Starting phenix.real_space_refine on Fri Jan 16 10:10:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mh1_23833/01_2026/7mh1_23833_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mh1_23833/01_2026/7mh1_23833.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/7mh1_23833/01_2026/7mh1_23833_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mh1_23833/01_2026/7mh1_23833_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mh1_23833/01_2026/7mh1_23833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mh1_23833/01_2026/7mh1_23833.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= 0.212 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 92 5.16 5 C 11308 2.51 5 N 3072 2.21 5 O 3332 1.98 5 H 17800 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35636 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 8849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 8849 Classifications: {'peptide': 557} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'CTP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: J, K, L Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU H 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU H 155 " occ=0.75 residue: pdb=" N CYS H 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS H 243 " occ=0.75 residue: pdb=" N GLU J 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU J 155 " occ=0.75 residue: pdb=" N CYS J 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS J 243 " occ=0.75 residue: pdb=" N GLU K 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU K 155 " occ=0.75 residue: pdb=" N CYS K 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS K 243 " occ=0.75 residue: pdb=" N GLU L 155 " occ=0.75 ... (13 atoms not shown) pdb=" HG3 GLU L 155 " occ=0.75 residue: pdb=" N CYS L 243 " occ=0.75 ... (9 atoms not shown) pdb=" HG CYS L 243 " occ=0.75 Time building chain proxies: 12.39, per 1000 atoms: 0.35 Number of scatterers: 35636 At special positions: 0 Unit cell: (122.85, 141.75, 91.35, 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 92 16.00 P 24 15.00 Mg 8 11.99 O 3332 8.00 N 3072 7.00 C 11308 6.00 H 17800 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: 3.28 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 4112 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 20 sheets defined 45.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'H' and resid 15 through 30 Processing helix chain 'H' and resid 69 through 78 removed outlier: 3.573A pdb=" N TYR H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 90 through 104 Processing helix chain 'H' and resid 115 through 130 removed outlier: 3.504A pdb=" N LYS H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 170 removed outlier: 4.628A pdb=" N PHE H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS H 169 " --> pdb=" O GLN H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 208 Processing helix chain 'H' and resid 223 through 235 Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 252 through 260 Processing helix chain 'H' and resid 261 through 270 removed outlier: 3.652A pdb=" N TYR H 265 " --> pdb=" O SER H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.939A pdb=" N TRP H 285 " --> pdb=" O LEU H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 340 through 349 removed outlier: 6.240A pdb=" N LYS H 344 " --> pdb=" O ASP H 341 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE H 345 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU H 347 " --> pdb=" O LYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 363 Processing helix chain 'H' and resid 377 through 391 Processing helix chain 'H' and resid 399 through 414 removed outlier: 3.674A pdb=" N PHE H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 468 Processing helix chain 'H' and resid 486 through 493 removed outlier: 3.712A pdb=" N ILE H 489 " --> pdb=" O PRO H 486 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS H 490 " --> pdb=" O ASN H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 531 removed outlier: 3.721A pdb=" N PHE H 529 " --> pdb=" O HIS H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 549 Processing helix chain 'H' and resid 550 through 555 Processing helix chain 'J' and resid 15 through 30 Processing helix chain 'J' and resid 69 through 78 removed outlier: 3.574A pdb=" N TYR J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 85 No H-bonds generated for 'chain 'J' and resid 83 through 85' Processing helix chain 'J' and resid 90 through 104 Processing helix chain 'J' and resid 115 through 130 removed outlier: 3.503A pdb=" N LYS J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 170 removed outlier: 4.628A pdb=" N PHE J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS J 169 " --> pdb=" O GLN J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 223 through 235 Processing helix chain 'J' and resid 237 through 239 No H-bonds generated for 'chain 'J' and resid 237 through 239' Processing helix chain 'J' and resid 249 through 251 No H-bonds generated for 'chain 'J' and resid 249 through 251' Processing helix chain 'J' and resid 252 through 260 Processing helix chain 'J' and resid 261 through 270 removed outlier: 3.652A pdb=" N TYR J 265 " --> pdb=" O SER J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 293 removed outlier: 3.939A pdb=" N TRP J 285 " --> pdb=" O LEU J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 328 Processing helix chain 'J' and resid 340 through 349 removed outlier: 6.241A pdb=" N LYS J 344 " --> pdb=" O ASP J 341 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE J 345 " --> pdb=" O LEU J 342 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU J 347 " --> pdb=" O LYS J 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 363 Processing helix chain 'J' and resid 377 through 391 Processing helix chain 'J' and resid 399 through 414 removed outlier: 3.674A pdb=" N PHE J 409 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 486 through 493 removed outlier: 3.711A pdb=" N ILE J 489 " --> pdb=" O PRO J 486 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS J 490 " --> pdb=" O ASN J 487 " (cutoff:3.500A) Processing helix chain 'J' and resid 526 through 531 removed outlier: 3.721A pdb=" N PHE J 529 " --> pdb=" O HIS J 526 " (cutoff:3.500A) Processing helix chain 'J' and resid 537 through 549 Processing helix chain 'J' and resid 550 through 555 Processing helix chain 'K' and resid 15 through 30 Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.573A pdb=" N TYR K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 90 through 104 Processing helix chain 'K' and resid 115 through 130 removed outlier: 3.503A pdb=" N LYS K 130 " --> pdb=" O MET K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 170 removed outlier: 4.628A pdb=" N PHE K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS K 169 " --> pdb=" O GLN K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 208 Processing helix chain 'K' and resid 223 through 235 Processing helix chain 'K' and resid 237 through 239 No H-bonds generated for 'chain 'K' and resid 237 through 239' Processing helix chain 'K' and resid 249 through 251 No H-bonds generated for 'chain 'K' and resid 249 through 251' Processing helix chain 'K' and resid 252 through 260 Processing helix chain 'K' and resid 261 through 270 removed outlier: 3.652A pdb=" N TYR K 265 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 281 through 293 removed outlier: 3.939A pdb=" N TRP K 285 " --> pdb=" O LEU K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 328 Processing helix chain 'K' and resid 340 through 349 removed outlier: 6.241A pdb=" N LYS K 344 " --> pdb=" O ASP K 341 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE K 345 " --> pdb=" O LEU K 342 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU K 347 " --> pdb=" O LYS K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 363 Processing helix chain 'K' and resid 377 through 391 Processing helix chain 'K' and resid 399 through 414 removed outlier: 3.675A pdb=" N PHE K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 486 through 493 removed outlier: 3.712A pdb=" N ILE K 489 " --> pdb=" O PRO K 486 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS K 490 " --> pdb=" O ASN K 487 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 531 removed outlier: 3.721A pdb=" N PHE K 529 " --> pdb=" O HIS K 526 " (cutoff:3.500A) Processing helix chain 'K' and resid 537 through 549 Processing helix chain 'K' and resid 550 through 555 Processing helix chain 'L' and resid 15 through 30 Processing helix chain 'L' and resid 69 through 78 removed outlier: 3.574A pdb=" N TYR L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 90 through 103 Processing helix chain 'L' and resid 115 through 130 removed outlier: 3.503A pdb=" N LYS L 130 " --> pdb=" O MET L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 170 removed outlier: 4.628A pdb=" N PHE L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS L 169 " --> pdb=" O GLN L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 208 Processing helix chain 'L' and resid 223 through 235 Processing helix chain 'L' and resid 237 through 239 No H-bonds generated for 'chain 'L' and resid 237 through 239' Processing helix chain 'L' and resid 249 through 251 No H-bonds generated for 'chain 'L' and resid 249 through 251' Processing helix chain 'L' and resid 252 through 260 Processing helix chain 'L' and resid 261 through 270 removed outlier: 3.652A pdb=" N TYR L 265 " --> pdb=" O SER L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 281 through 293 removed outlier: 3.939A pdb=" N TRP L 285 " --> pdb=" O LEU L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 