Starting phenix.real_space_refine on Mon Jul 6 13:30:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mh1_23833/07_2026/7mh1_23833_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mh1_23833/07_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_23833/07_2026/7mh1_23833_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mh1_23833/07_2026/7mh1_23833_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mh1_23833/07_2026/7mh1_23833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mh1_23833/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35636 Number of models: 1 Model: "" Number of chains: 8 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: "J" 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: "K" 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: "L" 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} 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: 6.39, per 1000 atoms: 0.18 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: 3.37 Conformation dependent library (CDL) restraints added in 1.2 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: 0.91 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: 8.93 Time building geometry restraints manager: 4.62 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: 53503 2.65 - 5.29: 9446 5.29 - 7.94: 2147 7.94 - 10.59: 128 10.59 - 13.24: 48 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 - 17.75: 15008 17.75 - 35.51: 1202 35.51 - 53.26: 503 53.26 - 71.02: 291 71.02 - 88.77: 28 Dihedral angle restraints: 17032 sinusoidal: 9580 harmonic: 7452 Sorted by residual: dihedral pdb=" CA LEU L 310 " pdb=" C LEU L 310 " pdb=" N ARG L 311 " pdb=" CA ARG L 311 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU K 310 " pdb=" C LEU K 310 " pdb=" N ARG K 311 " pdb=" CA ARG K 311 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU H 310 " pdb=" C LEU H 310 " pdb=" N ARG H 311 " pdb=" CA ARG H 311 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 17029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1561 0.080 - 0.161: 764 0.161 - 0.241: 347 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: 5272 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 5269 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: 2.030 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: 0.240 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 34.830 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.142 18208 Z= 0.786 Angle : 2.004 11.390 24688 Z= 1.335 Chirality : 0.110 0.402 2748 Planarity : 0.016 0.155 3164 Dihedral : 15.627 88.771 7076 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/Z covalent geometry : bond 0.01272 / 0.79 (18208) covalent geometry : angle 2.00424 / 1.34 (24688) hydrogen bonds : bond 0.18312 / 12.15 ( 731) hydrogen bonds : angle 7.61362 / 5.31 ( 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 : 0.979 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: 1.1339 time to fit residues: 630.0067 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 : 0.966 ------------------------------------------------------------------------------- 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... 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 = 0.3826 r_free = 0.3826 target = 0.167106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123274 restraints weight = 55391.822| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.91 r_work: 0.3192 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (16 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18208 Z= 0.161 Angle : 0.667 6.019 24688 Z= 0.348 Chirality : 0.047 0.153 2748 Planarity : 0.005 0.050 3164 Dihedral : 9.275 57.541 2724 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.14 % Allowed : 14.18 % Favored : 82.68 % 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 (0.17), residues: 2220 helix: 0.13 (0.16), residues: 904 sheet: -0.43 (0.24), residues: 392 loop : -0.22 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 252 TYR 0.012 0.002 TYR H 265 PHE 0.019 0.002 PHE L 424 TRP 0.012 0.001 TRP K 358 HIS 0.006 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (18208) covalent geometry : angle 0.66676 / 0.35 (24688) hydrogen bonds : bond 0.04599 / 3.05 ( 731) hydrogen bonds : angle 5.23979 / 3.70 ( 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 446 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 385 time to evaluate : 1.060 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: 0.7745 (tptp) cc_final: 0.7496 (tttp) REVERT: H 49 THR cc_start: 0.9006 (m) cc_final: 0.8627 (p) REVERT: H 54 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6817 (mt-10) REVERT: H 78 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7827 (mp) REVERT: H 123 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7616 (mt-10) REVERT: H 157 MET cc_start: 0.8610 (mmt) cc_final: 0.8348 (mmt) REVERT: H 212 ASP cc_start: 0.8772 (m-30) cc_final: 0.8486 (m-30) REVERT: H 224 MET cc_start: 0.7581 (tpt) cc_final: 0.7027 (tpp) REVERT: H 227 LYS cc_start: 0.8005 (mttt) cc_final: 0.7657 (mttp) REVERT: H 228 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7689 (mt-10) REVERT: H 258 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7013 (tp30) REVERT: H 500 VAL cc_start: 0.9081 (m) cc_final: 0.8640 (p) REVERT: H 543 LEU cc_start: 0.8300 (tm) cc_final: 0.7993 (tt) REVERT: J 49 THR cc_start: 0.9007 (m) cc_final: 0.8642 (p) REVERT: J 54 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6833 (mt-10) REVERT: J 78 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (mp) REVERT: J 123 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7782 (tt0) REVERT: J 172 ARG cc_start: 0.7784 (tpt90) cc_final: 0.7374 (tpt170) REVERT: J 212 ASP cc_start: 0.8768 (m-30) cc_final: 0.8454 (m-30) REVERT: J 224 MET cc_start: 0.7556 (tpt) cc_final: 0.7004 (tpp) REVERT: J 228 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: J 239 GLU cc_start: 0.7786 (mp0) cc_final: 0.7518 (mp0) REVERT: J 500 VAL cc_start: 0.9066 (m) cc_final: 0.8615 (p) REVERT: J 507 ASP cc_start: 0.7151 (m-30) cc_final: 0.6902 (m-30) REVERT: J 513 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6475 (tt0) REVERT: J 543 LEU cc_start: 0.8337 (tm) cc_final: 0.8018 (tt) REVERT: K 49 THR cc_start: 0.8996 (m) cc_final: 0.8642 (p) REVERT: K 54 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7027 (mt-10) REVERT: K 78 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7766 (mp) REVERT: K 123 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7664 (mt-10) REVERT: K 157 MET cc_start: 0.8628 (mmt) cc_final: 0.8352 (mmt) REVERT: K 212 ASP cc_start: 0.8772 (m-30) cc_final: 0.8486 (m-30) REVERT: K 224 MET cc_start: 0.7587 (tpt) cc_final: 0.6816 (tpp) REVERT: K 227 LYS cc_start: 0.7984 (mttt) cc_final: 0.7646 (mttp) REVERT: K 228 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: K 322 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7496 (mt-10) REVERT: K 329 ASN cc_start: 0.7258 (OUTLIER) cc_final: 0.6774 (t0) REVERT: K 500 VAL cc_start: 0.9081 (m) cc_final: 0.8613 (p) REVERT: K 543 LEU cc_start: 0.8340 (tm) cc_final: 0.8022 (tt) REVERT: L 49 THR cc_start: 0.9007 (m) cc_final: 0.8595 (p) REVERT: L 123 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7674 (mt-10) REVERT: L 157 MET cc_start: 0.8611 (mmt) cc_final: 0.8327 (mmt) REVERT: L 224 MET cc_start: 0.7543 (tpt) cc_final: 0.7020 (tpp) REVERT: L 227 LYS cc_start: 0.7996 (mttt) cc_final: 0.7693 (mtpp) REVERT: L 228 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: L 258 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6999 (tp30) REVERT: L 322 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7318 (mt-10) REVERT: L 329 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6713 (t0) REVERT: L 500 VAL cc_start: 0.9069 (m) cc_final: 0.8628 (p) REVERT: L 509 MET cc_start: 0.7566 (mmt) cc_final: 0.7280 (mmm) REVERT: L 543 LEU cc_start: 0.8335 (tm) cc_final: 0.8030 (tt) outliers start: 61 outliers final: 10 residues processed: 422 average time/residue: 1.1515 time to fit residues: 557.1050 Evaluate side-chains 373 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 352 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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: 0.8980 chunk 105 optimal weight: 0.0570 chunk 166 optimal weight: 0.0970 chunk 174 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 136 ASN H 287 ASN H 323 HIS K 136 ASN K 323 HIS L 287 ASN L 323 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.165886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.121869 restraints weight = 55129.661| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.91 r_work: 0.3162 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18208 Z= 0.139 Angle : 0.589 5.478 24688 Z= 0.305 Chirality : 0.045 0.151 2748 Planarity : 0.005 0.054 3164 Dihedral : 8.063 57.688 2722 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 15.98 % Favored : 81.44 % 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: 0.22 (0.18), residues: 2220 helix: 0.72 (0.17), residues: 912 sheet: -0.45 (0.24), residues: 388 loop : 0.03 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 252 TYR 0.013 0.002 TYR J 265 PHE 0.012 0.001 PHE H 163 TRP 0.012 0.002 TRP J 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (18208) covalent geometry : angle 0.58936 / 0.31 (24688) hydrogen bonds : bond 0.03945 / 2.61 ( 731) hydrogen bonds : angle 4.75320 / 3.36 ( 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 414 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 1.155 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: 0.9073 (m) cc_final: 0.8732 (p) REVERT: H 78 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7695 (mp) REVERT: H 109 LYS cc_start: 0.8666 (mttm) cc_final: 0.8425 (mttm) REVERT: H 123 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7827 (tt0) REVERT: H 224 MET cc_start: 0.7601 (tpt) cc_final: 0.7072 (tpp) REVERT: H 228 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: H 252 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.8025 (ttm-80) REVERT: H 258 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6983 (tp30) REVERT: H 261 SER cc_start: 0.8745 (t) cc_final: 0.8284 (p) REVERT: H 500 VAL cc_start: 0.9062 (m) cc_final: 0.8575 (p) REVERT: H 543 LEU cc_start: 0.8267 (tm) cc_final: 0.7953 (tt) REVERT: J 49 THR cc_start: 0.9090 (m) cc_final: 0.8763 (p) REVERT: J 54 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6754 (mt-10) REVERT: J 78 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7659 (mp) REVERT: J 123 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7887 (tt0) REVERT: J 172 ARG cc_start: 0.7796 (tpt90) cc_final: 0.7301 (tpt170) REVERT: J 224 MET cc_start: 0.7530 (tpt) cc_final: 0.7014 (tpp) REVERT: J 228 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: J 239 GLU cc_start: 0.7788 (mp0) cc_final: 0.7549 (mp0) REVERT: J 252 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8197 (ttm-80) REVERT: J 261 SER cc_start: 0.8832 (t) cc_final: 0.8594 (p) REVERT: J 475 GLU cc_start: 0.7885 (tt0) cc_final: 0.7661 (mt-10) REVERT: J 500 VAL cc_start: 0.9068 (m) cc_final: 0.8568 (p) REVERT: J 543 LEU cc_start: 0.8309 (tm) cc_final: 0.7975 (tt) REVERT: K 49 THR cc_start: 0.9076 (m) cc_final: 0.8712 (p) REVERT: K 54 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6895 (mt-10) REVERT: K 78 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7703 (mp) REVERT: K 123 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7930 (mt-10) REVERT: K 224 MET cc_start: 0.7585 (tpt) cc_final: 0.6821 (tpp) REVERT: K 228 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7697 (mm-30) REVERT: K 252 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: K 261 SER cc_start: 0.8785 (t) cc_final: 0.8550 (p) REVERT: K 329 ASN cc_start: 0.7406 (t0) cc_final: 0.7184 (t0) REVERT: K 365 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7332 (t0) REVERT: K 500 VAL cc_start: 0.9080 (m) cc_final: 0.8568 (p) REVERT: K 543 LEU cc_start: 0.8302 (tm) cc_final: 0.7975 (tt) REVERT: L 1 MET cc_start: 0.8304 (ttm) cc_final: 0.8070 (ttm) REVERT: L 49 THR cc_start: 0.9036 (m) cc_final: 0.8716 (p) REVERT: L 123 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7777 (tt0) REVERT: L 224 MET cc_start: 0.7559 (tpt) cc_final: 0.6991 (tpp) REVERT: L 227 LYS cc_start: 0.8060 (mttt) cc_final: 0.7826 (mtpp) REVERT: L 228 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: L 252 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8192 (ttm-80) REVERT: L 258 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: L 261 SER cc_start: 0.8816 (t) cc_final: 0.8460 (p) REVERT: L 322 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7455 (mt-10) REVERT: L 329 