N SER B 217 " pdb=" C SER B 217 " pdb=" CB SER B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA SER D 217 " pdb=" N SER D 217 " pdb=" C SER D 217 " pdb=" CB SER D 217 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 2781 not shown) Planarity restraints: 5264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 488 " 0.145 9.50e-02 1.11e+02 1.05e-01 1.96e+02 pdb=" NE ARG B 488 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 488 " 0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG B 488 " 0.064 2.00e-02 2.50e+03 pdb=" NH2 ARG B 488 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG B 488 " -0.190 2.00e-02 2.50e+03 pdb="HH12 ARG B 488 " 0.080 2.00e-02 2.50e+03 pdb="HH21 ARG B 488 " -0.131 2.00e-02 2.50e+03 pdb="HH22 ARG B 488 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 488 " 0.145 9.50e-02 1.11e+02 1.05e-01 1.96e+02 pdb=" NE ARG A 488 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 488 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 488 " 0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG A 488 " 0.054 2.00e-02 2.50e+03 pdb="HH11 ARG A 488 " -0.190 2.00e-02 2.50e+03 pdb="HH12 ARG A 488 " 0.079 2.00e-02 2.50e+03 pdb="HH21 ARG A 488 " -0.131 2.00e-02 2.50e+03 pdb="HH22 ARG A 488 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 488 " -0.145 9.50e-02 1.11e+02 1.05e-01 1.96e+02 pdb=" NE ARG D 488 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG D 488 " -0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG D 488 " -0.064 2.00e-02 2.50e+03 pdb=" NH2 ARG D 488 " -0.054 2.00e-02 2.50e+03 pdb="HH11 ARG D 488 " 0.190 2.00e-02 2.50e+03 pdb="HH12 ARG D 488 " -0.079 2.00e-02 2.50e+03 pdb="HH21 ARG D 488 " 0.131 2.00e-02 2.50e+03 pdb="HH22 ARG D 488 " 0.024 2.00e-02 2.50e+03 ... (remaining 5261 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.12: 1672 2.12 - 2.74: 56975 2.74 - 3.36: 107123 3.36 - 3.98: 144050 3.98 - 4.60: 211948 Nonbonded interactions: 521768 Sorted by model distance: nonbonded pdb=" HE1 HIS D 233 " pdb="HE21 GLN A 165 " model vdw 1.506 2.100 nonbonded pdb=" HE1 HIS B 233 " pdb="HE21 GLN C 165 " model vdw 1.508 2.100 nonbonded pdb="HE21 GLN D 165 " pdb=" HE1 HIS A 233 " model vdw 1.510 2.100 nonbonded pdb="HE21 GLN B 165 " pdb=" HE1 HIS C 233 " model vdw 1.536 2.100 nonbonded pdb=" H LYS A 193 " pdb=" O3G UTP B 602 " model vdw 1.555 2.450 ... (remaining 521763 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 571 or resid 604)) selection = (chain 'B' and (resid 1 through 571 or resid 604)) selection = (chain 'C' and (resid 1 through 571 or resid 604)) selection = (chain 'D' and (resid 1 through 571 or resid 604)) } 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.190 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 34.710 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 0.013 0.134 18136 Z= 0.790 Angle : 1.943 15.312 24620 Z= 1.297 Chirality : 0.107 0.938 2784 Planarity : 0.015 0.128 3136 Dihedral : 16.949 93.792 6960 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 0.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.64 % Allowed : 6.15 % Favored : 92.21 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: -0.45 (0.17), residues: 2220 helix: -0.44 (0.15), residues: 936 sheet: 0.06 (0.26), residues: 332 loop : -0.05 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG B 215 TYR 0.080 0.021 TYR A 74 PHE 0.077 0.015 PHE B 168 TRP 0.108 0.028 TRP A 472 HIS 0.029 0.006 HIS B 179 Details of bonding type rmsd/Z covalent geometry : bond 0.01263 / 0.79 (18136) covalent geometry : angle 1.94276 / 1.30 (24620) hydrogen bonds : bond 0.14444 / 10.04 ( 848) hydrogen bonds : angle 7.08717 / 5.00 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 431 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 ARG cc_start: 0.7699 (ttp-110) cc_final: 0.7275 (mtm-85) REVERT: D 105 ASP cc_start: 0.7432 (m-30) cc_final: 0.7069 (m-30) REVERT: D 146 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: D 165 GLN cc_start: 0.8479 (mt0) cc_final: 0.8108 (mt0) REVERT: D 201 ASP cc_start: 0.7703 (m-30) cc_final: 0.7475 (m-30) REVERT: D 241 ASN cc_start: 0.8109 (t0) cc_final: 0.7867 (t0) REVERT: D 287 LEU cc_start: 0.7839 (tp) cc_final: 0.7552 (tm) REVERT: D 443 ILE cc_start: 0.6597 (OUTLIER) cc_final: 0.6345 (tp) REVERT: D 548 SER cc_start: 0.8545 (t) cc_final: 0.8259 (t) REVERT: A 103 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7298 (mtm-85) REVERT: A 105 ASP cc_start: 0.7327 (m-30) cc_final: 0.7126 (m-30) REVERT: A 146 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 165 GLN cc_start: 0.8474 (mt0) cc_final: 0.8106 (mt0) REVERT: A 201 ASP cc_start: 0.7699 (m-30) cc_final: 0.7474 (m-30) REVERT: A 257 LYS cc_start: 0.7980 (ptmm) cc_final: 0.7736 (ptmm) REVERT: A 443 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6355 (tp) REVERT: B 103 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7333 (mtm-85) REVERT: B 105 ASP cc_start: 0.7369 (m-30) cc_final: 0.7026 (m-30) REVERT: B 146 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 165 GLN cc_start: 0.8460 (mt0) cc_final: 0.8085 (mt0) REVERT: B 201 ASP cc_start: 0.7666 (m-30) cc_final: 0.7445 (m-30) REVERT: B 241 ASN cc_start: 