328 Processing helix chain 'L' and resid 340 through 349 removed outlier: 6.241A pdb=" N LYS L 344 " --> pdb=" O ASP L 341 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE L 345 " --> pdb=" O LEU L 342 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU L 347 " --> pdb=" O LYS L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 363 Processing helix chain 'L' and resid 377 through 391 Processing helix chain 'L' and resid 399 through 414 removed outlier: 3.674A pdb=" N PHE L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 486 through 493 removed outlier: 3.713A pdb=" N ILE L 489 " --> pdb=" O PRO L 486 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS L 490 " --> pdb=" O ASN L 487 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 531 removed outlier: 3.721A pdb=" N PHE L 529 " --> pdb=" O HIS L 526 " (cutoff:3.500A) Processing helix chain 'L' and resid 537 through 549 Processing helix chain 'L' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'H' and resid 87 through 89 removed outlier: 8.112A pdb=" N ILE H 88 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS H 38 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY H 8 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY H 149 " --> pdb=" O GLY H 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR H 3 " --> pdb=" O CYS H 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU H 213 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASN H 177 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL H 215 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS H 179 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG H 217 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER H 181 " --> pdb=" O ARG H 217 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE H 214 " --> pdb=" O ILE H 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE H 244 " --> pdb=" O ILE H 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS H 216 " --> pdb=" O ILE H 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AA3, first strand: chain 'H' and resid 331 through 338 removed outlier: 6.388A pdb=" N CYS H 299 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET H 335 " --> pdb=" O CYS H 299 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE H 301 " --> pdb=" O MET H 335 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE H 337 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU H 303 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N GLY H 366 " --> pdb=" O ILE H 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER H 300 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU H 368 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA H 302 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE H 367 " --> pdb=" O LEU H 396 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL H 398 " --> pdb=" O ILE H 367 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL H 369 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE H 395 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL H 523 " --> pdb=" O PHE H 395 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY H 397 " --> pdb=" O VAL H 523 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE H 520 " --> pdb=" O LEU H 514 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET H 509 " --> pdb=" O GLN H 502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 502 " --> pdb=" O MET H 509 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE H 511 " --> pdb=" O VAL H 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 419 through 420 removed outlier: 3.690A pdb=" N ASP H 420 " --> pdb=" O VAL H 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 433 through 435 Processing sheet with id=AA6, first strand: chain 'J' and resid 87 through 89 removed outlier: 8.112A pdb=" N ILE J 88 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS J 38 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY J 8 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY J 149 " --> pdb=" O GLY J 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR J 3 " --> pdb=" O CYS J 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE J 178 " --> pdb=" O TYR J 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU J 5 " --> pdb=" O ILE J 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL J 180 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR J 7 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU J 182 " --> pdb=" O THR J 7 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU J 213 " --> pdb=" O PHE J 175 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN J 177 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL J 215 " --> pdb=" O ASN J 177 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS J 179 " --> pdb=" O VAL J 215 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG J 217 " --> pdb=" O HIS J 179 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER J 181 " --> pdb=" O ARG J 217 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE J 214 " --> pdb=" O ILE J 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE J 244 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS J 216 " --> pdb=" O ILE J 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 58 through 60 Processing sheet with id=AA8, first strand: chain 'J' and resid 331 through 338 removed outlier: 6.388A pdb=" N CYS J 299 " --> pdb=" O ASN J 333 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N MET J 335 " --> pdb=" O CYS J 299 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE J 301 " --> pdb=" O MET J 335 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE J 337 " --> pdb=" O ILE J 301 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU J 303 " --> pdb=" O ILE J 337 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N GLY J 366 " --> pdb=" O ILE J 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER J 300 " --> pdb=" O GLY J 366 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU J 368 " --> pdb=" O SER J 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA J 302 " --> pdb=" O LEU J 368 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE J 367 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL J 398 " --> pdb=" O ILE J 367 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL J 369 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE J 395 " --> pdb=" O VAL J 521 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL J 523 " --> pdb=" O PHE J 395 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY J 397 " --> pdb=" O VAL J 523 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE J 520 " --> pdb=" O LEU J 514 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET J 509 " --> pdb=" O GLN J 502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN J 502 " --> pdb=" O MET J 509 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE J 511 " --> pdb=" O VAL J 500 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 419 through 420 removed outlier: 3.691A pdb=" N ASP J 420 " --> pdb=" O VAL J 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'J' and resid 433 through 435 Processing sheet with id=AB2, first strand: chain 'K' and resid 87 through 89 removed outlier: 8.112A pdb=" N ILE K 88 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS K 38 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY K 8 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY K 149 " --> pdb=" O GLY K 8 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR K 3 " --> pdb=" O CYS K 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE K 178 " --> pdb=" O TYR K 3 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU K 5 " --> pdb=" O ILE K 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL K 180 " --> pdb=" O LEU K 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR K 7 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LEU K 182 " --> pdb=" O THR K 7 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LEU K 213 " --> pdb=" O PHE K 175 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN K 177 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL K 215 " --> pdb=" O ASN K 177 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS K 179 " --> pdb=" O VAL K 215 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ARG K 217 " --> pdb=" O HIS K 179 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER K 181 " --> pdb=" O ARG K 217 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE K 214 " --> pdb=" O ILE K 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE K 244 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS K 216 " --> pdb=" O ILE K 244 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'K' and resid 331 through 338 removed outlier: 6.387A pdb=" N CYS K 299 " --> pdb=" O ASN K 333 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET K 335 " --> pdb=" O CYS K 299 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE K 301 " --> pdb=" O MET K 335 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE K 337 " --> pdb=" O ILE K 301 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU K 303 " --> pdb=" O ILE K 337 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N GLY K 366 " --> pdb=" O ILE K 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER K 300 " --> pdb=" O GLY K 366 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEU K 368 " --> pdb=" O SER K 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA K 302 " --> pdb=" O LEU K 368 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE K 367 " --> pdb=" O LEU K 396 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL K 398 " --> pdb=" O ILE K 367 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL K 369 " --> pdb=" O VAL K 398 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE K 395 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL K 523 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY K 397 " --> pdb=" O VAL K 523 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE K 520 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET K 509 " --> pdb=" O GLN K 502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN K 502 " --> pdb=" O MET K 509 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE K 511 " --> pdb=" O VAL K 500 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 419 through 420 removed outlier: 3.690A pdb=" N ASP K 420 " --> pdb=" O VAL K 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'K' and resid 433 through 435 Processing sheet with id=AB7, first strand: chain 'L' and resid 87 through 89 removed outlier: 8.112A pdb=" N ILE L 88 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS L 38 " --> pdb=" O ILE L 88 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY L 8 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY L 149 " --> pdb=" O GLY L 8 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR L 3 " --> pdb=" O CYS L 176 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE L 178 " --> pdb=" O TYR L 3 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU L 5 " --> pdb=" O ILE L 178 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL L 180 " --> pdb=" O LEU L 5 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR L 7 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU L 182 " --> pdb=" O THR L 7 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU L 213 " --> pdb=" O PHE L 175 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN L 177 " --> pdb=" O LEU L 213 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL L 215 " --> pdb=" O ASN L 177 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N HIS L 179 " --> pdb=" O VAL L 215 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG L 217 " --> pdb=" O HIS L 179 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER L 181 " --> pdb=" O ARG L 217 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE L 214 " --> pdb=" O ILE L 242 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE L 244 " --> pdb=" O ILE L 214 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N CYS L 216 " --> pdb=" O ILE L 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 58 through 60 Processing sheet with id=AB9, first strand: chain 'L' and resid 331 through 338 removed outlier: 6.388A pdb=" N CYS L 299 " --> pdb=" O ASN L 333 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N MET L 335 " --> pdb=" O CYS L 299 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE L 301 " --> pdb=" O MET L 335 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE L 337 " --> pdb=" O ILE L 301 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU L 303 " --> pdb=" O ILE L 337 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N GLY L 366 " --> pdb=" O ILE L 298 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER L 300 " --> pdb=" O GLY L 366 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU L 368 " --> pdb=" O SER L 300 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA L 302 " --> pdb=" O LEU L 368 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE L 367 " --> pdb=" O LEU L 396 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL L 398 " --> pdb=" O ILE L 367 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL L 369 " --> pdb=" O VAL L 398 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE L 395 " --> pdb=" O VAL L 521 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL L 523 " --> pdb=" O PHE L 395 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY L 397 " --> pdb=" O VAL L 523 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE L 520 " --> pdb=" O LEU L 514 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET L 509 " --> pdb=" O GLN L 502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN L 502 " --> pdb=" O MET L 509 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE L 511 " --> pdb=" O VAL L 500 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 419 through 420 removed outlier: 3.690A pdb=" N ASP L 420 " --> pdb=" O VAL L 430 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'L' and resid 433 through 435 731 hydrogen bonds defined for protein. 2073 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: 9.48 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 1731 1.01 - 1.21: 16033 1.21 - 1.41: 7498 1.41 - 1.61: 10602 1.61 - 1.81: 144 Bond restraints: 36008 Sorted by residual: bond pdb=" N VAL K 97 " pdb=" H VAL K 97 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N ASN J 412 " pdb=" H ASN J 412 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N TYR K 106 " pdb=" H TYR K 106 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" NE ARG K 508 " pdb=" HE ARG K 508 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CD2 HIS J 96 " pdb=" HD2 HIS J 96 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 36003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 53505 2.65 - 5.29: 9393 5.29 - 7.94: 2176 7.94 - 10.59: 146 10.59 - 13.24: 52 Bond angle restraints: 65272 Sorted by residual: angle pdb=" N PRO K 538 " pdb=" CA PRO K 538 " pdb=" C PRO K 538 " ideal model delta sigma weight residual 110.70 118.62 -7.92 1.22e+00 6.72e-01 4.21e+01 angle pdb=" N PRO H 538 " pdb=" CA PRO H 538 " pdb=" C PRO H 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO J 538 " pdb=" CA PRO J 538 " pdb=" C PRO J 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO L 538 " pdb=" CA PRO L 538 " pdb=" C PRO L 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" CA ASN K 443 " pdb=" CB ASN K 443 " pdb=" CG ASN K 443 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.00e+00 1.00e+00 4.12e+01 ... (remaining 65267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16052 35.09 - 70.19: 724 70.19 - 105.28: 46 105.28 - 140.37: 8 140.37 - 175.46: 10 Dihedral angle restraints: 16840 sinusoidal: 9388 harmonic: 7452 Sorted by residual: dihedral pdb=" O1G CTP J 604 " pdb=" O3B CTP J 604 " pdb=" PG CTP J 604 " pdb=" PB CTP J 604 " ideal model delta sinusoidal sigma weight residual 82.72 -101.82 -175.46 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1G CTP K 603 " pdb=" O3B CTP K 603 " pdb=" PG CTP K 603 " pdb=" PB CTP K 603 " ideal model delta sinusoidal sigma weight residual 82.72 -101.87 -175.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A CTP K 601 " pdb=" O3B CTP K 601 " pdb=" PB CTP K 601 " pdb=" PG CTP K 601 " ideal model delta sinusoidal sigma weight residual 204.50 46.10 158.40 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1568 0.080 - 0.161: 756 0.161 - 0.241: 348 0.241 - 0.321: 60 0.321 - 0.402: 16 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CA PRO K 538 " pdb=" N PRO K 538 " pdb=" C PRO K 538 " pdb=" CB PRO K 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA PRO H 538 " pdb=" N PRO H 538 " pdb=" C PRO H 538 " pdb=" CB PRO H 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA PRO J 538 " pdb=" N PRO J 538 " pdb=" C PRO J 538 " pdb=" CB PRO J 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 2745 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 269 " 0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG J 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG J 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG J 269 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG J 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG J 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG J 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG J 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG J 269 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 269 " -0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG L 269 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG L 269 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG L 269 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG L 269 " 0.109 2.00e-02 2.50e+03 pdb="HH11 ARG L 269 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG L 269 " 0.050 2.00e-02 2.50e+03 pdb="HH21 ARG L 269 " 0.044 2.00e-02 2.50e+03 pdb="HH22 ARG L 269 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 269 " 0.522 9.50e-02 1.11e+02 1.90e-01 1.56e+02 pdb=" NE ARG H 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG H 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG H 269 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG H 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG H 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG H 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG H 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG H 269 " 0.173 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1171 2.06 - 2.70: 49467 2.70 - 3.33: 111381 3.33 - 3.97: 147939 3.97 - 4.60: 217689 Nonbonded interactions: 527647 Sorted by model distance: nonbonded pdb="HD21 ASN K 44 " pdb=" HE1 PHE K 50 " model vdw 1.426 2.100 nonbonded pdb="HD21 ASN J 44 " pdb=" HE1 PHE J 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN H 44 " pdb=" HE1 PHE H 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN L 44 " pdb=" HE1 PHE L 50 " model vdw 1.427 2.100 nonbonded pdb=" HG1 THR H 49 " pdb=" OE2 GLU K 101 " model vdw 1.579 2.450 ... (remaining 527642 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'H' and resid 1 through 557) selection = (chain 'J' and resid 1 through 557) selection = (chain 'K' and resid 1 through 557) selection = (chain 'L' and resid 1 through 557) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 40.730 