ASN cc_start: 0.7348 (t0) cc_final: 0.6816 (t0) REVERT: L 500 VAL cc_start: 0.9091 (m) cc_final: 0.8609 (p) REVERT: L 509 MET cc_start: 0.7532 (mmt) cc_final: 0.7302 (mmm) REVERT: L 543 LEU cc_start: 0.8290 (tm) cc_final: 0.7960 (tt) outliers start: 50 outliers final: 21 residues processed: 396 average time/residue: 1.2197 time to fit residues: 549.9777 Evaluate side-chains 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 424 PHE Chi-restraints excluded: chain J residue 71 LEU 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 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 71 LEU 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 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 71 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 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: 0.7980 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 135 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 517 HIS J 287 ASN J 517 HIS K 517 HIS L 517 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.168680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125010 restraints weight = 54958.570| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.91 r_work: 0.3184 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18208 Z= 0.110 Angle : 0.537 5.901 24688 Z= 0.276 Chirality : 0.044 0.156 2748 Planarity : 0.005 0.051 3164 Dihedral : 7.235 55.958 2722 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.78 % Allowed : 16.34 % Favored : 80.88 % 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: 0.52 (0.18), residues: 2220 helix: 1.09 (0.18), residues: 920 sheet: -0.50 (0.24), residues: 388 loop : 0.14 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 252 TYR 0.014 0.001 TYR L 265 PHE 0.011 0.001 PHE J 409 TRP 0.011 0.001 TRP J 358 HIS 0.003 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (18208) covalent geometry : angle 0.53665 / 0.28 (24688) hydrogen bonds : bond 0.03328 / 2.21 ( 731) hydrogen bonds : angle 4.48644 / 3.18 ( 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 382 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 328 time to evaluate : 1.003 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: 0.9087 (m) cc_final: 0.8777 (p) REVERT: H 109 LYS cc_start: 0.8654 (mttm) cc_final: 0.8418 (mttm) REVERT: H 123 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7844 (tt0) REVERT: H 224 MET cc_start: 0.7648 (tpt) cc_final: 0.7152 (tpp) REVERT: H 252 ARG cc_start: 0.8328 (ttm-80) cc_final: 0.8048 (ttm-80) REVERT: H 258 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6993 (tp30) REVERT: H 260 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: H 261 SER cc_start: 0.8739 (t) cc_final: 0.8318 (p) REVERT: H 500 VAL cc_start: 0.9059 (m) cc_final: 0.8552 (p) REVERT: J 49 THR cc_start: 0.9104 (m) cc_final: 0.8789 (p) REVERT: J 123 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7901 (tt0) REVERT: J 172 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7284 (tpt170) REVERT: J 224 MET cc_start: 0.7603 (tpt) cc_final: 0.7093 (tpp) REVERT: J 239 GLU cc_start: 0.7817 (mp0) cc_final: 0.7584 (mp0) REVERT: J 252 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: J 260 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: J 291 ARG cc_start: 0.7198 (ttp-170) cc_final: 0.6995 (ttp-170) REVERT: J 376 ARG cc_start: 0.6729 (tmm-80) cc_final: 0.6524 (tmm-80) REVERT: J 475 GLU cc_start: 0.7952 (tt0) cc_final: 0.7694 (mt-10) REVERT: J 500 VAL cc_start: 0.9071 (m) cc_final: 0.8556 (p) REVERT: K 49 THR cc_start: 0.9042 (m) cc_final: 0.8730 (p) REVERT: K 123 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7829 (tt0) REVERT: K 224 MET cc_start: 0.7605 (tpt) cc_final: 0.6805 (tpp) REVERT: K 228 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7568 (mm-30) REVERT: K 239 GLU cc_start: 0.8057 (mp0) cc_final: 0.7752 (pm20) REVERT: K 252 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8170 (ttm-80) REVERT: K 260 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: K 365 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7336 (t0) REVERT: K 481 ARG cc_start: 0.6993 (mtp180) cc_final: 0.6531 (mtp85) REVERT: K 500 VAL cc_start: 0.9074 (m) cc_final: 0.8536 (p) REVERT: L 49 THR cc_start: 0.9018 (m) cc_final: 0.8693 (p) REVERT: L 54 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6866 (mt-10) REVERT: L 123 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7857 (tt0) REVERT: L 224 MET cc_start: 0.7643 (tpt) cc_final: 0.6788 (tpp) REVERT: L 227 LYS cc_start: 0.8008 (mttt) cc_final: 0.7726 (mtpp) REVERT: L 228 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7573 (mm-30) REVERT: L 252 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8207 (ttm-80) REVERT: L 258 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7007 (tp30) REVERT: L 260 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: L 261 SER cc_start: 0.8783 (t) cc_final: 0.8479 (p) REVERT: L 329 ASN cc_start: 0.7367 (t0) cc_final: 0.6797 (t0) REVERT: L 500 VAL cc_start: 0.9086 (m) cc_final: 0.8580 (p) REVERT: L 509 MET cc_start: 0.7501 (mmt) cc_final: 0.7189 (mmm) REVERT: L 535 LYS cc_start: 0.8080 (pptt) cc_final: 0.7829 (pttp) outliers start: 54 outliers final: 17 residues processed: 367 average time/residue: 1.2774 time to fit residues: 532.9276 Evaluate side-chains 338 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 314 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN 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 213 LEU Chi-restraints excluded: chain J residue 240 GLN 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 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 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: 1.9990 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: 3.9990 chunk 76 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 185 GLN J 323 HIS K 333 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 = 0.3772 r_free = 0.3772 target = 0.162302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117534 restraints weight = 55063.121| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 18208 Z= 0.252 Angle : 0.636 6.214 24688 Z= 0.326 Chirality : 0.047 0.148 2748 Planarity : 0.006 0.051 3164 Dihedral : 8.259 56.392 2708 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 16.24 % Favored : 80.88 % 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 (0.18), residues: 2220 helix: 0.90 (0.18), residues: 920 sheet: -0.49 (0.26), residues: 348 loop : -0.05 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 269 TYR 0.013 0.002 TYR K 336 PHE 0.017 0.002 PHE K 163 TRP 0.012 0.002 TRP L 285 HIS 0.007 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (18208) covalent geometry : angle 0.63610 / 0.33 (24688) hydrogen bonds : bond 0.04068 / 2.71 ( 731) hydrogen bonds : angle 4.61278 / 3.27 ( 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 415 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 359 time to evaluate : 0.980 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: 0.9121 (m) cc_final: 0.8781 (p) REVERT: H 78 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7652 (mp) REVERT: H 109 LYS cc_start: 0.8761 (mttm) cc_final: 0.8531 (mttm) REVERT: H 224 MET cc_start: 0.7656 (tpt) cc_final: 0.7182 (tpp) REVERT: H 228 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: H 252 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8185 (ttm-80) REVERT: H 258 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: H 260 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: H 261 SER cc_start: 0.8789 (t) cc_final: 0.8333 (p) REVERT: H 286 ARG cc_start: 0.7031 (ttt90) cc_final: 0.6425 (ttp-110) REVERT: H 389 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.7111 (ttp-110) REVERT: H 481 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6125 (mtp85) REVERT: H 500 VAL cc_start: 0.9081 (m) cc_final: 0.8537 (p) REVERT: H 543 LEU cc_start: 0.8338 (tm) cc_final: 0.8006 (tt) REVERT: J 78 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7674 (mp) REVERT: J 123 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7924 (tt0) REVERT: J 172 ARG cc_start: 0.7878 (tpt90) cc_final: 0.7488 (tpt170) REVERT: J 224 MET cc_start: 0.7615 (tpt) cc_final: 0.7090 (tpp) REVERT: J 228 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: J 239 GLU cc_start: 0.7883 (mp0) cc_final: 0.7547 (mp0) REVERT: J 260 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: J 286 ARG cc_start: 0.7048 (ttt90) cc_final: 0.6453 (ttp-110) REVERT: J 465 ARG cc_start: 0.7513 (ttt-90) cc_final: 0.7255 (ttt-90) REVERT: J 475 GLU cc_start: 0.7849 (tt0) cc_final: 0.7624 (mt-10) REVERT: J 500 VAL cc_start: 0.9081 (m) cc_final: 0.8529 (p) REVERT: J 543 LEU cc_start: 0.8341 (tm) cc_final: 0.8000 (tt) REVERT: K 28 LYS cc_start: 0.7864 (tptp) cc_final: 0.7642 (tttp) REVERT: K 78 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7705 (mp) REVERT: K 109 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8582 (mmtp) REVERT: K 123 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7939 (tt0) REVERT: K 224 MET cc_start: 0.7623 (tpt) cc_final: 0.7107 (tpp) REVERT: K 228 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: K 260 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: K 267 LYS cc_start: 0.7930 (tttm) cc_final: 0.7456 (tttt) REVERT: K 286 ARG cc_start: 0.7045 (ttt90) cc_final: 0.6405 (ttp-110) REVERT: K 481 ARG cc_start: 0.7325 (mtp180) cc_final: 0.6783 (mtp85) REVERT: K 543 LEU cc_start: 0.8336 (tm) cc_final: 0.7999 (tt) REVERT: L 54 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6825 (mt-10) REVERT: L 78 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7652 (mp) REVERT: L 102 ARG cc_start: 0.8492 (mmm160) cc_final: 0.8283 (mmp-170) REVERT: L 123 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7962 (tt0) REVERT: L 224 MET cc_start: 0.7659 (tpt) cc_final: 0.7080 (tpp) REVERT: L 228 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: L 258 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6967 (tp30) REVERT: L 260 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: L 261 SER cc_start: 0.8845 (t) cc_final: 0.8483 (p) REVERT: L 329 ASN cc_start: 0.7390 (t0) cc_final: 0.6868 (t0) REVERT: L 465 ARG cc_start: 0.7488 (ttt-90) cc_final: 0.7223 (ttt-90) REVERT: L 481 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6063 (mtp85) REVERT: L 500 VAL cc_start: 0.9092 (m) cc_final: 0.8549 (p) REVERT: L 509 MET cc_start: 0.7625 (mmt) cc_final: 0.7406 (mmm) REVERT: L 535 LYS cc_start: 0.8187 (pptt) cc_final: 0.7914 (pttp) REVERT: L 543 LEU cc_start: 0.8358 (tm) cc_final: 0.8025 (tt) outliers start: 56 outliers final: 21 residues processed: 401 average time/residue: 1.3338 time to fit residues: 605.1970 Evaluate side-chains 388 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 353 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 228 GLU 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 367 ILE 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 228 GLU Chi-restraints excluded: chain J residue 240 GLN 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 228 GLU Chi-restraints excluded: chain K residue 260 GLN 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 L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 213 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 188 optimal weight: 0.1980 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 287 ASN J 287 ASN K 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 = 0.3795 r_free = 0.3795 target = 0.164523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119673 restraints weight = 54809.709| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.92 r_work: 0.3138 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18208 Z= 0.136 Angle : 0.552 5.241 24688 Z= 0.283 Chirality : 0.044 0.146 2748 Planarity : 0.005 0.063 3164 Dihedral : 7.765 57.581 2708 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.73 % Allowed : 17.47 % Favored : 79.79 % 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: 0.52 (0.18), residues: 2220 helix: 1.18 (0.18), residues: 920 sheet: -0.53 (0.26), residues: 348 loop : 0.01 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 252 TYR 0.012 0.001 TYR K 265 PHE 0.011 0.001 PHE H 163 TRP 0.009 0.001 TRP J 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (18208) covalent geometry : angle 0.55227 / 0.28 (24688) hydrogen bonds : bond 0.03408 / 2.27 ( 731) hydrogen bonds : angle 4.41118 / 3.13 ( 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 390 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 337 time to evaluate : 1.003 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: 0.9123 (m) cc_final: 0.8797 (p) REVERT: H 78 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7543 (mp) REVERT: H 109 LYS cc_start: 0.8745 (mttm) cc_final: 0.8502 (mttm) REVERT: H 224 MET cc_start: 0.7638 (tpt) cc_final: 0.7130 (tpp) REVERT: H 258 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: H 260 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: H 261 SER cc_start: 0.8747 (t) cc_final: 0.8313 (p) REVERT: H 481 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6051 (mtp85) REVERT: H 500 VAL cc_start: 0.9057 (m) cc_final: 0.8518 (p) REVERT: H 535 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7842 (pptt) REVERT: H 543 LEU cc_start: 0.8317 (tm) cc_final: 0.8005 (tt) REVERT: J 18 ILE cc_start: 0.9231 (tp) cc_final: 0.8995 (tp) REVERT: J 49 THR cc_start: 0.9150 (m) cc_final: 0.8838 (p) REVERT: J 78 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7566 (mp) REVERT: J 123 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7959 (tt0) REVERT: J 134 ASP cc_start: 0.7152 (t70) cc_final: 0.6505 (p0) REVERT: J 172 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7430 (tpt170) REVERT: J 224 MET cc_start: 0.7573 (tpt) cc_final: 0.7057 (tpp) REVERT: J 239 GLU cc_start: 0.7928 (mp0) cc_final: 0.7599 (mp0) REVERT: J 260 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: J 333 ASN cc_start: 0.8021 (t0) cc_final: 0.7688 (t0) REVERT: J 475 GLU cc_start: 0.7846 (tt0) cc_final: 0.7618 (mt-10) REVERT: J 481 ARG cc_start: 0.6936 (mmm-85) cc_final: 0.6482 (mtm110) REVERT: J 500 VAL cc_start: 0.9054 (m) cc_final: 0.8503 (p) REVERT: J 535 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7815 (pptt) REVERT: J 543 LEU cc_start: 0.8317 (tm) cc_final: 0.7997 (tt) REVERT: K 18 ILE cc_start: 0.9242 (tp) cc_final: 0.8997 (tp) REVERT: K 78 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7563 (mp) REVERT: K 123 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7901 (tt0) REVERT: K 171 LYS cc_start: 0.7683 (mptt) cc_final: 0.6975 (mtpp) REVERT: K 224 MET cc_start: 0.7611 (tpt) cc_final: 0.7111 (tpp) REVERT: K 259 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7569 (mt-10) REVERT: K 260 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8123 (mt0) REVERT: K 481 ARG cc_start: 0.7298 (mtp180) cc_final: 0.6746 (mtp85) REVERT: K 543 LEU cc_start: 0.8350 (tm) cc_final: 0.8021 (tt) REVERT: L 54 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6764 (mt-10) REVERT: L 123 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7919 (tt0) REVERT: L 134 ASP cc_start: 0.7108 (t70) cc_final: 0.6511 (p0) REVERT: L 171 LYS cc_start: 0.7641 (mptt) cc_final: 0.6941 (mtpp) REVERT: L 224 MET cc_start: 0.7600 (tpt) cc_final: 0.7092 (tpp) REVERT: L 258 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6918 (tp30) REVERT: L 260 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: L 261 SER cc_start: 0.8828 (t) cc_final: 0.8490 (p) REVERT: L 329 ASN cc_start: 0.7346 (t0) cc_final: 0.6811 (t0) REVERT: L 465 ARG cc_start: 0.7501 (ttt-90) cc_final: 0.7162 (ttt-90) REVERT: L 481 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6037 (mtp85) REVERT: L 500 VAL cc_start: 0.9072 (m) cc_final: 0.8535 (p) REVERT: L 535 LYS cc_start: 0.8160 (pptt) cc_final: 0.7887 (pttp) REVERT: L 543 LEU cc_start: 0.8358 (tm) cc_final: 0.8024 (tt) outliers start: 53 outliers final: 22 residues processed: 377 average time/residue: 1.3323 time to fit residues: 570.2579 Evaluate side-chains 365 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU 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 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 282 LEU 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 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 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 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: 0.3980 chunk 108 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 167 GLN J 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.119745 restraints weight = 54792.760| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.90 r_work: 0.3141 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- 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 = 0.82 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 = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18208 Z= 0.143 Angle : 0.551 5.214 24688 Z= 0.281 Chirality : 0.044 0.147 2748 Planarity : 0.005 0.106 3164 Dihedral : 7.592 56.464 2708 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.73 % Allowed : 17.63 % 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: 0.61 (0.18), residues: 2220 helix: 1.30 (0.18), residues: 920 sheet: -0.53 (0.26), residues: 348 loop : 0.02 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 252 TYR 0.012 0.002 TYR L 265 PHE 0.012 0.001 PHE H 163 TRP 0.008 0.001 TRP K 358 HIS 0.004 0.001 HIS K 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (18208) covalent geometry : angle 0.55138 / 0.28 (24688) hydrogen bonds : bond 0.03326 / 2.22 ( 731) hydrogen bonds : angle 4.35793 / 3.10 ( 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 389 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 336 time to evaluate : 1.082 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 18 ILE cc_start: 0.9242 (tp) cc_final: 0.9022 (tp) REVERT: H 49 THR cc_start: 0.9138 (m) cc_final: 0.8818 (p) REVERT: H 78 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7548 (mp) REVERT: H 109 LYS cc_start: 0.8756 (mttm) cc_final: 0.8497 (mttm) REVERT: H 224 MET cc_start: 0.7642 (tpt) cc_final: 0.7168 (tpp) REVERT: H 228 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: H 258 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6915 (tp30) REVERT: H 260 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: H 261 SER cc_start: 0.8752 (t) cc_final: 0.8309 (p) REVERT: H 500 VAL cc_start: 0.9060 (m) cc_final: 0.8506 (p) REVERT: H 535 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7872 (pptt) REVERT: H 543 LEU cc_start: 0.8360 (tm) cc_final: 0.8049 (tt) REVERT: J 18 ILE cc_start: 0.9230 (tp) cc_final: 0.9004 (tp) REVERT: J 78 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7605 (mp) REVERT: J 172 ARG cc_start: 0.7803 (tpt90) cc_final: 0.7378 (tpt170) REVERT: J 224 MET cc_start: 0.7591 (tpt) cc_final: 0.7115 (tpp) REVERT: J 239 GLU cc_start: 0.7913 (mp0) cc_final: 0.7680 (mp0) REVERT: J 260 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: J 333 ASN