Starting phenix.real_space_refine on Sat Mar 7 00:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mh1_23833/03_2026/7mh1_23833_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mh1_23833/03_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_23833/03_2026/7mh1_23833_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mh1_23833/03_2026/7mh1_23833_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mh1_23833/03_2026/7mh1_23833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mh1_23833/03_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-5986/lib/python3.9/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: 5.49, per 1000 atoms: 0.15 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: 3.03 Conformation dependent library (CDL) restraints added in 887.5 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.88 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: 10.31 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 1731 1.01 - 1.21: 16033 1.21 - 1.41: 7498 1.41 - 1.61: 10602 1.61 - 1.81: 144 Bond restraints: 36008 Sorted by residual: bond pdb=" N VAL K 97 " pdb=" H VAL K 97 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N ASN J 412 " pdb=" H ASN J 412 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N TYR K 106 " pdb=" H TYR K 106 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" NE ARG K 508 " pdb=" HE ARG K 508 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" CD2 HIS J 96 " pdb=" HD2 HIS J 96 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 36003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 53505 2.65 - 5.29: 9393 5.29 - 7.94: 2176 7.94 - 10.59: 146 10.59 - 13.24: 52 Bond angle restraints: 65272 Sorted by residual: angle pdb=" N PRO K 538 " pdb=" CA PRO K 538 " pdb=" C PRO K 538 " ideal model delta sigma weight residual 110.70 118.62 -7.92 1.22e+00 6.72e-01 4.21e+01 angle pdb=" N PRO H 538 " pdb=" CA PRO H 538 " pdb=" C PRO H 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO J 538 " pdb=" CA PRO J 538 " pdb=" C PRO J 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" N PRO L 538 " pdb=" CA PRO L 538 " pdb=" C PRO L 538 " ideal model delta sigma weight residual 110.70 118.59 -7.89 1.22e+00 6.72e-01 4.18e+01 angle pdb=" CA ASN K 443 " pdb=" CB ASN K 443 " pdb=" CG ASN K 443 " ideal model delta sigma weight residual 112.60 119.02 -6.42 1.00e+00 1.00e+00 4.12e+01 ... (remaining 65267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16052 35.09 - 70.19: 724 70.19 - 105.28: 46 105.28 - 140.37: 8 140.37 - 175.46: 10 Dihedral angle restraints: 16840 sinusoidal: 9388 harmonic: 7452 Sorted by residual: dihedral pdb=" O1G CTP J 604 " pdb=" O3B CTP J 604 " pdb=" PG CTP J 604 " pdb=" PB CTP J 604 " ideal model delta sinusoidal sigma weight residual 82.72 -101.82 -175.46 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1G CTP K 603 " pdb=" O3B CTP K 603 " pdb=" PG CTP K 603 " pdb=" PB CTP K 603 " ideal model delta sinusoidal sigma weight residual 82.72 -101.87 -175.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O3A CTP K 601 " pdb=" O3B CTP K 601 " pdb=" PB CTP K 601 " pdb=" PG CTP K 601 " ideal model delta sinusoidal sigma weight residual 204.50 46.10 158.40 1 2.00e+01 2.50e-03 4.63e+01 ... (remaining 16837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1568 0.080 - 0.161: 756 0.161 - 0.241: 348 0.241 - 0.321: 60 0.321 - 0.402: 16 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CA PRO K 538 " pdb=" N PRO K 538 " pdb=" C PRO K 538 " pdb=" CB PRO K 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA PRO H 538 " pdb=" N PRO H 538 " pdb=" C PRO H 538 " pdb=" CB PRO H 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA PRO J 538 " pdb=" N PRO J 538 " pdb=" C PRO J 538 " pdb=" CB PRO J 538 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 2745 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 269 " 0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG J 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG J 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG J 269 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG J 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG J 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG J 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG J 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG J 269 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 269 " -0.523 9.50e-02 1.11e+02 1.90e-01 1.57e+02 pdb=" NE ARG L 269 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG L 269 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG L 269 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG L 269 " 0.109 2.00e-02 2.50e+03 pdb="HH11 ARG L 269 " -0.010 2.00e-02 2.50e+03 pdb="HH12 ARG L 269 " 0.050 2.00e-02 2.50e+03 pdb="HH21 ARG L 269 " 0.044 2.00e-02 2.50e+03 pdb="HH22 ARG L 269 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 269 " 0.522 9.50e-02 1.11e+02 1.90e-01 1.56e+02 pdb=" NE ARG H 269 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG H 269 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG H 269 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG H 269 " -0.109 2.00e-02 2.50e+03 pdb="HH11 ARG H 269 " 0.010 2.00e-02 2.50e+03 pdb="HH12 ARG H 269 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG H 269 " -0.044 2.00e-02 2.50e+03 pdb="HH22 ARG H 269 " 0.173 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 1171 2.06 - 2.70: 49467 2.70 - 3.33: 111381 3.33 - 3.97: 147939 3.97 - 4.60: 217689 Nonbonded interactions: 527647 Sorted by model distance: nonbonded pdb="HD21 ASN K 44 " pdb=" HE1 PHE K 50 " model vdw 1.426 2.100 nonbonded pdb="HD21 ASN J 44 " pdb=" HE1 PHE J 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN H 44 " pdb=" HE1 PHE H 50 " model vdw 1.427 2.100 nonbonded pdb="HD21 ASN L 44 " pdb=" HE1 PHE L 50 " model vdw 1.427 2.100 nonbonded pdb=" HG1 THR H 49 " pdb=" OE2 GLU K 101 " model vdw 1.579 2.450 ... (remaining 527642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'H' and resid 1 through 557) selection = (chain 'J' and resid 1 through 557) selection = (chain 'K' and resid 1 through 557) selection = (chain 'L' and resid 1 through 557) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 33.930 Find NCS groups from input model: 0.640 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:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.053 18208 Z= 0.766 Angle : 2.030 12.894 24688 Z= 1.339 Chirality : 0.110 0.402 2748 Planarity : 0.016 0.155 3172 Dihedral : 16.816 175.465 6884 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.44 % Allowed : 7.22 % Favored : 91.34 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2220 helix: -0.97 (0.15), residues: 880 sheet: -0.74 (0.24), residues: 372 loop : -0.34 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG K 269 TYR 0.135 0.021 TYR L 307 PHE 0.085 0.013 PHE K 163 TRP 0.100 0.023 TRP K 285 HIS 0.011 0.004 HIS L 235 Details of bonding type rmsd covalent geometry : bond 0.01221 (18208) covalent geometry : angle 2.02984 (24688) hydrogen bonds : bond 0.18312 ( 731) hydrogen bonds : angle 7.61362 ( 2073) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 465 time to evaluate : 0.602 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: 1.1199 time to fit residues: 616.2855 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 : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 86 ASN H 165 GLN H 185 GLN H 287 ASN H 440 ASN H 443 ASN J 86 ASN J 165 GLN J 185 GLN J 287 ASN J 440 ASN J 443 ASN K 86 ASN K 165 GLN K 287 ASN K 440 ASN K 443 ASN L 86 ASN L 165 GLN L 185 GLN L 440 ASN L 443 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.167153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123220 restraints weight = 55236.077| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.91 r_work: 0.3203 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- 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 = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18208 Z= 0.154 Angle : 0.694 7.005 24688 Z= 0.352 Chirality : 0.048 0.152 2748 Planarity : 0.005 0.052 3172 Dihedral : 14.354 179.018 2532 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.14 % Allowed : 14.23 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2220 helix: 0.13 (0.16), residues: 904 sheet: -0.44 (0.24), residues: 392 loop : -0.23 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 252 TYR 0.013 0.002 TYR H 265 PHE 0.019 0.002 PHE J 424 TRP 0.011 0.001 TRP K 358 HIS 0.006 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00356 (18208) covalent geometry : angle 0.69424 (24688) hydrogen bonds : bond 0.04577 ( 731) hydrogen bonds : angle 5.23303 ( 2073) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 0.826 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: 0.7754 (tptp) cc_final: 0.7511 (tttp) REVERT: H 49 THR cc_start: 0.9013 (m) cc_final: 0.8636 (p) REVERT: H 54 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6861 (mt-10) REVERT: H 78 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7826 (mp) REVERT: H 123 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7625 (mt-10) REVERT: H 157 MET cc_start: 0.8608 (mmt) cc_final: 0.8352 (mmt) REVERT: H 212 ASP cc_start: 0.8768 (m-30) cc_final: 0.8484 (m-30) REVERT: H 224 MET cc_start: 0.7597 (tpt) cc_final: 0.7050 (tpp) REVERT: H 228 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: H 258 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7023 (tp30) REVERT: H 500 VAL cc_start: 0.9082 (m) cc_final: 0.8650 (p) REVERT: H 543 LEU cc_start: 0.8317 (tm) cc_final: 0.8011 (tt) REVERT: J 49 THR cc_start: 0.9015 (m) cc_final: 0.8650 (p) REVERT: J 54 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6833 (mt-10) REVERT: J 78 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7755 (mp) REVERT: J 123 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7766 (tt0) REVERT: J 172 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7369 (tpt170) REVERT: J 212 ASP cc_start: 0.8770 (m-30) cc_final: 0.8463 (m-30) REVERT: J 224 MET cc_start: 0.7559 (tpt) cc_final: 0.7015 (tpp) REVERT: J 228 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: J 239 GLU cc_start: 0.7779 (mp0) cc_final: 0.7529 (mp0) REVERT: J 500 VAL cc_start: 0.9067 (m) cc_final: 0.8627 (p) REVERT: J 507 ASP cc_start: 0.7146 (m-30) cc_final: 0.6897 (m-30) REVERT: J 513 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6438 (tt0) REVERT: J 543 LEU cc_start: 0.8346 (tm) cc_final: 0.8030 (tt) REVERT: K 49 THR cc_start: 0.9002 (m) cc_final: 0.8649 (p) REVERT: K 54 GLU cc_start: 0.7255 (mm-30) cc_final: 0.7031 (mt-10) REVERT: K 78 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7770 (mp) REVERT: K 123 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7667 (mt-10) REVERT: K 157 MET cc_start: 0.8614 (mmt) cc_final: 0.8342 (mmt) REVERT: K 212 ASP cc_start: 0.8767 (m-30) cc_final: 0.8486 (m-30) REVERT: K 224 MET cc_start: 0.7581 (tpt) cc_final: 0.6809 (tpp) REVERT: K 227 LYS cc_start: 0.7993 (mttt) cc_final: 0.7652 (mttp) REVERT: K 228 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: K 322 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7507 (mt-10) REVERT: K 329 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.7032 (t0) REVERT: K 500 VAL cc_start: 0.9087 (m) cc_final: 0.8629 (p) REVERT: K 543 LEU cc_start: 0.8346 (tm) cc_final: 0.8029 (tt) REVERT: L 49 THR cc_start: 0.9016 (m) cc_final: 0.8608 (p) REVERT: L 123 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7670 (mt-10) REVERT: L 224 MET cc_start: 0.7536 (tpt) cc_final: 0.7016 (tpp) REVERT: L 227 LYS cc_start: 0.7999 (mttt) cc_final: 0.7701 (mtpp) REVERT: L 228 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: L 258 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: L 322 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7337 (mt-10) REVERT: L 329 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6741 (t0) REVERT: L 500 VAL cc_start: 0.9070 (m) cc_final: 0.8641 (p) REVERT: L 543 LEU cc_start: 0.8349 (tm) cc_final: 0.8044 (tt) outliers start: 61 outliers final: 10 residues processed: 419 average time/residue: 1.1488 time to fit residues: 545.5461 Evaluate side-chains 365 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 344 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 261 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 240 GLN Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 329 