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.012 0.053 18208 Z= 0.766 Angle : 2.030 12.894 24688 Z= 1.339 Chirality : 0.110 0.402 2748 Planarity : 0.016 0.155 3172 Dihedral : 16.816 175.465 6884 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.44 % Allowed : 7.22 % Favored : 91.34 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 3.45 % 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: -1.16 (0.16), residues: 2220 helix: -0.97 (0.15), residues: 880 sheet: -0.74 (0.24), residues: 372 loop : -0.34 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG K 269 TYR 0.135 0.021 TYR L 307 PHE 0.085 0.013 PHE K 163 TRP 0.100 0.023 TRP K 285 HIS 0.011 0.004 HIS L 235 Details of bonding type rmsd covalent geometry : bond 0.01221 (18208) covalent geometry : angle 2.02984 (24688) hydrogen bonds : bond 0.18312 ( 731) hydrogen bonds : angle 7.61362 ( 2073) *********************** 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 **************************** Evaluate side-chains 493 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 465 time to evaluate : 0.865 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: 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: 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: H 68 ASP cc_start: 0.6846 (t0) cc_final: 0.6467 (t0) REVERT: H 75 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7723 (mt-10) REVERT: H 78 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8150 (mp) REVERT: H 123 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6704 (mt-10) REVERT: H 134 ASP cc_start: 0.7293 (t0) cc_final: 0.7092 (t70) REVERT: H 172 ARG cc_start: 0.7537 (tpt170) cc_final: 0.7293 (tpt90) REVERT: H 224 MET cc_start: 0.6998 (tpt) cc_final: 0.6680 (tpp) REVERT: H 322 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6995 (mt-10) REVERT: H 402 MET cc_start: 0.8501 (tmt) cc_final: 0.7810 (tmt) REVERT: H 513 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6404 (tm-30) REVERT: H 514 LEU cc_start: 0.7909 (tp) cc_final: 0.7348 (tp) REVERT: J 68 ASP cc_start: 0.6847 (t0) cc_final: 0.6438 (t0) REVERT: J 78 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8156 (mp) REVERT: J 123 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6764 (mt-10) REVERT: J 224 MET cc_start: 0.6945 (tpt) cc_final: 0.6654 (tpp) REVERT: J 322 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6982 (mt-10) REVERT: J 402 MET cc_start: 0.8497 (tmt) cc_final: 0.7844 (tmt) REVERT: J 507 ASP cc_start: 0.6878 (m-30) cc_final: 0.6617 (m-30) REVERT: J 513 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6338 (tt0) REVERT: K 68 ASP cc_start: 0.6827 (t0) cc_final: 0.6447 (t0) REVERT: K 75 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7685 (mt-10) REVERT: K 78 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8143 (mp) REVERT: K 123 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6773 (mt-10) REVERT: K 134 ASP cc_start: 0.7361 (t0) cc_final: 0.7128 (t70) REVERT: K 224 MET cc_start: 0.6975 (tpt) cc_final: 0.6648 (tpp) REVERT: K 322 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7041 (mt-10) REVERT: K 402 MET cc_start: 0.8510 (tmt) cc_final: 0.7857 (tmt) REVERT: K 408 GLU cc_start: 0.7468 (pp20) cc_final: 0.7177 (pp20) REVERT: K 513 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6412 (tm-30) REVERT: K 514 LEU cc_start: 0.7903 (tp) cc_final: 0.7367 (tp) REVERT: L 68 ASP cc_start: 0.6825 (t0) cc_final: 0.6454 (t0) REVERT: L 75 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7671 (mt-10) REVERT: L 78 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8139 (mp) REVERT: L 123 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6785 (mt-10) REVERT: L 224 MET cc_start: 0.6965 (tpt) cc_final: 0.6653 (tpp) REVERT: L 322 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7074 (mt-10) REVERT: L 408 GLU cc_start: 0.7476 (pp20) cc_final: 0.7273 (pp20) REVERT: L 476 GLU cc_start: 0.7306 (mm-30) cc_final: 0.7087 (mm-30) REVERT: L 509 MET cc_start: 0.6612 (mmt) cc_final: 0.6408 (mmm) REVERT: L 513 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6402 (tm-30) REVERT: L 514 LEU cc_start: 0.7923 (tp) cc_final: 0.7382 (tp) outliers start: 28 outliers final: 4 residues processed: 485 average time/residue: 1.2485 time to fit residues: 686.1813 Evaluate side-chains 369 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 361 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 ASN H 165 GLN H 185 GLN H 287 ASN H 440 ASN H 443 ASN J 86 ASN J 165 GLN J 185 GLN J 287 ASN J 440 ASN J 443 ASN K 86 ASN K 165 GLN K 287 ASN K 440 ASN K 443 ASN L 86 ASN L 165 GLN L 185 GLN L 440 ASN L 443 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123208 restraints weight = 55235.627| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.91 r_work: 0.3204 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18208 Z= 0.154 Angle : 0.694 7.005 24688 Z= 0.352 Chirality : 0.048 0.152 2748 Planarity : 0.005 0.052 3172 Dihedral : 14.355 179.014 2532 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.14 % Allowed : 14.23 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.31 (0.17), residues: 2220 helix: 0.13 (0.16), residues: 904 sheet: -0.44 (0.24), residues: 392 loop : -0.23 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 252 TYR 0.013 0.002 TYR H 265 PHE 0.019 0.002 PHE J 424 TRP 0.011 0.001 TRP K 358 HIS 0.006 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00356 (18208) covalent geometry : angle 0.69425 (24688) hydrogen bonds : bond 0.04577 ( 731) hydrogen bonds : angle 5.23309 ( 2073) *********************** 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 **************************** Evaluate side-chains 443 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 28 LYS cc_start: 0.7749 (tptp) cc_final: 0.7503 (tttp) REVERT: H 49 THR cc_start: 0.9014 (m) cc_final: 0.8637 (p) REVERT: H 54 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6856 (mt-10) REVERT: H 78 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7824 (mp) REVERT: H 123 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7616 (mt-10) REVERT: H 157 MET cc_start: 0.8607 (mmt) cc_final: 0.8350 (mmt) REVERT: H 212 ASP cc_start: 0.8769 (m-30) cc_final: 0.8484 (m-30) REVERT: H 224 MET cc_start: 0.7602 (tpt) cc_final: 0.7057 (tpp) REVERT: H 228 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: H 258 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: H 500 VAL cc_start: 0.9081 (m) cc_final: 0.8647 (p) REVERT: H 543 LEU cc_start: 0.8310 (tm) cc_final: 0.8005 (tt) REVERT: J 49 THR cc_start: 0.9014 (m) cc_final: 0.8649 (p) REVERT: J 54 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6830 (mt-10) REVERT: J 78 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7751 (mp) REVERT: J 123 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7759 (tt0) REVERT: J 172 ARG cc_start: 0.7778 (tpt90) cc_final: 0.7370 (tpt170) REVERT: J 212 ASP cc_start: 0.8770 (m-30) cc_final: 0.8462 (m-30) REVERT: J 224 MET cc_start: 0.7564 (tpt) cc_final: 0.7022 (tpp) REVERT: J 228 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: J 239 GLU cc_start: 0.7776 (mp0) cc_final: 0.7524 (mp0) REVERT: J 500 VAL cc_start: 0.9068 (m) cc_final: 0.8626 (p) REVERT: J 507 ASP cc_start: 0.7147 (m-30) cc_final: 0.6897 (m-30) REVERT: J 513 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6434 (tt0) REVERT: J 543 LEU cc_start: 0.8340 (tm) cc_final: 0.8025 (tt) REVERT: K 49 THR cc_start: 0.9002 (m) cc_final: 0.8650 (p) REVERT: K 54 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7026 (mt-10) REVERT: K 78 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7765 (mp) REVERT: K 123 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7664 (mt-10) REVERT: K 157 MET cc_start: 0.8614 (mmt) cc_final: 0.8343 (mmt) REVERT: K 212 ASP cc_start: 0.8767 (m-30) cc_final: 0.8483 (m-30) REVERT: K 224 MET cc_start: 0.7581 (tpt) cc_final: 0.6810 (tpp) REVERT: K 227 LYS cc_start: 0.7992 (mttt) cc_final: 0.7651 (mttp) REVERT: K 228 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: K 322 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7498 (mt-10) REVERT: K 329 ASN cc_start: 0.7253 (OUTLIER) cc_final: 0.7033 (t0) REVERT: K 500 VAL cc_start: 0.9086 (m) cc_final: 0.8627 (p) REVERT: K 543 LEU cc_start: 0.8344 (tm) cc_final: 0.8026 (tt) REVERT: L 49 THR cc_start: 0.9015 (m) cc_final: 0.8606 (p) REVERT: L 123 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7665 (mt-10) REVERT: L 224 MET cc_start: 0.7539 (tpt) cc_final: 0.7022 (tpp) REVERT: L 227 LYS cc_start: 0.8002 (mttt) cc_final: 0.7703 (mtpp) REVERT: L 228 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: L 258 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6996 (tp30) REVERT: L 322 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7324 (mt-10) REVERT: L 329 ASN cc_start: 0.7224 (OUTLIER) cc_final: 0.6741 (t0) REVERT: L 500 VAL cc_start: 0.9069 (m) cc_final: 0.8639 (p) REVERT: L 543 LEU cc_start: 0.8343 (tm) cc_final: 0.8037 (tt) outliers start: 61 outliers final: 10 residues processed: 419 average time/residue: 1.2724 time to fit residues: 603.6068 Evaluate side-chains 365 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 344 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 329 ASN Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 87 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN H 287 ASN H 323 HIS J 323 HIS K 136 ASN K 323 HIS L 287 ASN L 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118148 restraints weight = 54831.385| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.92 r_work: 0.3115 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18208 Z= 0.223 Angle : 0.690 6.937 