cc_start: 0.8004 (t0) cc_final: 0.7626 (t0) REVERT: J 475 GLU cc_start: 0.7850 (tt0) cc_final: 0.7622 (mt-10) REVERT: J 481 ARG cc_start: 0.6911 (mmm-85) cc_final: 0.6464 (mtm110) REVERT: J 500 VAL cc_start: 0.9056 (m) cc_final: 0.8489 (p) REVERT: J 535 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7858 (pptt) REVERT: J 543 LEU cc_start: 0.8357 (tm) cc_final: 0.8038 (tt) REVERT: K 18 ILE cc_start: 0.9244 (tp) cc_final: 0.9008 (tp) REVERT: K 78 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7595 (mp) REVERT: K 123 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7922 (tt0) REVERT: K 224 MET cc_start: 0.7644 (tpt) cc_final: 0.7155 (tpp) REVERT: K 228 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: K 259 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7569 (mt-10) REVERT: K 260 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: K 481 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6727 (mtp85) REVERT: K 543 LEU cc_start: 0.8353 (tm) cc_final: 0.8030 (tt) REVERT: L 18 ILE cc_start: 0.9243 (tp) cc_final: 0.9027 (tp) REVERT: L 54 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6805 (mt-10) REVERT: L 109 LYS cc_start: 0.8765 (mttm) cc_final: 0.8548 (mttm) REVERT: L 123 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7928 (tt0) REVERT: L 171 LYS cc_start: 0.7655 (mptt) cc_final: 0.7126 (mmmm) REVERT: L 224 MET cc_start: 0.7602 (tpt) cc_final: 0.7138 (tpp) REVERT: L 258 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: L 260 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: L 261 SER cc_start: 0.8840 (t) cc_final: 0.8490 (p) REVERT: L 329 ASN cc_start: 0.7358 (t0) cc_final: 0.6835 (t0) REVERT: L 481 ARG cc_start: 0.6898 (mtm-85) cc_final: 0.6121 (mtp85) REVERT: L 500 VAL cc_start: 0.9068 (m) cc_final: 0.8507 (p) REVERT: L 535 LYS cc_start: 0.8179 (pptt) cc_final: 0.7931 (pttp) REVERT: L 543 LEU cc_start: 0.8345 (tm) cc_final: 0.8028 (tt) outliers start: 53 outliers final: 21 residues processed: 375 average time/residue: 1.2510 time to fit residues: 531.0587 Evaluate side-chains 372 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 535 LYS Chi-restraints excluded: chain J residue 78 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 367 ILE Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 78 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 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 51 SER 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 367 ILE Chi-restraints excluded: chain L residue 424 PHE 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: 0.9980 chunk 0 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 287 ASN K 167 GLN L 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.164599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119853 restraints weight = 54575.861| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.91 r_work: 0.3141 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18208 Z= 0.147 Angle : 0.550 5.658 24688 Z= 0.280 Chirality : 0.044 0.149 2748 Planarity : 0.005 0.066 3164 Dihedral : 7.572 56.800 2708 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.42 % Allowed : 17.78 % Favored : 79.79 % 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: 1.33 (0.18), residues: 920 sheet: -0.47 (0.26), residues: 340 loop : 0.07 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 252 TYR 0.011 0.002 TYR H 42 PHE 0.013 0.001 PHE J 424 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (18208) covalent geometry : angle 0.54992 / 0.28 (24688) hydrogen bonds : bond 0.03284 / 2.19 ( 731) hydrogen bonds : angle 4.31572 / 3.08 ( 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 380 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 333 time to evaluate : 1.014 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: 0.9141 (m) cc_final: 0.8814 (p) REVERT: H 78 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7549 (mp) REVERT: H 109 LYS cc_start: 0.8753 (mttm) cc_final: 0.8521 (mttm) REVERT: H 224 MET cc_start: 0.7630 (tpt) cc_final: 0.7171 (tpp) REVERT: H 258 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: H 260 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: H 261 SER cc_start: 0.8742 (t) cc_final: 0.8302 (p) REVERT: H 376 ARG cc_start: 0.6795 (ttm-80) cc_final: 0.6268 (tmm-80) REVERT: H 500 VAL cc_start: 0.9060 (m) cc_final: 0.8498 (p) REVERT: H 535 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7983 (pptt) REVERT: H 543 LEU cc_start: 0.8354 (tm) cc_final: 0.8055 (tt) REVERT: J 18 ILE cc_start: 0.9224 (tp) cc_final: 0.9005 (tp) REVERT: J 49 THR cc_start: 0.9157 (m) cc_final: 0.8854 (p) REVERT: J 78 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7572 (mp) REVERT: J 134 ASP cc_start: 0.7191 (t70) cc_final: 0.6543 (p0) REVERT: J 172 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7396 (tpt170) REVERT: J 224 MET cc_start: 0.7590 (tpt) cc_final: 0.7071 (tpp) REVERT: J 228 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: J 239 GLU cc_start: 0.7903 (mp0) cc_final: 0.7583 (mp0) REVERT: J 260 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8188 (mt0) REVERT: J 333 ASN cc_start: 0.7980 (t0) cc_final: 0.7588 (t0) REVERT: J 465 ARG cc_start: 0.7580 (ttt-90) cc_final: 0.7280 (ttt-90) REVERT: J 475 GLU cc_start: 0.7851 (tt0) cc_final: 0.7620 (mt-10) REVERT: J 500 VAL cc_start: 0.9052 (m) cc_final: 0.8479 (p) REVERT: J 535 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7954 (pptt) REVERT: J 543 LEU cc_start: 0.8348 (tm) cc_final: 0.8043 (tt) REVERT: K 78 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7559 (mp) REVERT: K 224 MET cc_start: 0.7628 (tpt) cc_final: 0.7140 (tpp) REVERT: K 228 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: K 260 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: K 481 ARG cc_start: 0.7257 (mtp180) cc_final: 0.6712 (mtp85) REVERT: K 543 LEU cc_start: 0.8336 (tm) cc_final: 0.8028 (tt) REVERT: L 18 ILE cc_start: 0.9232 (tp) cc_final: 0.9009 (tp) REVERT: L 54 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6867 (mt-10) REVERT: L 109 LYS cc_start: 0.8765 (mttm) cc_final: 0.8559 (mttm) REVERT: L 123 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7923 (tt0) REVERT: L 224 MET cc_start: 0.7621 (tpt) cc_final: 0.7129 (tpp) REVERT: L 258 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: L 260 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: L 261 SER cc_start: 0.8828 (t) cc_final: 0.8444 (p) REVERT: L 329 ASN cc_start: 0.7362 (t0) cc_final: 0.6849 (t0) REVERT: L 481 ARG cc_start: 0.6909 (mtm-85) cc_final: 0.6111 (mtp85) REVERT: L 500 VAL cc_start: 0.9068 (m) cc_final: 0.8501 (p) REVERT: L 535 LYS cc_start: 0.8177 (pptt) cc_final: 0.7915 (pttp) REVERT: L 543 LEU cc_start: 0.8342 (tm) cc_final: 0.8039 (tt) outliers start: 47 outliers final: 22 residues processed: 366 average time/residue: 1.3189 time to fit residues: 546.3354 Evaluate side-chains 363 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 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 H residue 535 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 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 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 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 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 408 GLU Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 51 SER 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 367 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 155 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 105 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 287 ASN L 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.164599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.119699 restraints weight = 54528.086| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.92 r_work: 0.3145 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4641 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= 0.138 Angle : 0.545 5.322 24688 Z= 0.277 Chirality : 0.044 0.149 2748 Planarity : 0.005 0.065 3164 Dihedral : 7.458 56.405 2708 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.01 % Allowed : 18.61 % Favored : 79.38 % 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: 0.75 (0.18), residues: 2220 helix: 1.41 (0.18), residues: 920 sheet: -0.44 (0.27), residues: 340 loop : 0.10 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 389 TYR 0.012 0.001 TYR L 42 PHE 0.013 0.001 PHE L 424 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (18208) covalent geometry : angle 0.54476 / 0.28 (24688) hydrogen bonds : bond 0.03200 / 2.14 ( 731) hydrogen bonds : angle 4.27867 / 3.05 ( 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 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 331 time to evaluate : 0.876 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: 0.9130 (m) cc_final: 0.8805 (p) REVERT: H 78 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7528 (mp) REVERT: H 109 LYS cc_start: 0.8766 (mttm) cc_final: 0.8527 (mttm) REVERT: H 224 MET cc_start: 0.7642 (tpt) cc_final: 0.7152 (tpp) REVERT: H 228 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: H 258 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6895 (tp30) REVERT: H 260 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: H 261 SER cc_start: 0.8719 (t) cc_final: 0.8287 (p) REVERT: H 365 ASP cc_start: 0.7745 (t0) cc_final: 0.7417 (t0) REVERT: H 376 ARG cc_start: 0.6786 (ttm-80) cc_final: 0.6232 (tmm-80) REVERT: H 500 VAL cc_start: 0.9041 (m) cc_final: 0.8470 (p) REVERT: H 535 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7974 (pptt) REVERT: H 543 LEU cc_start: 0.8351 (tm) cc_final: 0.8062 (tt) REVERT: J 18 ILE cc_start: 0.9214 (tp) cc_final: 0.9001 (tp) REVERT: J 49 THR cc_start: 0.9142 (m) cc_final: 0.8841 (p) REVERT: J 78 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7542 (mp) REVERT: J 134 ASP cc_start: 0.7160 (t70) cc_final: 0.6504 (p0) REVERT: J 172 ARG cc_start: 0.7831 (tpt90) cc_final: 0.7384 (tpt170) REVERT: J 224 MET cc_start: 0.7625 (tpt) cc_final: 0.7119 (tpp) REVERT: J 228 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: J 239 GLU cc_start: 0.7904 (mp0) cc_final: 0.7581 (mp0) REVERT: J 260 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: J 333 ASN cc_start: 0.7928 (t0) cc_final: 0.7499 (t0) REVERT: J 465 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.7223 (ttt-90) REVERT: J 475 GLU cc_start: 0.7858 (tt0) cc_final: 0.7628 (mt-10) REVERT: J 481 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6495 (mtm110) REVERT: J 500 VAL cc_start: 0.9047 (m) cc_final: 0.8471 (p) REVERT: J 535 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7932 (pptt) REVERT: J 543 LEU cc_start: 0.8347 (tm) cc_final: 0.8053 (tt) REVERT: K 78 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7582 (mp) REVERT: K 224 MET cc_start: 0.7623 (tpt) cc_final: 0.7157 (tpp) REVERT: K 260 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: K 481 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6710 (mtp85) REVERT: K 543 LEU cc_start: 0.8337 (tm) cc_final: 0.8040 (tt) REVERT: L 18 ILE cc_start: 0.9228 (tp) cc_final: 0.9010 (tp) REVERT: L 54 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6876 (mt-10) REVERT: L 123 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7930 (tt0) REVERT: L 224 MET cc_start: 0.7620 (tpt) cc_final: 0.7130 (tpp) REVERT: L 258 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6889 (tp30) REVERT: L 260 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8016 (mt0) REVERT: L 261 SER cc_start: 0.8842 (t) cc_final: 0.8450 (p) REVERT: L 329 ASN cc_start: 0.7352 (t0) cc_final: 0.6843 (t0) REVERT: L 389 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7134 (ttp-110) REVERT: L 481 ARG cc_start: 0.6872 (mtm-85) cc_final: 0.6076 (mtp85) REVERT: L 500 VAL cc_start: 0.9063 (m) cc_final: 0.8494 (p) REVERT: L 535 LYS cc_start: 0.8206 (pptt) cc_final: 0.7952 (pttp) REVERT: L 543 LEU cc_start: 0.8346 (tm) cc_final: 0.8050 (tt) outliers start: 39 outliers final: 20 residues processed: 358 average time/residue: 1.2217 time to fit residues: 495.4565 Evaluate side-chains 358 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 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 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU 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 408 GLU Chi-restraints excluded: chain L residue 51 SER 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 367 ILE 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: 0.2980 chunk 205 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 44 ASN J 333 ASN K 44 ASN K 323 HIS 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 = 0.165376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120746 