0.8088 (t0) cc_final: 0.7864 (t0) REVERT: B 287 LEU cc_start: 0.7838 (tp) cc_final: 0.7553 (tm) REVERT: B 443 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6386 (tp) REVERT: C 103 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7251 (mtm-85) REVERT: C 105 ASP cc_start: 0.7461 (m-30) cc_final: 0.7118 (m-30) REVERT: C 146 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: C 165 GLN cc_start: 0.8479 (mt0) cc_final: 0.8250 (mt0) REVERT: C 201 ASP cc_start: 0.7698 (m-30) cc_final: 0.7488 (m-30) REVERT: C 222 ARG cc_start: 0.7229 (mmt180) cc_final: 0.7001 (tpp-160) REVERT: C 241 ASN cc_start: 0.8077 (t0) cc_final: 0.7853 (t0) REVERT: C 287 LEU cc_start: 0.7843 (tp) cc_final: 0.7533 (tm) REVERT: C 443 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6331 (tp) outliers start: 32 outliers final: 4 residues processed: 455 average time/residue: 1.1048 time to fit residues: 574.3239 Evaluate side-chains 340 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 328 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 443 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 116 HIS D 167 GLN D 285 GLN A 116 HIS A 285 GLN B 116 HIS C 116 HIS C 241 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.179861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.131132 restraints weight = 55777.299| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.93 r_work: 0.3236 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18136 Z= 0.154 Angle : 0.648 5.981 24620 Z= 0.341 Chirality : 0.048 0.387 2784 Planarity : 0.005 0.032 3136 Dihedral : 12.115 62.199 2716 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.92 % Allowed : 11.68 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2220 helix: 0.88 (0.16), residues: 952 sheet: 0.11 (0.27), residues: 332 loop : 0.11 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 334 TYR 0.016 0.002 TYR B 312 PHE 0.010 0.002 PHE D 175 TRP 0.009 0.001 TRP A 290 HIS 0.010 0.002 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (18136) covalent geometry : angle 0.64827 / 0.34 (24620) hydrogen bonds : bond 0.03917 / 2.66 ( 848) hydrogen bonds : angle 5.34810 / 3.73 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 425 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 368 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 103 ARG cc_start: 0.7977 (ttp-110) cc_final: 0.7580 (ttm110) REVERT: D 105 ASP cc_start: 0.8085 (m-30) cc_final: 0.7601 (m-30) REVERT: D 201 ASP cc_start: 0.8405 (m-30) cc_final: 0.8150 (m-30) REVERT: D 222 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7360 (tpp-160) REVERT: D 248 THR cc_start: 0.8718 (p) cc_final: 0.8308 (m) REVERT: D 272 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7305 (mt-10) REVERT: D 287 LEU cc_start: 0.7807 (tp) cc_final: 0.7520 (tm) REVERT: D 338 GLU cc_start: 0.8130 (tt0) cc_final: 0.7883 (tt0) REVERT: D 443 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.6056 (OUTLIER) REVERT: D 476 ARG cc_start: 0.8091 (tmt90) cc_final: 0.7797 (ttt-90) REVERT: A 54 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6206 (mt-10) REVERT: A 70 ASP cc_start: 0.8614 (m-30) cc_final: 0.8366 (m-30) REVERT: A 103 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7625 (ttm110) REVERT: A 105 ASP cc_start: 0.8078 (m-30) cc_final: 0.7645 (m-30) REVERT: A 201 ASP cc_start: 0.8400 (m-30) cc_final: 0.8146 (m-30) REVERT: A 222 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7342 (tpp-160) REVERT: A 248 THR cc_start: 0.8699 (p) cc_final: 0.8283 (m) REVERT: A 272 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7308 (mt-10) REVERT: A 443 ILE cc_start: 0.6449 (OUTLIER) cc_final: 0.6174 (OUTLIER) REVERT: A 476 ARG cc_start: 0.8093 (tmt90) cc_final: 0.7749 (ttt-90) REVERT: A 546 GLU cc_start: 0.8071 (tt0) cc_final: 0.7852 (pt0) REVERT: B 70 ASP cc_start: 0.8620 (m-30) cc_final: 0.8362 (m-30) REVERT: B 201 ASP cc_start: 0.8381 (m-30) cc_final: 0.8139 (m-30) REVERT: B 248 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8297 (m) REVERT: B 272 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7316 (mt-10) REVERT: B 287 LEU cc_start: 0.7796 (tp) cc_final: 0.7480 (tm) REVERT: B 336 GLN cc_start: 0.7212 (tp40) cc_final: 0.7010 (tm-30) REVERT: B 338 GLU cc_start: 0.8078 (tt0) cc_final: 0.7835 (tt0) REVERT: B 443 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6106 (tp) REVERT: B 476 ARG cc_start: 0.8091 (tmt90) cc_final: 0.7773 (ttt-90) REVERT: C 70 ASP cc_start: 0.8626 (m-30) cc_final: 0.8396 (m-30) REVERT: C 103 ARG cc_start: 0.7962 (ttp-110) cc_final: 0.7611 (ttm110) REVERT: C 105 ASP cc_start: 0.8122 (m-30) cc_final: 0.7735 (m-30) REVERT: C 201 ASP cc_start: 0.8395 (m-30) cc_final: 0.8158 (m-30) REVERT: C 248 THR cc_start: 0.8694 (p) cc_final: 0.8303 (m) REVERT: C 272 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7319 (mt-10) REVERT: C 287 LEU cc_start: 0.7665 (tp) cc_final: 0.7378 (tm) REVERT: C 443 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.6055 (OUTLIER) REVERT: C 476 ARG cc_start: 0.8093 (tmt90) cc_final: 0.7802 (ttt-90) REVERT: C 546 GLU cc_start: 0.8045 (tt0) cc_final: 0.7841 (pt0) outliers start: 57 outliers final: 22 residues processed: 401 