24688 Z= 0.346 Chirality : 0.048 0.148 2748 Planarity : 0.005 0.056 3172 Dihedral : 12.981 173.217 2530 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.09 % Allowed : 15.57 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.05 (0.18), residues: 2220 helix: 0.56 (0.17), residues: 912 sheet: -0.56 (0.24), residues: 388 loop : -0.03 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 252 TYR 0.014 0.002 TYR J 265 PHE 0.015 0.002 PHE L 163 TRP 0.012 0.002 TRP J 358 HIS 0.006 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00527 (18208) covalent geometry : angle 0.68965 (24688) hydrogen bonds : bond 0.04421 ( 731) hydrogen bonds : angle 4.87998 ( 2073) *********************** 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 **************************** Evaluate side-chains 429 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 369 time to evaluate : 1.004 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: H 49 THR cc_start: 0.9140 (m) cc_final: 0.8802 (p) REVERT: H 54 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6826 (mt-10) REVERT: H 78 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7737 (mp) REVERT: H 102 ARG cc_start: 0.8384 (mmm160) cc_final: 0.8155 (mmp-170) REVERT: H 109 LYS cc_start: 0.8741 (mttm) cc_final: 0.8533 (mttm) REVERT: H 123 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7892 (tt0) REVERT: H 224 MET cc_start: 0.7571 (tpt) cc_final: 0.7059 (tpp) REVERT: H 228 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: H 252 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8141 (ttm-80) REVERT: H 258 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: H 267 LYS cc_start: 0.7913 (tttm) cc_final: 0.7447 (tttt) REVERT: H 500 VAL cc_start: 0.9083 (m) cc_final: 0.8576 (p) REVERT: H 543 LEU cc_start: 0.8262 (tm) cc_final: 0.7935 (tt) REVERT: J 49 THR cc_start: 0.9141 (m) cc_final: 0.8804 (p) REVERT: J 54 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6794 (mt-10) REVERT: J 78 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7716 (mp) REVERT: J 123 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7900 (tt0) REVERT: J 172 ARG cc_start: 0.7854 (tpt90) cc_final: 0.7300 (tpt170) REVERT: J 224 MET cc_start: 0.7529 (tpt) cc_final: 0.7005 (tpp) REVERT: J 228 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: J 239 GLU cc_start: 0.7819 (mp0) cc_final: 0.7490 (mp0) REVERT: J 252 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: J 260 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: J 475 GLU cc_start: 0.7846 (tt0) cc_final: 0.7618 (mt-10) REVERT: J 500 VAL cc_start: 0.9087 (m) cc_final: 0.8570 (p) REVERT: J 543 LEU cc_start: 0.8293 (tm) cc_final: 0.7954 (tt) REVERT: K 49 THR cc_start: 0.9128 (m) cc_final: 0.8795 (p) REVERT: K 54 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6858 (mt-10) REVERT: K 78 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7735 (mp) REVERT: K 123 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7888 (mt-10) REVERT: K 224 MET cc_start: 0.7558 (tpt) cc_final: 0.7031 (tpp) REVERT: K 228 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: K 252 ARG cc_start: 0.8481 (ttm-80) cc_final: 0.8277 (ttm-80) REVERT: K 260 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: K 261 SER cc_start: 0.8805 (t) cc_final: 0.8562 (p) REVERT: K 267 LYS cc_start: 0.7895 (tttm) cc_final: 0.7426 (tttt) REVERT: K 322 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7652 (mt-10) REVERT: K 365 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7489 (t0) REVERT: K 481 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6708 (mtp85) REVERT: K 500 VAL cc_start: 0.9093 (m) cc_final: 0.8562 (p) REVERT: K 543 LEU cc_start: 0.8303 (tm) cc_final: 0.7958 (tt) REVERT: L 49 THR cc_start: 0.9103 (m) cc_final: 0.8763 (p) REVERT: L 54 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6939 (mt-10) REVERT: L 78 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7682 (mp) REVERT: L 123 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7859 (tt0) REVERT: L 224 MET cc_start: 0.7531 (tpt) cc_final: 0.7019 (tpp) REVERT: L 228 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: L 252 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8260 (ttm-80) REVERT: L 258 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: L 260 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: L 267 LYS cc_start: 0.7957 (tttm) cc_final: 0.7499 (tttt) REVERT: L 322 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7443 (mt-10) REVERT: L 329 ASN cc_start: 0.7444 (t0) cc_final: 0.6917 (t0) REVERT: L 500 VAL cc_start: 0.9089 (m) cc_final: 0.8586 (p) REVERT: L 543 LEU cc_start: 0.8286 (tm) cc_final: 0.7956 (tt) outliers start: 60 outliers final: 20 residues processed: 408 average time/residue: 1.3905 time to fit residues: 637.8785 Evaluate side-chains 380 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 346 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN H 517 HIS J 287 ASN L 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.163235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118010 restraints weight = 54597.316| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.93 r_work: 0.3118 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18208 Z= 0.194 Angle : 0.641 6.954 24688 Z= 0.320 Chirality : 0.046 0.149 2748 Planarity : 0.005 0.052 3172 Dihedral : 12.486 167.085 2530 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.40 % Allowed : 15.88 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.18 (0.18), residues: 2220 helix: 0.75 (0.17), residues: 920 sheet: -0.64 (0.24), residues: 388 loop : 0.01 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 252 TYR 0.014 0.002 TYR H 265 PHE 0.014 0.001 PHE K 163 TRP 0.009 0.002 TRP J 358 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00454 (18208) covalent geometry : angle 0.64147 (24688) hydrogen bonds : bond 0.03883 ( 731) hydrogen bonds : angle 4.68283 ( 2073) *********************** 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 **************************** Evaluate side-chains 416 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 350 time to evaluate : 0.926 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: H 49 THR cc_start: 0.9151 (m) cc_final: 0.8804 (p) REVERT: H 78 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7714 (mp) REVERT: H 123 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7936 (tt0) REVERT: H 224 MET cc_start: 0.7630 (tpt) cc_final: 0.7116 (tpp) REVERT: H 228 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: H 252 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8120 (ttm-80) REVERT: H 258 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: H 260 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: H 500 VAL cc_start: 0.9091 (m) cc_final: 0.8568 (p) REVERT: H 543 LEU cc_start: 0.8293 (tm) cc_final: 0.7969 (tt) REVERT: J 49 THR cc_start: 0.9153 (m) cc_final: 0.8816 (p) REVERT: J 78 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7697 (mp) REVERT: J 123 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7958 (tt0) REVERT: J 172 ARG cc_start: 0.7869 (tpt90) cc_final: 0.7489 (tpt170) REVERT: J 224 MET cc_start: 0.7538 (tpt) cc_final: 0.7014 (tpp) REVERT: J 228 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: J 239 GLU cc_start: 0.7850 (mp0) cc_final: 0.7488 (mp0) REVERT: J 252 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: J 260 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: J 261 SER cc_start: 0.8834 (t) cc_final: 0.8604 (p) REVERT: J 475 GLU cc_start: 0.7990 (tt0) cc_final: 0.7742 (mt-10) REVERT: J 500 VAL cc_start: 0.9070 (m) cc_final: 0.8524 (p) REVERT: J 543 LEU cc_start: 0.8310 (tm) cc_final: 0.7990 (tt) REVERT: K 49 THR cc_start: 0.9143 (m) cc_final: 0.8795 (p) REVERT: K 78 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7695 (mp) REVERT: K 123 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7931 (tt0) REVERT: K 224 MET cc_start: 0.7607 (tpt) cc_final: 0.7042 (tpp) REVERT: K 228 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: K 260 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: K 261 SER cc_start: 0.8825 (t) cc_final: 0.8585 (p) REVERT: K 267 LYS cc_start: 0.7903 (tttm) cc_final: 0.7452 (tttt) REVERT: K 291 ARG cc_start: 0.7099 (ttp-170) cc_final: 0.6515 (ttp80) REVERT: K 322 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7437 (mt-10) REVERT: K 365 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7368 (t0) REVERT: K 481 ARG cc_start: 0.7251 (mtp180) cc_final: 0.6737 (mtp85) REVERT: K 543 LEU cc_start: 0.8304 (tm) cc_final: 0.7987 (tt) REVERT: K 544 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8035 (mp) REVERT: L 49 THR cc_start: 0.9134 (m) cc_final: 0.8788 (p) REVERT: L 78 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7633 (mp) REVERT: L 123 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7926 (tt0) REVERT: L 171 LYS cc_start: 0.7621 (mptt) cc_final: 0.6894 (mtpp) REVERT: L 224 MET cc_start: 0.7561 (tpt) cc_final: 0.7046 (tpp) REVERT: L 228 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: L 252 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8311 (ttm-80) REVERT: L 258 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: L 260 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: L 261 SER cc_start: 0.8843 (t) cc_final: 0.8614 (m) REVERT: L 322 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7445 (mt-10) REVERT: L 329 ASN cc_start: 0.7354 (t0) cc_final: 0.6816 (t0) REVERT: L 473 PHE cc_start: 0.8218 (p90) cc_final: 0.7939 (p90) REVERT: L 481 ARG cc_start: 0.6966 (mmm-85) cc_final: 0.6155 (mtp85) REVERT: L 500 VAL cc_start: 0.9102 (m) cc_final: 0.8572 (p) REVERT: L 543 LEU cc_start: 0.8304 (tm) cc_final: 0.7979 (tt) outliers start: 66 outliers final: 29 residues processed: 400 average time/residue: 1.3803 time to fit residues: 620.3530 Evaluate side-chains 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 343 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 365 ASP Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 0.0980 chunk 157 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 214 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 287 ASN J 517 HIS K 287 ASN K 517 HIS L 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.163800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118801 restraints weight = 54733.722| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.93 r_work: 0.3127 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18208 Z= 0.164 Angle : 0.612 6.864 24688 Z= 0.303 Chirality : 0.045 0.147 2748 Planarity : 0.005 0.050 3172 Dihedral : 11.958 160.262 2530 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.76 % Allowed : 16.19 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.30 (0.18), residues: 2220 helix: 0.99 (0.18), residues: 920 sheet: -0.65 (0.25), residues: 348 loop : -0.09 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 389 TYR 0.011 0.001 TYR H 42 PHE 0.012 0.001 PHE K 163 TRP 0.010 0.002 TRP K 358 HIS 0.004 0.001 HIS L 96 Details of bonding type rmsd covalent geometry : bond 0.00386 (18208) covalent geometry : angle 0.61207 (24688) hydrogen bonds : bond 0.03596 ( 731) hydrogen bonds : angle 4.51051 ( 2073) *********************** 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 **************************** Evaluate side-chains 426 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 353 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 THR cc_start: 0.9161 (m) cc_final: 0.8808 (p) REVERT: H 54 GLU cc_start: 0.7312 (mp0) cc_final: 0.7087 (mt-10) REVERT: H 78 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7673 (mp) REVERT: H 123 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7933 (tt0) REVERT: H 224 MET cc_start: 0.7608 (tpt) cc_final: 0.7097 (tpp) REVERT: H 228 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: H 252 ARG cc_start: 0.8394 (ttm-80) cc_final: 0.8138 (ttm-80) REVERT: H 258 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6939 (tp30) REVERT: H 260 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8116 (mt0) REVERT: H 500 VAL cc_start: 0.9070 (m) cc_final: 0.8531 (p) REVERT: H 543 LEU cc_start: 0.8287 (tm) cc_final: 0.7993 (tt) REVERT: H 544 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8010 (mp) REVERT: J 49 THR cc_start: 0.9162 (m) cc_final: 0.8821 (p) REVERT: J 78 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7663 (mp) REVERT: J 123 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7948 (tt0) REVERT: J 172 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7469 (tpt170) REVERT: J 224 MET cc_start: 0.7575 (tpt) cc_final: 0.7048 (tpp) REVERT: J 228 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: J 239 GLU cc_start: 0.7895 (mp0) cc_final: 0.7596 (mp0) REVERT: J 252 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8241 (ttm-80) REVERT: J 258 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7190 (tp30) REVERT: J 260 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: J 261 SER cc_start: 0.8846 (t) cc_final: 0.8607 (p) REVERT: J 475 GLU cc_start: 0.7839 (tt0) cc_final: 0.7594 (mt-10) REVERT: J 481 ARG cc_start: 0.6948 (mtm-85) cc_final: 0.6560 (mtm110) REVERT: J 500 VAL cc_start: 0.9061 (m) cc_final: 0.8513 (p) REVERT: J 543 LEU cc_start: 0.8378 (tm) cc_final: 0.8035 (tt) REVERT: K 28 LYS cc_start: 0.7870 (tptp) cc_final: 0.7620 (tttp) REVERT: K 49 THR cc_start: 0.9176 (m) cc_final: 0.8845 (p) REVERT: K 123 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7920 (tt0) REVERT: K 224 MET cc_start: 0.7591 (tpt) cc_final: 0.7058 (tpp) REVERT: K 228 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: K 261 SER cc_start: 0.8809 (t) cc_final: 0.8561 (p) REVERT: K 267 LYS cc_start: 0.7904 (tttm) cc_final: 0.7436 (tttt) REVERT: K 481 ARG cc_start: 0.7290 (mtp180) cc_final: 0.6773 (mtp85) REVERT: K 543 LEU cc_start: 0.8283 (tm) cc_final: 0.7986 (tt) REVERT: K 544 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.8009 (mp) REVERT: L 78 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7604 (mp) REVERT: L 123 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7943 (tt0) REVERT: L 224 MET cc_start: 0.7612 (tpt) cc_final: 0.7063 (tpp) REVERT: L 228 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: L 258 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: L 260 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: L 261 SER cc_start: 0.8852 (t) cc_final: 0.8498 (p) REVERT: L 322 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7348 (mt-10) REVERT: L 329 ASN cc_start: 0.7346 (t0) cc_final: 0.6810 (t0) REVERT: L 481 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6085 (mtp85) REVERT: L 500 VAL cc_start: 0.9079 (m) cc_final: 0.8541 (p) REVERT: L 543 LEU cc_start: 0.8332 (tm) cc_final: 0.7996 (tt) REVERT: L 544 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8023 (mp) outliers start: 73 outliers final: 32 residues processed: 406 average time/residue: 1.3165 time to fit residues: 602.3830 Evaluate side-chains 391 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 344 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 544 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 544 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 168 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 287 ASN L 287 ASN L 517 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.117555 restraints weight = 54468.033| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.94 r_work: 0.3115 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18208 Z= 0.196 Angle : 0.626 6.889 24688 Z= 0.310 Chirality : 0.046 0.145 2748 Planarity : 0.005 0.052 3172 Dihedral : 11.953 163.864 2528 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.35 % Allowed : 16.75 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.30 (0.18), residues: 2220 helix: 0.99 (0.18), residues: 920 sheet: -0.62 (0.26), residues: 348 loop : -0.11 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 389 TYR 0.012 0.002 TYR H 42 PHE 0.013 0.001 PHE K 163 TRP 0.008 0.002 TRP J 358 HIS 0.005 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00462 (18208) covalent geometry : angle 0.62637 (24688) hydrogen bonds : bond 0.03672 ( 731) hydrogen bonds : angle 4.49659 ( 2073) *********************** 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 **************************** Evaluate side-chains 412 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 347 time to evaluate : 0.894 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: H 54 GLU cc_start: 0.7323 (mp0) cc_final: 0.7086 (mt-10) REVERT: H 78 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7685 (mp) REVERT: H 224 MET cc_start: 0.7699 (tpt) cc_final: 0.7156 (tpp) REVERT: H 228 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: H 252 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8146 (ttm-80) REVERT: H 258 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: H 260 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: H 286 ARG cc_start: 0.7022 (ttt90) cc_final: 0.6525 (ttp-110) REVERT: H 365 ASP cc_start: 0.7697 (t0) cc_final: 0.7337 (t0) REVERT: H 481 ARG cc_start: 0.7061 (mtm-85) cc_final: 0.6190 (mtp85) REVERT: H 500 VAL cc_start: 0.9059 (m) cc_final: 0.8505 (p) REVERT: H 543 LEU cc_start: 0.8346 (tm) cc_final: 0.8005 (tt) REVERT: J 78 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7670 (mp) REVERT: J 123 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7962 (tt0) REVERT: J 172 ARG cc_start: 0.7960 (tpt90) cc_final: 0.7521 (tpt170) REVERT: J 224 MET cc_start: 0.7649 (tpt) cc_final: 0.7087 (tpp) REVERT: J 228 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: J 239 GLU cc_start: 0.7915 (mp0) cc_final: 0.7586 (mp0) REVERT: J 252 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: J 260 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: J 261 SER cc_start: 0.8889 (t) cc_final: 0.8618 (p) REVERT: J 286 ARG cc_start: 0.7011 (ttt90) cc_final: 0.6467 (ttp-110) REVERT: J 365 ASP cc_start: 0.7743 (t0) cc_final: 0.7246 (t0) REVERT: J 481 ARG cc_start: 0.6964 (mtm-85) cc_final: 0.6552 (mtm110) REVERT: J 535 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7840 (pptt) REVERT: J 543 LEU cc_start: 0.8410 (tm) cc_final: 0.8066 (tt) REVERT: K 28 LYS cc_start: 0.7901 (tptp) cc_final: 0.7648 (tttp) REVERT: K 123 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7939 (tt0) REVERT: K 224 MET cc_start: 0.7642 (tpt) cc_final: 0.7113 (tpp) REVERT: K 228 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: K 261 SER cc_start: 0.8820 (t) cc_final: 0.8565 (p) REVERT: K 481 ARG cc_start: 0.7292 (mtp180) cc_final: 0.6748 (mtp85) REVERT: K 543 LEU cc_start: 0.8344 (tm) cc_final: 0.7997 (tt) REVERT: L 78 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7605 (mp) REVERT: L 123 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7937 (tt0) REVERT: L 171 LYS cc_start: 0.7565 (mptt) cc_final: 0.6934 (mmmm) REVERT: L 224 MET cc_start: 0.7670 (tpt) cc_final: 0.7111 (tpp) REVERT: L 228 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: L 258 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: L 260 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: L 261 SER cc_start: 0.8883 (t) cc_final: 0.8496 (p) REVERT: L 329 ASN cc_start: 0.7343 (t0) cc_final: 0.6791 (t0) REVERT: L 365 ASP cc_start: 0.7741 (t0) cc_final: 0.7290 (t0) REVERT: L 473 PHE cc_start: 0.8183 (p90) cc_final: 0.7889 (p90) REVERT: L 481 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6160 (mtp85) REVERT: L 500 VAL cc_start: 0.9078 (m) cc_final: 0.8524 (p) REVERT: L 535 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (pptt) REVERT: L 543 LEU cc_start: 0.8344 (tm) cc_final: 0.8003 (tt) outliers start: 65 outliers final: 29 residues processed: 399 average time/residue: 1.3578 time to fit residues: 609.8552 Evaluate side-chains 389 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 346 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 104 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 1 optimal weight: 0.0970 chunk 187 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 167 GLN J 287 ASN L 167 GLN L 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.119959 restraints weight = 54619.427| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.92 r_work: 0.3148 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18208 Z= 0.135 Angle : 0.586 6.768 24688 Z= 0.288 Chirality : 0.045 0.150 2748 Planarity : 0.005 0.052 3172 Dihedral : 11.375 154.678 2528 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.99 % Allowed : 17.37 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.49 (0.18), residues: 2220 helix: 1.20 (0.18), residues: 920 sheet: -0.64 (0.26), residues: 348 loop : -0.01 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 389 TYR 0.012 0.001 TYR K 265 PHE 0.012 0.001 PHE J 409 TRP 0.008 0.001 TRP K 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00317 (18208) covalent geometry : angle 0.58553 (24688) hydrogen bonds : bond 0.03302 ( 731) hydrogen bonds : angle 4.35754 ( 2073) *********************** 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 **************************** Evaluate side-chains 404 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.967 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: H 18 ILE cc_start: 0.9312 (tp) cc_final: 0.9083 (tp) REVERT: H 54 GLU cc_start: 0.7365 (mp0) cc_final: 0.7154 (mt-10) REVERT: H 78 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7656 (mp) REVERT: H 224 MET cc_start: 0.7645 (tpt) cc_final: 0.7161 (tpp) REVERT: H 252 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8146 (ttm-80) REVERT: H 258 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6953 (tp30) REVERT: H 260 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: H 261 SER cc_start: 0.8600 (m) cc_final: 0.8194 (p) REVERT: H 286 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6534 (ttp-110) REVERT: H 365 ASP cc_start: 0.7678 (t0) cc_final: 0.7385 (t0) REVERT: H 500 VAL cc_start: 0.9063 (m) cc_final: 0.8511 (p) REVERT: H 543 LEU cc_start: 0.8345 (tm) cc_final: 0.8016 (tt) REVERT: J 18 ILE cc_start: 0.9334 (tp) cc_final: 0.9120 (tp) REVERT: J 78 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7616 (mp) REVERT: J 172 ARG cc_start: 0.7882 (tpt90) cc_final: 0.7452 (tpt170) REVERT: J 224 MET cc_start: 0.7582 (tpt) cc_final: 0.7027 (tpp) REVERT: J 239 GLU cc_start: 0.7885 (mp0) cc_final: 0.7591 (mp0) REVERT: J 252 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8264 (ttm-80) REVERT: J 260 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: J 261 SER cc_start: 0.8822 (t) cc_final: 0.8583 (p) REVERT: J 365 ASP cc_start: 0.7671 (t0) cc_final: 0.7283 (t0) REVERT: J 481 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6542 (mtm110) REVERT: J 500 VAL cc_start: 0.9011 (m) cc_final: 0.8445 (p) REVERT: J 535 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7849 (pptt) REVERT: J 543 LEU cc_start: 0.8400 (tm) cc_final: 0.8061 (tt) REVERT: K 18 ILE cc_start: 0.9330 (tp) cc_final: 0.9118 (tp) REVERT: K 123 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7926 (tt0) REVERT: K 224 MET cc_start: 0.7693 (tpt) cc_final: 0.7175 (tpp) REVERT: K 260 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: K 261 SER cc_start: 0.8811 (t) cc_final: 0.8569 (p) REVERT: K 481 ARG cc_start: 0.7337 (mtp180) cc_final: 0.6787 (mtp85) REVERT: K 543 LEU cc_start: 0.8344 (tm) cc_final: 0.8021 (tt) REVERT: L 18 ILE cc_start: 0.9317 (tp) cc_final: 0.9106 (tp) REVERT: L 78 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7611 (mp) REVERT: L 123 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7921 (tt0) REVERT: L 224 MET cc_start: 0.7623 (tpt) cc_final: 0.7107 (tpp) REVERT: L 258 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: L 260 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: L 261 SER cc_start: 0.8860 (t) cc_final: 0.8526 (p) REVERT: L 329 ASN cc_start: 0.7334 (t0) cc_final: 0.6808 (t0) REVERT: L 365 ASP cc_start: 0.7713 (t0) cc_final: 0.7305 (t0) REVERT: L 481 ARG cc_start: 0.6899 (mtm-85) cc_final: 0.6098 (mtp85) REVERT: L 500 VAL cc_start: 0.9075 (m) cc_final: 0.8539 (p) REVERT: L 535 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7825 (pptt) REVERT: L 543 LEU cc_start: 0.8338 (tm) cc_final: 0.8011 (tt) outliers start: 58 outliers final: 31 residues processed: 391 average time/residue: 1.3570 time to fit residues: 595.5821 Evaluate side-chains 379 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 167 GLN H 287 ASN K 167 GLN L 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.121036 restraints weight = 54403.040| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.91 r_work: 0.3171 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18208 Z= 0.119 Angle : 0.570 6.730 24688 Z= 0.278 Chirality : 0.044 0.150 2748 Planarity : 0.005 0.058 3172 Dihedral : 10.844 147.841 2528 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.27 % Allowed : 18.45 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.65 (0.18), residues: 2220 helix: 1.37 (0.18), residues: 920 sheet: -0.60 (0.26), residues: 348 loop : 0.05 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 389 TYR 0.011 0.001 TYR K 307 PHE 0.012 0.001 PHE J 424 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00279 (18208) covalent geometry : angle 0.56953 (24688) hydrogen bonds : bond 0.03129 ( 731) hydrogen bonds : angle 4.27705 ( 2073) *********************** 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 **************************** Evaluate side-chains 381 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 337 time to evaluate : 1.016 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: H 18 ILE cc_start: 0.9302 (tp) cc_final: 0.9078 (tp) REVERT: H 54 GLU cc_start: 0.7351 (mp0) cc_final: 0.7119 (mt-10) REVERT: H 78 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7628 (mp) REVERT: H 224 MET cc_start: 0.7659 (tpt) cc_final: 0.7200 (tpp) REVERT: H 252 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.8131 (ttm-80) REVERT: H 258 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6908 (tp30) REVERT: H 260 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: H 261 SER cc_start: 0.8564 (m) cc_final: 0.8202 (p) REVERT: H 286 ARG cc_start: 0.6986 (ttt90) cc_final: 0.6501 (ttp-110) REVERT: H 365 ASP cc_start: 0.7671 (t0) cc_final: 0.7419 (t0) REVERT: H 500 VAL cc_start: 0.9054 (m) cc_final: 0.8503 (p) REVERT: H 543 LEU cc_start: 0.8363 (tm) cc_final: 0.8048 (tt) REVERT: J 49 THR cc_start: 0.9159 (m) cc_final: 0.8866 (p) REVERT: J 78 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7603 (mp) REVERT: J 172 ARG cc_start: 0.7854 (tpt90) cc_final: 0.7420 (tpt170) REVERT: J 224 MET cc_start: 0.7564 (tpt) cc_final: 0.7090 (tpp) REVERT: J 239 GLU cc_start: 0.7881 (mp0) cc_final: 0.7594 (mp0) REVERT: J 252 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8221 (ttm-80) REVERT: J 260 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: J 261 SER cc_start: 0.8846 (t) cc_final: 0.8604 (p) REVERT: J 365 ASP cc_start: 0.7652 (t0) cc_final: 0.7386 (t0) REVERT: J 465 ARG cc_start: 0.7508 (ttt-90) cc_final: 0.7241 (ttt-90) REVERT: J 481 ARG cc_start: 0.6871 (mtm-85) cc_final: 0.6495 (mtm110) REVERT: J 500 VAL cc_start: 0.9005 (m) cc_final: 0.8444 (p) REVERT: J 535 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7940 (pptt) REVERT: J 543 LEU cc_start: 0.8377 (tm) cc_final: 0.8058 (tt) REVERT: K 18 ILE cc_start: 0.9317 (tp) cc_final: 0.9097 (tp) REVERT: K 123 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7896 (tt0) REVERT: K 224 MET cc_start: 0.7637 (tpt) cc_final: 0.7203 (tpp) REVERT: K 261 SER cc_start: 0.8831 (t) cc_final: 0.8628 (p) REVERT: K 481 ARG cc_start: 0.7288 (mtp180) cc_final: 0.6743 (mtp85) REVERT: K 543 LEU cc_start: 0.8362 (tm) cc_final: 0.8040 (tt) REVERT: L 18 ILE cc_start: 0.9310 (tp) cc_final: 0.9084 (tp) REVERT: L 134 ASP cc_start: 0.6960 (t70) cc_final: 0.6350 (p0) REVERT: L 224 MET cc_start: 0.7636 (tpt) cc_final: 0.7174 (tpp) REVERT: L 258 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: L 260 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: L 261 SER cc_start: 0.8821 (t) cc_final: 0.8493 (p) REVERT: L 329 ASN cc_start: 0.7378 (t0) cc_final: 0.6856 (t0) REVERT: L 365 ASP cc_start: 0.7724 (t0) cc_final: 0.7422 (t0) REVERT: L 481 ARG cc_start: 0.6914 (mtm-85) cc_final: 0.6134 (mtp85) REVERT: L 500 VAL cc_start: 0.9071 (m) cc_final: 0.8519 (p) REVERT: L 535 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7911 (pptt) REVERT: L 543 LEU cc_start: 0.8358 (tm) cc_final: 0.8054 (tt) outliers start: 44 outliers final: 28 residues processed: 370 average time/residue: 1.4011 time to fit residues: 580.9332 Evaluate side-chains 367 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 330 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 155 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 ASN H 287 ASN J 287 ASN K 44 ASN L 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.164826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.119792 