restraints weight = 54623.978| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.92 r_work: 0.3141 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 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 = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4713 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= 0.136 Angle : 0.544 5.391 24688 Z= 0.277 Chirality : 0.044 0.147 2748 Planarity : 0.005 0.063 3164 Dihedral : 7.377 56.182 2708 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.91 % Allowed : 18.87 % Favored : 79.23 % 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: 0.81 (0.18), residues: 2220 helix: 1.47 (0.18), residues: 920 sheet: -0.44 (0.27), residues: 340 loop : 0.13 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 389 TYR 0.012 0.001 TYR H 42 PHE 0.013 0.001 PHE K 424 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS L 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (18208) covalent geometry : angle 0.54355 / 0.28 (24688) hydrogen bonds : bond 0.03169 / 2.12 ( 731) hydrogen bonds : angle 4.26344 / 3.04 ( 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 371 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 334 time to evaluate : 0.962 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: H 78 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7505 (mp) REVERT: H 109 LYS cc_start: 0.8757 (mttm) cc_final: 0.8516 (mttm) REVERT: H 224 MET cc_start: 0.7645 (tpt) cc_final: 0.7150 (tpp) REVERT: H 228 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: H 258 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6931 (tp30) REVERT: H 260 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: H 261 SER cc_start: 0.8714 (t) cc_final: 0.8273 (p) REVERT: H 365 ASP cc_start: 0.7764 (t0) cc_final: 0.7444 (t0) REVERT: H 376 ARG cc_start: 0.6840 (ttm-80) cc_final: 0.6267 (tmm-80) REVERT: H 483 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6584 (mp0) REVERT: H 500 VAL cc_start: 0.9031 (m) cc_final: 0.8454 (p) REVERT: H 535 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7978 (pptt) REVERT: H 543 LEU cc_start: 0.8347 (tm) cc_final: 0.8065 (tt) REVERT: J 18 ILE cc_start: 0.9223 (tp) cc_final: 0.9007 (tp) REVERT: J 49 THR cc_start: 0.9151 (m) cc_final: 0.8898 (p) REVERT: J 78 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7570 (mp) REVERT: J 134 ASP cc_start: 0.7210 (t70) cc_final: 0.6564 (p0) REVERT: J 172 ARG cc_start: 0.7834 (tpt90) cc_final: 0.7357 (tpt170) REVERT: J 224 MET cc_start: 0.7621 (tpt) cc_final: 0.7112 (tpp) REVERT: J 228 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7830 (mt-10) REVERT: J 239 GLU cc_start: 0.7915 (mp0) cc_final: 0.7585 (mp0) REVERT: J 260 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: J 333 ASN cc_start: 0.7900 (t0) cc_final: 0.7406 (t0) REVERT: J 465 ARG cc_start: 0.7528 (ttt-90) cc_final: 0.7282 (ttt-90) REVERT: J 475 GLU cc_start: 0.7878 (tt0) cc_final: 0.7656 (mt-10) REVERT: J 481 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6471 (mtm110) REVERT: J 500 VAL cc_start: 0.9033 (m) cc_final: 0.8451 (p) REVERT: J 535 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7932 (pptt) REVERT: J 543 LEU cc_start: 0.8336 (tm) cc_final: 0.8060 (tt) REVERT: K 78 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (mp) REVERT: K 224 MET cc_start: 0.7712 (tpt) cc_final: 0.7218 (tpp) REVERT: K 260 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: K 481 ARG cc_start: 0.7266 (mtp180) cc_final: 0.6705 (mtp85) REVERT: K 543 LEU cc_start: 0.8330 (tm) cc_final: 0.8042 (tt) REVERT: L 18 ILE cc_start: 0.9218 (tp) cc_final: 0.9001 (tp) REVERT: L 54 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6865 (mt-10) REVERT: L 123 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7924 (tt0) REVERT: L 134 ASP cc_start: 0.7119 (t70) cc_final: 0.6525 (p0) REVERT: L 224 MET cc_start: 0.7645 (tpt) cc_final: 0.7153 (tpp) REVERT: L 258 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6887 (tp30) REVERT: L 260 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: L 261 SER cc_start: 0.8853 (t) cc_final: 0.8461 (p) REVERT: L 329 ASN cc_start: 0.7357 (t0) cc_final: 0.6847 (t0) REVERT: L 389 ARG cc_start: 0.7372 (ttp-110) cc_final: 0.7125 (ttp-110) REVERT: L 481 ARG cc_start: 0.6873 (mtm-85) cc_final: 0.6095 (mtp85) REVERT: L 500 VAL cc_start: 0.9058 (m) cc_final: 0.8478 (p) REVERT: L 535 LYS cc_start: 0.8219 (pptt) cc_final: 0.7961 (pttp) REVERT: L 543 LEU cc_start: 0.8339 (tm) cc_final: 0.8042 (tt) outliers start: 37 outliers final: 16 residues processed: 360 average time/residue: 1.2079 time to fit residues: 492.4209 Evaluate side-chains 359 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 330 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 228 GLU 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 H residue 535 LYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 228 GLU 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 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain L residue 51 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 170 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 181 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 323 HIS K 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117709 restraints weight = 54492.889| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.92 r_work: 0.3113 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4743 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= 0.201 Angle : 0.587 5.925 24688 Z= 0.299 Chirality : 0.046 0.145 2748 Planarity : 0.005 0.064 3164 Dihedral : 7.716 55.685 2708 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.86 % Allowed : 19.28 % Favored : 78.87 % 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: 0.69 (0.18), residues: 2220 helix: 1.32 (0.18), residues: 920 sheet: -0.44 (0.27), residues: 340 loop : 0.10 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 389 TYR 0.013 0.002 TYR K 251 PHE 0.013 0.001 PHE K 163 TRP 0.008 0.002 TRP H 285 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (18208) covalent geometry : angle 0.58747 / 0.30 (24688) hydrogen bonds : bond 0.03523 / 2.36 ( 731) hydrogen bonds : angle 4.34221 / 3.10 ( 2073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14138.56 seconds wall clock time: 239 minutes 30.64 seconds (14370.64 seconds total)