average time/residue: 1.0097 time to fit residues: 468.1144 Evaluate side-chains 362 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 335 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 490 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 GLN A 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.128583 restraints weight = 56255.336| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.84 r_work: 0.3157 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18136 Z= 0.217 Angle : 0.602 5.204 24620 Z= 0.318 Chirality : 0.049 0.379 2784 Planarity : 0.004 0.041 3136 Dihedral : 9.618 62.952 2700 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.28 % Allowed : 12.24 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.36 (0.18), residues: 2220 helix: 0.87 (0.17), residues: 980 sheet: -0.34 (0.26), residues: 332 loop : -0.07 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 334 TYR 0.015 0.002 TYR C 42 PHE 0.014 0.002 PHE D 523 TRP 0.011 0.001 TRP A 124 HIS 0.008 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (18136) covalent geometry : angle 0.60185 / 0.32 (24620) hydrogen bonds : bond 0.03633 / 2.48 ( 848) hydrogen bonds : angle 4.97195 / 3.46 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 340 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 195 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8592 (t) REVERT: D 201 ASP cc_start: 0.8478 (m-30) cc_final: 0.8224 (m-30) REVERT: D 222 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7334 (tpp-160) REVERT: D 248 THR cc_start: 0.8724 (p) cc_final: 0.8403 (m) REVERT: D 287 LEU cc_start: 0.7849 (tp) cc_final: 0.7582 (tm) REVERT: D 311 LYS cc_start: 0.7367 (mtmt) cc_final: 0.7011 (mtmm) REVERT: D 476 ARG cc_start: 0.8224 (tmt90) cc_final: 0.7838 (ttt-90) REVERT: D 486 HIS cc_start: 0.8170 (m90) cc_final: 0.7890 (m90) REVERT: A 195 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8604 (t) REVERT: A 201 ASP cc_start: 0.8460 (m-30) cc_final: 0.8205 (m-30) REVERT: A 222 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7303 (tpp-160) REVERT: A 248 THR cc_start: 0.8722 (p) cc_final: 0.8407 (m) REVERT: A 311 LYS cc_start: 0.7335 (mtmt) cc_final: 0.6968 (mtmm) REVERT: A 476 ARG cc_start: 0.8155 (tmt90) cc_final: 0.7881 (ttt-90) REVERT: A 486 HIS cc_start: 0.8247 (m90) cc_final: 0.7974 (m90) REVERT: B 195 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8593 (t) REVERT: B 201 ASP cc_start: 0.8444 (m-30) cc_final: 0.8191 (m-30) REVERT: B 248 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8432 (m) REVERT: B 287 LEU cc_start: 0.7867 (tp) cc_final: 0.7599 (tm) REVERT: B 311 LYS cc_start: 0.7354 (mtmt) cc_final: 0.7004 (mtmm) REVERT: B 338 GLU cc_start: 0.8208 (tt0) cc_final: 0.7829 (tt0) REVERT: B 476 ARG cc_start: 0.8214 (tmt90) cc_final: 0.7829 (ttt-90) REVERT: C 201 ASP cc_start: 0.8448 (m-30) cc_final: 0.8212 (m-30) REVERT: C 248 THR cc_start: 0.8734 (p) cc_final: 0.8413 (m) REVERT: C 287 LEU cc_start: 0.7708 (tp) cc_final: 0.7449 (tm) REVERT: C 311 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7011 (mtmm) REVERT: C 476 ARG cc_start: 0.8205 (tmt90) cc_final: 0.7823 (ttt-90) REVERT: C 486 HIS cc_start: 0.8210 (m90) cc_final: 0.7956 (m90) REVERT: C 546 GLU cc_start: 0.8056 (tt0) cc_final: 0.7828 (pt0) outliers start: 64 outliers final: 22 residues processed: 385 average time/residue: 0.9992 time to fit residues: 447.1804 Evaluate side-chains 338 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 310 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 42 TYR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 211 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 165 GLN D 328 HIS D 535 GLN A 165 GLN B 165 GLN B 285 GLN B 535 GLN C 165 GLN C 535 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.177402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.128693 restraints weight = 55648.984| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.91 r_work: 0.3172 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18136 Z= 0.136 Angle : 0.524 4.484 24620 Z= 0.275 Chirality : 0.046 0.375 2784 Planarity : 0.004 0.050 3136 Dihedral : 9.093 63.938 2692 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.46 % Allowed : 14.04 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2220 helix: 1.19 (0.17), residues: 980 sheet: -0.58 (0.25), residues: 332 loop : 0.05 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 334 TYR 0.013 0.001 TYR C 42 PHE 0.010 0.001 PHE D 523 TRP 0.007 0.001 TRP D 124 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (18136) covalent geometry : angle 0.52380 / 0.27 (24620) hydrogen bonds : bond 0.03058 / 2.08 ( 848) hydrogen bonds : angle 4.73018 / 3.29 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 376 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 328 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 ASP cc_start: 0.8088 (m-30) cc_final: 0.7598 (m-30) REVERT: D 130 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8639 (mtpm) REVERT: D 201 ASP cc_start: 0.8379 (m-30) cc_final: 0.8101 (m-30) REVERT: D 222 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7225 (tpp-160) REVERT: D 248 THR cc_start: 0.8686 (p) cc_final: 