restraints weight = 54199.763| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.93 r_work: 0.3141 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18208 Z= 0.152 Angle : 0.588 6.780 24688 Z= 0.288 Chirality : 0.045 0.148 2748 Planarity : 0.005 0.064 3172 Dihedral : 11.064 156.083 2528 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 18.81 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.68 (0.18), residues: 2220 helix: 1.36 (0.18), residues: 920 sheet: -0.54 (0.27), residues: 348 loop : 0.08 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 389 TYR 0.012 0.001 TYR L 42 PHE 0.014 0.001 PHE K 424 TRP 0.006 0.001 TRP K 358 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00356 (18208) covalent geometry : angle 0.58820 (24688) hydrogen bonds : bond 0.03266 ( 731) hydrogen bonds : angle 4.29050 ( 2073) *********************** 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 **************************** Evaluate side-chains 374 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 332 time to evaluate : 1.079 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: H 54 GLU cc_start: 0.7308 (mp0) cc_final: 0.7052 (mt-10) REVERT: H 78 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7635 (mp) REVERT: H 224 MET cc_start: 0.7645 (tpt) cc_final: 0.7180 (tpp) REVERT: H 252 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8138 (ttm-80) REVERT: H 258 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6948 (tp30) REVERT: H 260 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8119 (mt0) REVERT: H 261 SER cc_start: 0.8614 (m) cc_final: 0.8254 (p) REVERT: H 286 ARG cc_start: 0.7009 (ttt90) cc_final: 0.6505 (ttp-110) REVERT: H 365 ASP cc_start: 0.7674 (t0) cc_final: 0.7382 (t0) REVERT: H 500 VAL cc_start: 0.9036 (m) cc_final: 0.8464 (p) REVERT: H 543 LEU cc_start: 0.8379 (tm) cc_final: 0.8075 (tt) REVERT: J 78 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7617 (mp) REVERT: J 172 ARG cc_start: 0.7911 (tpt90) cc_final: 0.7429 (tpt170) REVERT: J 224 MET cc_start: 0.7570 (tpt) cc_final: 0.7095 (tpp) REVERT: J 239 GLU cc_start: 0.7876 (mp0) cc_final: 0.7561 (mp0) REVERT: J 260 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: J 261 SER cc_start: 0.8866 (t) cc_final: 0.8611 (p) REVERT: J 286 ARG cc_start: 0.7008 (ttt90) cc_final: 0.6491 (ttp-110) REVERT: J 365 ASP cc_start: 0.7721 (t0) cc_final: 0.7433 (t0) REVERT: J 465 ARG cc_start: 0.7543 (ttt-90) cc_final: 0.7280 (ttt-90) REVERT: J 481 ARG cc_start: 0.6901 (mtm-85) cc_final: 0.6517 (mtm110) REVERT: J 500 VAL cc_start: 0.9008 (m) cc_final: 0.8437 (p) REVERT: J 535 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7955 (pptt) REVERT: J 543 LEU cc_start: 0.8391 (tm) cc_final: 0.8084 (tt) REVERT: K 49 THR cc_start: 0.9144 (m) cc_final: 0.8884 (p) REVERT: K 224 MET cc_start: 0.7695 (tpt) cc_final: 0.7242 (tpp) REVERT: K 260 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: K 261 SER cc_start: 0.8842 (t) cc_final: 0.8626 (p) REVERT: K 286 ARG cc_start: 0.7014 (ttt90) cc_final: 0.6479 (ttp-110) REVERT: K 481 ARG cc_start: 0.7301 (mtp180) cc_final: 0.7026 (mtm110) REVERT: K 543 LEU cc_start: 0.8378 (tm) cc_final: 0.8070 (tt) REVERT: L 134 ASP cc_start: 0.7132 (t70) cc_final: 0.6538 (p0) REVERT: L 224 MET cc_start: 0.7624 (tpt) cc_final: 0.7128 (tpp) REVERT: L 258 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6892 (tp30) REVERT: L 260 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: L 261 SER cc_start: 0.8873 (t) cc_final: 0.8532 (p) REVERT: L 329 ASN cc_start: 0.7352 (t0) cc_final: 0.6835 (t0) REVERT: L 365 ASP cc_start: 0.7719 (t0) cc_final: 0.7397 (t0) REVERT: L 481 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6155 (mtp85) REVERT: L 500 VAL cc_start: 0.9088 (m) cc_final: 0.8527 (p) REVERT: L 535 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7948 (pptt) REVERT: L 543 LEU cc_start: 0.8379 (tm) cc_final: 0.8083 (tt) outliers start: 42 outliers final: 27 residues processed: 364 average time/residue: 1.4161 time to fit residues: 577.3650 Evaluate side-chains 363 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 217 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN L 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.163942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119181 restraints weight = 54454.856| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.91 r_work: 0.3186 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18208 Z= 0.177 Angle : 0.607 6.870 24688 Z= 0.298 Chirality : 0.045 0.144 2748 Planarity : 0.005 0.066 3172 Dihedral : 11.367 162.986 2528 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.16 % Allowed : 19.38 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.65 (0.18), residues: 2220 helix: 1.32 (0.18), residues: 920 sheet: -0.52 (0.27), residues: 340 loop : 0.07 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 389 TYR 0.012 0.002 TYR J 42 PHE 0.014 0.001 PHE J 424 TRP 0.006 0.001 TRP L 285 HIS 0.005 0.001 HIS J 116 Details of bonding type rmsd covalent geometry : bond 0.00416 (18208) covalent geometry : angle 0.60650 (24688) hydrogen bonds : bond 0.03411 ( 731) hydrogen bonds : angle 4.33594 ( 2073) ********************** 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 **************************** Evaluate side-chains 379 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 0.969 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: H 49 THR cc_start: 0.9165 (m) cc_final: 0.8899 (p) REVERT: H 54 GLU cc_start: 0.7253 (mp0) cc_final: 0.7011 (mt-10) REVERT: H 78 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (mp) REVERT: H 224 MET cc_start: 0.7689 (tpt) cc_final: 0.7248 (tpp) REVERT: H 252 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8174 (ttm-80) REVERT: H 258 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: H 260 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: H 261 SER cc_start: 0.8619 (m) cc_final: 0.8234 (p) REVERT: H 286 ARG cc_start: 0.7028 (ttt90) cc_final: 0.6440 (ttp-110) REVERT: H 365 ASP cc_start: 0.7750 (t0) cc_final: 0.7402 (t0) REVERT: H 465 ARG cc_start: 0.7493 (ttt-90) cc_final: 0.7248 (ttt-90) REVERT: H 543 LEU cc_start: 0.8391 (tm) cc_final: 0.8098 (tt) REVERT: J 78 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7624 (mp) REVERT: J 134 ASP cc_start: 0.7167 (t70) cc_final: 0.6538 (p0) REVERT: J 172 ARG cc_start: 0.7968 (tpt90) cc_final: 0.7493 (tpt170) REVERT: J 224 MET cc_start: 0.7579 (tpt) cc_final: 0.7108 (tpp) REVERT: J 239 GLU cc_start: 0.7893 (mp0) cc_final: 0.7613 (mp0) REVERT: J 260 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: J 261 SER cc_start: 0.8872 (t) cc_final: 0.8612 (p) REVERT: J 365 ASP cc_start: 0.7719 (t0) cc_final: 0.7397 (t0) REVERT: J 389 ARG cc_start: 0.7193 (ttp-110) cc_final: 0.6849 (ttp-110) REVERT: J 465 ARG cc_start: 0.7540 (ttt-90) cc_final: 0.7264 (ttt-90) REVERT: J 481 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6585 (mtm110) REVERT: J 500 VAL cc_start: 0.9018 (m) cc_final: 0.8453 (p) REVERT: J 535 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7946 (pptt) REVERT: J 543 LEU cc_start: 0.8380 (tm) cc_final: 0.8085 (tt) REVERT: K 49 THR cc_start: 0.9159 (m) cc_final: 0.8898 (p) REVERT: K 224 MET cc_start: 0.7710 (tpt) cc_final: 0.7219 (tpp) REVERT: K 260 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: K 261 SER cc_start: 0.8847 (t) cc_final: 0.8603 (p) REVERT: K 286 ARG cc_start: 0.6980 (ttt90) cc_final: 0.6378 (ttp-110) REVERT: K 481 ARG cc_start: 0.7285 (mtp180) cc_final: 0.7020 (mtm110) REVERT: K 543 LEU cc_start: 0.8388 (tm) cc_final: 0.8093 (tt) REVERT: L 134 ASP cc_start: 0.7213 (t70) cc_final: 0.6634 (p0) REVERT: L 224 MET cc_start: 0.7696 (tpt) cc_final: 0.7240 (tpp) REVERT: L 258 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: L 260 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: L 261 SER cc_start: 0.8864 (t) cc_final: 0.8497 (p) REVERT: L 286 ARG cc_start: 0.7007 (ttt90) cc_final: 0.6430 (ttp-110) REVERT: L 329 ASN cc_start: 0.7328 (t0) cc_final: 0.6813 (t0) REVERT: L 365 ASP cc_start: 0.7720 (t0) cc_final: 0.7373 (t0) REVERT: L 481 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6183 (mtp85) REVERT: L 535 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7927 (pptt) REVERT: L 543 LEU cc_start: 0.8390 (tm) cc_final: 0.8111 (tt) outliers start: 42 outliers final: 26 residues processed: 369 average time/residue: 1.4198 time to fit residues: 586.4597 Evaluate side-chains 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 170 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN K 323 HIS L 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.165151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120598 restraints weight = 54301.935| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.91 r_work: 0.3153 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18208 Z= 0.133 Angle : 0.580 6.687 24688 Z= 0.284 Chirality : 0.044 0.145 2748 Planarity : 0.005 0.073 3172 Dihedral : 10.960 154.887 2528 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.01 % Allowed : 20.00 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.39 (0.18), residues: 928 sheet: -0.58 (0.27), residues: 348 loop : 0.10 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 252 TYR 0.011 0.001 TYR L 42 PHE 0.012 0.001 PHE J 473 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00312 (18208) covalent geometry : angle 0.58010 (24688) hydrogen bonds : bond 0.03147 ( 731) hydrogen bonds : angle 4.26819 ( 2073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14998.45 seconds wall clock time: 253 minutes 35.38 seconds (15215.38 seconds total)