0.8382 (m) REVERT: D 287 LEU cc_start: 0.7701 (tp) cc_final: 0.7454 (tm) REVERT: D 311 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6949 (mtmm) REVERT: D 476 ARG cc_start: 0.8243 (tmt90) cc_final: 0.7816 (ttt-90) REVERT: D 486 HIS cc_start: 0.8276 (m90) cc_final: 0.8004 (m90) REVERT: A 105 ASP cc_start: 0.8086 (m-30) cc_final: 0.7574 (m-30) REVERT: A 201 ASP cc_start: 0.8368 (m-30) cc_final: 0.8105 (m-30) REVERT: A 222 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7329 (tpp-160) REVERT: A 248 THR cc_start: 0.8687 (p) cc_final: 0.8393 (m) REVERT: A 311 LYS cc_start: 0.7282 (mtmt) cc_final: 0.6912 (mtmm) REVERT: A 476 ARG cc_start: 0.8162 (tmt90) cc_final: 0.7831 (ttt-90) REVERT: B 103 ARG cc_start: 0.7923 (ttm170) cc_final: 0.7693 (ttm110) REVERT: B 130 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8619 (mtpm) REVERT: B 201 ASP cc_start: 0.8341 (m-30) cc_final: 0.8082 (m-30) REVERT: B 248 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8349 (m) REVERT: B 287 LEU cc_start: 0.7728 (tp) cc_final: 0.7472 (tm) REVERT: B 311 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6808 (mtmm) REVERT: B 476 ARG cc_start: 0.8238 (tmt90) cc_final: 0.7764 (ttt-90) REVERT: C 105 ASP cc_start: 0.8072 (m-30) cc_final: 0.7513 (m-30) REVERT: C 201 ASP cc_start: 0.8411 (m-30) cc_final: 0.8146 (m-30) REVERT: C 248 THR cc_start: 0.8700 (p) cc_final: 0.8384 (m) REVERT: C 287 LEU cc_start: 0.7696 (tp) cc_final: 0.7449 (tm) REVERT: C 311 LYS cc_start: 0.7339 (mtmt) cc_final: 0.6988 (mtmm) REVERT: C 476 ARG cc_start: 0.8222 (tmt90) cc_final: 0.7865 (ttt-90) REVERT: C 546 GLU cc_start: 0.8045 (tt0) cc_final: 0.7795 (pt0) outliers start: 48 outliers final: 12 residues processed: 356 average time/residue: 1.0826 time to fit residues: 447.0490 Evaluate side-chains 315 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 298 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 144 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 130 optimal weight: 0.0370 chunk 133 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 241 ASN D 285 GLN A 535 GLN B 44 ASN B 535 GLN C 535 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.175727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128561 restraints weight = 56457.466| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.84 r_work: 0.3165 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18136 Z= 0.164 Angle : 0.533 4.605 24620 Z= 0.279 Chirality : 0.047 0.377 2784 Planarity : 0.004 0.050 3136 Dihedral : 8.819 61.170 2692 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 15.16 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 2220 helix: 1.24 (0.17), residues: 980 sheet: -0.68 (0.25), residues: 332 loop : -0.03 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 334 TYR 0.015 0.002 TYR A 42 PHE 0.011 0.002 PHE B 523 TRP 0.008 0.001 TRP B 124 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (18136) covalent geometry : angle 0.53338 / 0.28 (24620) hydrogen bonds : bond 0.03102 / 2.12 ( 848) hydrogen bonds : angle 4.62699 / 3.21 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 357 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 309 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8272 (mtp180) REVERT: D 105 ASP cc_start: 0.8082 (m-30) cc_final: 0.7643 (m-30) REVERT: D 130 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8613 (mtpm) REVERT: D 201 ASP cc_start: 0.8458 (m-30) cc_final: 0.8200 (m-30) REVERT: D 222 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7279 (tpp-160) REVERT: D 248 THR cc_start: 0.8686 (p) cc_final: 0.8426 (m) REVERT: D 287 LEU cc_start: 0.7894 (tp) cc_final: 0.7660 (tm) REVERT: D 311 LYS cc_start: 0.7385 (mtmt) cc_final: 0.7079 (mtmm) REVERT: D 476 ARG cc_start: 0.8278 (tmt90) cc_final: 0.7908 (ttt-90) REVERT: D 486 HIS cc_start: 0.8317 (m90) cc_final: 0.8018 (m90) REVERT: A 105 ASP cc_start: 0.8044 (m-30) cc_final: 0.7569 (m-30) REVERT: A 201 ASP cc_start: 0.8449 (m-30) cc_final: 0.8189 (m-30) REVERT: A 222 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7340 (tpp-160) REVERT: A 248 THR cc_start: 0.8674 (p) cc_final: 0.8412 (m) REVERT: A 291 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7263 (mm-30) REVERT: A 311 LYS cc_start: 0.7398 (mtmt) cc_final: 0.7094 (mtmm) REVERT: A 476 ARG cc_start: 0.8168 (tmt90) cc_final: 0.7815 (ttt-90) REVERT: B 138 LEU cc_start: 0.8719 (mm) cc_final: 0.8390 (mt) REVERT: B 195 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8606 (t) REVERT: B 201 ASP cc_start: 0.8402 (m-30) cc_final: 0.8159 (m-30) REVERT: B 248 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8406 (m) REVERT: B 287 LEU cc_start: 0.7882 (tp) cc_final: 0.7655 (tm) REVERT: B 311 LYS cc_start: 0.7262 (mtmt) cc_final: 0.6935 (mtmm) REVERT: B 476 ARG cc_start: 0.8254 (tmt90) cc_final: 0.7779 (ttt-90) REVERT: C 100 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8293 (mtp180) REVERT: C 105 ASP cc_start: 0.8054 (m-30) cc_final: 0.7643 (m-30) REVERT: C 201 ASP cc_start: 0.8446 (m-30) cc_final: 0.8174 (m-30) REVERT: C 248 THR cc_start: 0.8706 (p) cc_final: 0.8416 (m) REVERT: C 311 LYS cc_start: 0.7411 (mtmt) cc_final: 0.7110 (mtmm) REVERT: C 476 ARG cc_start: 0.8247 (tmt90) cc_final: 0.7833 (ttt-90) REVERT: C 546 GLU cc_start: 0.8075 (tt0) cc_final: 0.7768 (pt0) outliers start: 48 outliers final: 21 residues processed: 338 average time/residue: 1.0306 time to fit residues: 402.7842 Evaluate side-chains 327 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 30 optimal weight: 0.2980 chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 ASN D 535 GLN A 535 GLN B 285 GLN B 535 GLN C 44 ASN C 535 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.175423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.128079 restraints weight = 56231.519| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.84 r_work: 0.3155 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 18136 Z= 0.161 Angle : 0.524 4.500 24620 Z= 0.273 Chirality : 0.046 0.379 2784 Planarity : 0.004 0.058 3136 Dihedral : 8.665 60.883 2692 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.66 % Allowed : 15.32 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.57 (0.18), residues: 2220 helix: 1.30 (0.17), residues: 980 sheet: -0.71 (0.26), residues: 332 loop : -0.07 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.025 0.002 TYR D 312 PHE 0.013 0.002 PHE A 523 TRP 0.007 0.001 TRP B 124 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (18136) covalent geometry : angle 0.52355 / 0.27 (24620) hydrogen bonds : bond 0.03008 / 2.05 ( 848) hydrogen bonds : angle 4.54577 / 3.14 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 364 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8353 (mtp180) REVERT: D 105 ASP cc_start: 0.8167 (m-30) cc_final: 0.7706 (m-30) REVERT: D 201 ASP cc_start: 0.8439 (m-30) cc_final: 0.8178 (m-30) REVERT: D 222 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7257 (tpp-160) REVERT: D 248 THR cc_start: 0.8672 (p) cc_final: 0.8420 (m) REVERT: D 287 LEU cc_start: 0.7874 (tp) cc_final: 0.7638 (tm) REVERT: D 311 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6914 (mtmm) REVERT: D 476 ARG cc_start: 0.8261 (tmt90) cc_final: 0.7907 (ttt-90) REVERT: D 521 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 100 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8233 (mtp180) REVERT: A 105 ASP cc_start: 0.8145 (m-30) cc_final: 0.7699 (m-30) REVERT: A 201 ASP cc_start: 0.8433 (m-30) cc_final: 0.8167 (m-30) REVERT: A 222 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7216 (tpp-160) REVERT: A 248 THR cc_start: 0.8658 (p) cc_final: 0.8366 (m) REVERT: A 311 LYS cc_start: 0.7320 (mtmt) cc_final: 0.6974 (mtmm) REVERT: A 476 ARG cc_start: 0.8152 (tmt90) cc_final: 0.7848 (ttt-90) REVERT: B 100 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8358 (mtp180) REVERT: B 138 LEU cc_start: 0.8687 (mm) cc_final: 0.8378 (mt) REVERT: B 195 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8606 (t) REVERT: B 201 ASP cc_start: 0.8400 (m-30) cc_final: 0.8153 (m-30) REVERT: B 248 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 287 LEU cc_start: 0.7889 (tp) cc_final: 0.7680 (tm) REVERT: B 311 LYS cc_start: 0.7272 (mtmt) cc_final: 0.6945 (mtmm) REVERT: B 476 ARG cc_start: 0.8246 (tmt90) cc_final: 0.7792 (ttt-90) REVERT: C 100 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8285 (mtp180) REVERT: C 105 ASP cc_start: 0.8223 (m-30) cc_final: 0.7765 (m-30) REVERT: C 200 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7949 (ttpp) REVERT: C 201 ASP cc_start: 0.8469 (m-30) cc_final: 0.8204 (m-30) REVERT: C 248 THR cc_start: 0.8711 (p) cc_final: 0.8441 (m) REVERT: C 311 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7018 (mtmm) REVERT: C 476 ARG cc_start: 0.8248 (tmt90) cc_final: 0.7868 (ttt-90) REVERT: C 546 GLU cc_start: 0.8048 (tt0) cc_final: 0.7717 (pt0) outliers start: 52 outliers final: 24 residues processed: 338 average time/residue: 1.1327 time to fit residues: 441.5887 Evaluate side-chains 340 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 307 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 160 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 GLN D 535 GLN A 285 GLN A 535 GLN B 535 GLN C 285 GLN C 535 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.176628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129773 restraints weight = 56455.114| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.83 r_work: 0.3191 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18136 Z= 0.117 Angle : 0.488 4.325 24620 Z= 0.255 Chirality : 0.045 0.376 2784 Planarity : 0.004 0.057 3136 Dihedral : 8.380 60.054 2692 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.00 % Allowed : 16.09 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.75 (0.18), residues: 2220 helix: 1.51 (0.17), residues: 984 sheet: -0.71 (0.26), residues: 332 loop : -0.02 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 334 TYR 0.013 0.001 TYR B 42 PHE 0.010 0.001 PHE D 523 TRP 0.006 0.001 TRP B 124 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (18136) covalent geometry : angle 0.48813 / 0.25 (24620) hydrogen bonds : bond 0.02743 / 1.87 ( 848) hydrogen bonds : angle 4.46315 / 3.08 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 355 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 316 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 ASP cc_start: 0.7948 (m-30) cc_final: 0.7704 (m-30) REVERT: D 201 ASP cc_start: 0.8392 (m-30) cc_final: 0.8122 (m-30) REVERT: D 222 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7250 (tpp-160) REVERT: D 248 THR cc_start: 0.8616 (p) cc_final: 0.8370 (m) REVERT: D 287 LEU cc_start: 0.7776 (tp) cc_final: 0.7524 (tm) REVERT: D 311 LYS cc_start: 0.7114 (mtmt) cc_final: 0.6825 (mtmm) REVERT: D 476 ARG cc_start: 0.8264 (tmt90) cc_final: 0.7923 (ttt-90) REVERT: D 486 HIS cc_start: 0.8325 (m90) cc_final: 0.8022 (m-70) REVERT: D 521 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7352 (mt-10) REVERT: D 534 THR cc_start: 0.7981 (p) cc_final: 0.7560 (p) REVERT: A 100 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8256 (mtp180) REVERT: A 200 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: A 201 ASP cc_start: 0.8388 (m-30) cc_final: 0.8122 (m-30) REVERT: A 222 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7160 (tpp-160) REVERT: A 240 VAL cc_start: 0.9227 (m) cc_final: 0.8955 (p) REVERT: A 248 THR cc_start: 0.8651 (p) cc_final: 0.8353 (m) REVERT: A 311 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6865 (mtmm) REVERT: A 476 ARG cc_start: 0.8170 (tmt90) cc_final: 0.7881 (ttt-90) REVERT: B 100 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (mtp180) REVERT: B 138 LEU cc_start: 0.8693 (mm) cc_final: 0.8378 (mt) REVERT: B 201 ASP cc_start: 0.8349 (m-30) cc_final: 0.8097 (m-30) REVERT: B 287 LEU cc_start: 0.7915 (tp) cc_final: 0.7686 (tm) REVERT: B 311 LYS cc_start: 0.7225 (mtmt) cc_final: 0.6912 (mtmm) REVERT: B 476 ARG cc_start: 0.8242 (tmt90) cc_final: 0.7789 (ttt-90) REVERT: B 534 THR cc_start: 0.7918 (p) cc_final: 0.7499 (p) REVERT: C 200 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7919 (ttpp) REVERT: C 201 ASP cc_start: 0.8402 (m-30) cc_final: 0.8143 (m-30) REVERT: C 248 THR cc_start: 0.8645 (p) cc_final: 0.8383 (m) REVERT: C 311 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6920 (mtmm) REVERT: C 476 ARG cc_start: 0.8250 (tmt90) cc_final: 0.7879 (ttt-90) REVERT: C 546 GLU cc_start: 0.7960 (tt0) cc_final: 0.7659 (pt0) outliers start: 39 outliers final: 21 residues processed: 333 average time/residue: 1.0870 time to fit residues: 418.8335 Evaluate side-chains 334 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 61 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 535 GLN A 535 GLN B 535 GLN C 535 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128265 restraints weight = 56385.020| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.86 r_work: 0.3158 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 18136 Z= 0.150 Angle : 0.510 4.401 24620 Z= 0.265 Chirality : 0.046 0.378 2784 Planarity : 0.004 0.062 3136 Dihedral : 8.371 59.251 2692 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.25 % Allowed : 16.19 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.70 (0.18), residues: 2220 helix: 1.46 (0.17), residues: 988 sheet: -0.64 (0.26), residues: 332 loop : -0.08 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 334 TYR 0.014 0.001 TYR A 42 PHE 0.012 0.002 PHE B 523 TRP 0.006 0.001 TRP B 124 HIS 0.005 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (18136) covalent geometry : angle 0.50951 / 0.27 (24620) hydrogen bonds : bond 0.02874 / 1.96 ( 848) hydrogen bonds : angle 4.46801 / 3.09 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 349 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 305 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8283 (mtp180) REVERT: D 105 ASP cc_start: 0.8070 (m-30) cc_final: 0.7870 (m-30) REVERT: D 201 ASP cc_start: 0.8413 (m-30) cc_final: 0.8157 (m-30) REVERT: D 222 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7269 (tpp-160) REVERT: D 248 THR cc_start: 0.8637 (p) cc_final: 0.8397 (m) REVERT: D 287 LEU cc_start: 0.7744 (tp) cc_final: 0.7500 (tm) REVERT: D 311 LYS cc_start: 0.7231 (mtmt) cc_final: 0.6935 (mtmm) REVERT: D 476 ARG cc_start: 0.8279 (tmt90) cc_final: 0.7950 (ttt-90) REVERT: D 486 HIS cc_start: 0.8311 (m90) cc_final: 0.8025 (m-70) REVERT: D 521 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 100 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8317 (mtp180) REVERT: A 200 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: A 201 ASP cc_start: 0.8434 (m-30) cc_final: 0.8169 (m-30) REVERT: A 222 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.7247 (tpp-160) REVERT: A 240 VAL cc_start: 0.9220 (m) cc_final: 0.8968 (p) REVERT: A 248 THR cc_start: 0.8665 (p) cc_final: 0.8360 (m) REVERT: A 311 LYS cc_start: 0.7268 (mtmt) cc_final: 0.6961 (mtmm) REVERT: A 476 ARG cc_start: 0.8176 (tmt90) cc_final: 0.7927 (ttt-90) REVERT: B 100 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8347 (mtp180) REVERT: B 138 LEU cc_start: 0.8687 (mm) cc_final: 0.8376 (mt) REVERT: B 201 ASP cc_start: 0.8379 (m-30) cc_final: 0.8143 (m-30) REVERT: B 248 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.8388 (m) REVERT: B 287 LEU cc_start: 0.7915 (tp) cc_final: 0.7709 (tm) REVERT: B 311 LYS cc_start: 0.7241 (mtmt) cc_final: 0.6934 (mtmm) REVERT: B 476 ARG cc_start: 0.8260 (tmt90) cc_final: 0.7819 (ttt-90) REVERT: C 75 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8587 (mt-10) REVERT: C 200 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.7936 (ttpp) REVERT: C 201 ASP cc_start: 0.8444 (m-30) cc_final: 0.8174 (m-30) REVERT: C 248 THR cc_start: 0.8655 (p) cc_final: 0.8411 (m) REVERT: C 272 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 311 LYS cc_start: 0.7292 (mtmt) cc_final: 0.6988 (mtmm) REVERT: C 476 ARG cc_start: 0.8252 (tmt90) cc_final: 0.7881 (ttt-90) REVERT: C 546 GLU cc_start: 0.7963 (tt0) cc_final: 0.7654 (pt0) outliers start: 44 outliers final: 25 residues processed: 329 average time/residue: 1.1154 time to fit residues: 424.3164 Evaluate side-chains 333 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 300 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 219 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 GLN D 535 GLN A 44 ASN A 285 GLN A 535 GLN B 535 GLN C 535 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.174479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126774 restraints weight = 56187.512| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.85 r_work: 0.3136 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18136 Z= 0.192 Angle : 0.539 4.539 24620 Z= 0.281 Chirality : 0.047 0.382 2784 Planarity : 0.004 0.064 3136 Dihedral : 8.496 58.086 2692 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2220 helix: 1.36 (0.17), residues: 984 sheet: -0.60 (0.27), residues: 332 loop : -0.15 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 334 TYR 0.017 0.002 TYR B 42 PHE 0.014 0.002 PHE D 523 TRP 0.007 0.001 TRP B 124 HIS 0.005 0.001 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (18136) covalent geometry : angle 0.53910 / 0.28 (24620) hydrogen bonds : bond 0.03064 / 2.09 ( 848) hydrogen bonds : angle 4.53668 / 3.13 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 348 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8357 (mtp180) REVERT: D 105 ASP cc_start: 0.8313 (m-30) cc_final: 0.7813 (m-30) REVERT: D 201 ASP cc_start: 0.8464 (m-30) cc_final: 0.8212 (m-30) REVERT: D 222 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7178 (tpp-160) REVERT: D 248 THR cc_start: 0.8658 (p) cc_final: 0.8435 (m) REVERT: D 287 LEU cc_start: 0.7877 (tp) cc_final: 0.7641 (tm) REVERT: D 311 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6948 (mtmm) REVERT: D 476 ARG cc_start: 0.8295 (tmt90) cc_final: 0.7965 (ttt-90) REVERT: D 486 HIS cc_start: 0.8301 (m90) cc_final: 0.8044 (m-70) REVERT: D 490 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8149 (ttt180) REVERT: D 521 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7211 (mt-10) REVERT: A 100 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8388 (mtp180) REVERT: A 200 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7908 (ttpp) REVERT: A 201 ASP cc_start: 0.8472 (m-30) cc_final: 0.8202 (m-30) REVERT: A 222 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7229 (tpp-160) REVERT: A 240 VAL cc_start: 0.9191 (m) cc_final: 0.8939 (p) REVERT: A 248 THR cc_start: 0.8698 (p) cc_final: 0.8399 (m) REVERT: A 311 LYS cc_start: 0.7331 (mtmt) cc_final: 0.7024 (mtmm) REVERT: A 476 ARG cc_start: 0.8178 (tmt90) cc_final: 0.7835 (ttt-90) REVERT: A 486 HIS cc_start: 0.8407 (m90) cc_final: 0.8107 (m-70) REVERT: A 490 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8269 (ttt180) REVERT: B 100 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8421 (mtp180) REVERT: B 138 LEU cc_start: 0.8719 (mm) cc_final: 0.8419 (mt) REVERT: B 201 ASP cc_start: 0.8417 (m-30) cc_final: 0.8178 (m-30) REVERT: B 248 THR cc_start: 0.8706 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 287 LEU cc_start: 0.7917 (tp) cc_final: 0.7691 (tm) REVERT: B 311 LYS cc_start: 0.7242 (mtmt) cc_final: 0.6945 (mtmm) REVERT: B 370 ASP cc_start: 0.7682 (m-30) cc_final: 0.7447 (m-30) REVERT: B 457 MET cc_start: 0.7231 (tpt) cc_final: 0.7004 (tpt) REVERT: B 476 ARG cc_start: 0.8239 (tmt90) cc_final: 0.7756 (ttt-90) REVERT: B 490 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8184 (ttt180) REVERT: C 200 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.7932 (ttpp) REVERT: C 201 ASP cc_start: 0.8487 (m-30) cc_final: 0.8222 (m-30) REVERT: C 248 THR cc_start: 0.8686 (p) cc_final: 0.8458 (m) REVERT: C 311 LYS cc_start: 0.7274 (mtmt) cc_final: 0.6946 (mtmm) REVERT: C 476 ARG cc_start: 0.8252 (tmt90) cc_final: 0.7924 (ttt-90) REVERT: C 546 GLU cc_start: 0.8001 (tt0) cc_final: 0.7663 (pt0) outliers start: 43 outliers final: 25 residues processed: 329 average time/residue: 1.0466 time to fit residues: 396.1093 Evaluate side-chains 333 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 43 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 135 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 535 GLN B 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.175687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.128302 restraints weight = 56370.011| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.85 r_work: 0.3152 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18136 Z= 0.138 Angle : 0.503 4.364 24620 Z= 0.263 Chirality : 0.046 0.377 2784 Planarity : 0.004 0.065 3136 Dihedral : 8.348 60.365 2692 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 16.65 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2220 helix: 1.45 (0.17), residues: 988 sheet: -0.59 (0.27), residues: 332 loop : -0.09 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 334 TYR 0.014 0.001 TYR A 42 PHE 0.012 0.001 PHE B 523 TRP 0.006 0.001 TRP B 124 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (18136) covalent geometry : angle 0.50317 / 0.26 (24620) hydrogen bonds : bond 0.02814 / 1.92 ( 848) hydrogen bonds : angle 4.47409 / 3.09 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Residue THR 433 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 100 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8234 (mtp180) REVERT: D 103 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: D 105 ASP cc_start: 0.8288 (m-30) cc_final: 0.7839 (m-30) REVERT: D 201 ASP cc_start: 0.8404 (m-30) cc_final: 0.8146 (m-30) REVERT: D 222 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7235 (tpp-160) REVERT: D 248 THR cc_start: 0.8622 (p) cc_final: 0.8396 (m) REVERT: D 285 GLN cc_start: 0.7520 (tp-100) cc_final: 0.7309 (tp-100) REVERT: D 287 LEU cc_start: 0.7713 (tp) cc_final: 0.7482 (tm) REVERT: D 311 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6871 (mtmm) REVERT: D 476 ARG cc_start: 0.8260 (tmt90) cc_final: 0.7875 (ttt-90) REVERT: D 486 HIS cc_start: 0.8301 (m90) cc_final: 0.8015 (m-70) REVERT: D 521 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7205 (mt-10) REVERT: D 534 THR cc_start: 0.7974 (p) cc_final: 0.7556 (p) REVERT: A 100 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (mtp180) REVERT: A 200 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7895 (ttpp) REVERT: A 201 ASP cc_start: 0.8413 (m-30) cc_final: 0.8152 (m-30) REVERT: A 222 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7227 (tpp-160) REVERT: A 240 VAL cc_start: 0.9178 (m) cc_final: 0.8938 (p) REVERT: A 248 THR cc_start: 0.8662 (p) cc_final: 0.8365 (m) REVERT: A 311 LYS cc_start: 0.7249 (mtmt) cc_final: 0.6951 (mtmm) REVERT: A 476 ARG cc_start: 0.8174 (tmt90) cc_final: 0.7829 (ttt-90) REVERT: A 486 HIS cc_start: 0.8412 (m90) cc_final: 0.8114 (m-70) REVERT: B 100 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8344 (mtp180) REVERT: B 138 LEU cc_start: 0.8712 (mm) cc_final: 0.8408 (mt) REVERT: B 201 ASP cc_start: 0.8384 (m-30) cc_final: 0.8145 (m-30) REVERT: B 248 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8411 (m) REVERT: B 287 LEU cc_start: 0.7906 (tp) cc_final: 0.7697 (tm) REVERT: B 311 LYS cc_start: 0.7162 (mtmt) cc_final: 0.6871 (mtmm) REVERT: B 370 ASP cc_start: 0.7708 (m-30) cc_final: 0.7480 (m-30) REVERT: B 476 ARG cc_start: 0.8237 (tmt90) cc_final: 0.7773 (ttt-90) REVERT: B 534 THR cc_start: 0.7908 (p) cc_final: 0.7484 (p) REVERT: C 200 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7916 (ttpp) REVERT: C 201 ASP cc_start: 0.8428 (m-30) cc_final: 0.8159 (m-30) REVERT: C 248 THR cc_start: 0.8657 (p) cc_final: 0.8433 (m) REVERT: C 311 LYS cc_start: 0.7173 (mtmt) cc_final: 0.6886 (mtmm) REVERT: C 476 ARG cc_start: 0.8247 (tmt90) cc_final: 0.7886 (ttt-90) REVERT: C 490 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8183 (ttt180) REVERT: C 546 GLU cc_start: 0.7982 (tt0) cc_final: 0.7644 (pt0) outliers start: 37 outliers final: 22 residues processed: 318 average time/residue: 1.1208 time to fit residues: 409.0862 Evaluate side-chains 331 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 100 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 222 ARG Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 539 GLU Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 100 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 100 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 539 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 0.5980 chunk 170 optimal weight: 1.9990 chunk 79 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 535 GLN B 535 GLN C 570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.176940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129927 restraints weight = 56186.624| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.84 r_work: 0.3190 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18136 Z= 0.109 Angle : 0.480 4.356 24620 Z= 0.250 Chirality : 0.045 0.377 2784 Planarity : 0.004 0.065 3136 Dihedral : 8.106 65.412 2692 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.79 % Allowed : 16.60 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % 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: 0.87 (0.18), residues: 2220 helix: 1.64 (0.17), residues: 988 sheet: -0.62 (0.26), residues: 332 loop : -0.02 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 334 TYR 0.011 0.001 TYR A 42 PHE 0.010 0.001 PHE B 523 TRP 0.006 0.001 TRP C 341 HIS 0.005 0.001 HIS D 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (18136) covalent geometry : angle 0.47970 / 0.25 (24620) hydrogen bonds : bond 0.02627 / 1.79 ( 848) hydrogen bonds : angle 4.39808 / 3.04 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12241.30 seconds wall clock time: 207 minutes 34.04 seconds (12454.04 seconds total)