ASN Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 329 ASN Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 87 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 136 ASN H 287 ASN H 323 HIS J 323 HIS K 136 ASN K 323 HIS L 287 ASN L 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.162907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.118070 restraints weight = 54864.913| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.91 r_work: 0.3114 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18208 Z= 0.233 Angle : 0.691 6.929 24688 Z= 0.347 Chirality : 0.048 0.145 2748 Planarity : 0.005 0.052 3172 Dihedral : 13.082 173.240 2530 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.20 % Allowed : 15.31 % Favored : 81.49 % 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: 0.03 (0.18), residues: 2220 helix: 0.53 (0.17), residues: 912 sheet: -0.56 (0.24), residues: 388 loop : -0.04 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 252 TYR 0.014 0.002 TYR K 265 PHE 0.015 0.002 PHE L 163 TRP 0.011 0.002 TRP J 358 HIS 0.006 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00549 (18208) covalent geometry : angle 0.69069 (24688) hydrogen bonds : bond 0.04454 ( 731) hydrogen bonds : angle 4.90615 ( 2073) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 367 time to evaluate : 0.903 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: H 49 THR cc_start: 0.9141 (m) cc_final: 0.8801 (p) REVERT: H 54 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6813 (mt-10) REVERT: H 78 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7746 (mp) REVERT: H 102 ARG cc_start: 0.8348 (mmm160) cc_final: 0.8104 (mmp-170) REVERT: H 109 LYS cc_start: 0.8731 (mttm) cc_final: 0.8525 (mttm) REVERT: H 123 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7897 (tt0) REVERT: H 224 MET cc_start: 0.7570 (tpt) cc_final: 0.7062 (tpp) REVERT: H 228 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7759 (mt-10) REVERT: H 252 ARG cc_start: 0.8476 (ttm-80) cc_final: 0.8167 (ttm-80) REVERT: H 258 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7019 (tp30) REVERT: H 267 LYS cc_start: 0.7907 (tttm) cc_final: 0.7444 (tttt) REVERT: H 500 VAL cc_start: 0.9081 (m) cc_final: 0.8574 (p) REVERT: H 543 LEU cc_start: 0.8268 (tm) cc_final: 0.7952 (tt) REVERT: J 49 THR cc_start: 0.9139 (m) cc_final: 0.8798 (p) REVERT: J 54 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6807 (mt-10) REVERT: J 78 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7724 (mp) REVERT: J 123 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7907 (tt0) REVERT: J 172 ARG cc_start: 0.7854 (tpt90) cc_final: 0.7304 (tpt170) REVERT: J 224 MET cc_start: 0.7528 (tpt) cc_final: 0.7007 (tpp) REVERT: J 228 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: J 239 GLU cc_start: 0.7821 (mp0) cc_final: 0.7493 (mp0) REVERT: J 252 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8171 (ttm-80) REVERT: J 500 VAL cc_start: 0.9086 (m) cc_final: 0.8574 (p) REVERT: J 507 ASP cc_start: 0.7173 (m-30) cc_final: 0.6958 (m-30) REVERT: J 543 LEU cc_start: 0.8289 (tm) cc_final: 0.7954 (tt) REVERT: K 49 THR cc_start: 0.9130 (m) cc_final: 0.8795 (p) REVERT: K 54 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6876 (mt-10) REVERT: K 78 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7738 (mp) REVERT: K 123 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7901 (mt-10) REVERT: K 224 MET cc_start: 0.7550 (tpt) cc_final: 0.6985 (tpp) REVERT: K 228 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: K 252 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8242 (ttm-80) REVERT: K 261 SER cc_start: 0.8801 (t) cc_final: 0.8550 (p) REVERT: K 267 LYS cc_start: 0.7903 (tttm) cc_final: 0.7423 (tttt) REVERT: K 322 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7652 (mt-10) REVERT: K 365 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7492 (t0) REVERT: K 481 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6700 (mtp85) REVERT: K 500 VAL cc_start: 0.9090 (m) cc_final: 0.8560 (p) REVERT: K 543 LEU cc_start: 0.8299 (tm) cc_final: 0.7960 (tt) REVERT: L 49 THR cc_start: 0.9097 (m) cc_final: 0.8757 (p) REVERT: L 78 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7703 (mp) REVERT: L 123 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7871 (tt0) REVERT: L 224 MET cc_start: 0.7529 (tpt) cc_final: 0.6981 (tpp) REVERT: L 228 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: L 252 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8262 (ttm-80) REVERT: L 258 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: L 260 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7966 (mt0) REVERT: L 267 LYS cc_start: 0.7965 (tttm) cc_final: 0.7496 (tttt) REVERT: L 322 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7507 (mt-10) REVERT: L 329 ASN cc_start: 0.7445 (t0) cc_final: 0.6913 (t0) REVERT: L 473 PHE cc_start: 0.8250 (p90) cc_final: 0.7984 (p90) REVERT: L 500 VAL cc_start: 0.9089 (m) cc_final: 0.8588 (p) REVERT: L 543 LEU cc_start: 0.8290 (tm) cc_final: 0.7962 (tt) outliers start: 62 outliers final: 25 residues processed: 407 average time/residue: 1.2683 time to fit residues: 580.1815 Evaluate side-chains 379 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 342 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 244 ILE 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 240 GLN Chi-restraints excluded: chain J residue 244 ILE 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 244 ILE 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 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 81 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN H 517 HIS J 287 ASN K 287 ASN L 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.164667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119742 restraints weight = 54525.370| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.92 r_work: 0.3142 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3930 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= 0.141 Angle : 0.608 6.847 24688 Z= 0.303 Chirality : 0.045 0.149 2748 Planarity : 0.005 0.051 3172 Dihedral : 12.235 166.265 2530 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.40 % Allowed : 15.88 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2220 helix: 0.84 (0.17), residues: 920 sheet: -0.64 (0.24), residues: 388 loop : 0.05 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 389 TYR 0.013 0.001 TYR H 265 PHE 0.012 0.001 PHE L 424 TRP 0.009 0.001 TRP J 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00327 (18208) covalent geometry : angle 0.60845 (24688) hydrogen bonds : bond 0.03651 ( 731) hydrogen bonds : angle 4.61427 ( 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 417 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 351 time to evaluate : 0.798 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: 0.9150 (m) cc_final: 0.8816 (p) REVERT: H 78 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7669 (mp) REVERT: H 109 LYS cc_start: 0.8691 (mttm) cc_final: 0.8484 (mttm) REVERT: H 123 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7922 (tt0) REVERT: H 224 MET cc_start: 0.7606 (tpt) cc_final: 0.7121 (tpp) REVERT: H 228 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: H 252 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8063 (ttm-80) REVERT: H 258 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: H 260 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8074 (mt0) REVERT: H 500 VAL cc_start: 0.9070 (m) cc_final: 0.8558 (p) REVERT: H 543 LEU cc_start: 0.8272 (tm) cc_final: 0.7950 (tt) REVERT: J 49 THR cc_start: 0.9141 (m) cc_final: 0.8813 (p) REVERT: J 78 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7644 (mp) REVERT: J 123 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7880 (tt0) REVERT: J 172 ARG cc_start: 0.7836 (tpt90) cc_final: 0.7448 (tpt170) REVERT: J 224 MET cc_start: 0.7533 (tpt) cc_final: 0.7037 (tpp) REVERT: J 228 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: J 239 GLU cc_start: 0.7836 (mp0) cc_final: 0.7538 (mp0) REVERT: J 252 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8290 (ttm-80) REVERT: J 260 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: J 261 SER cc_start: 0.8845 (t) cc_final: 0.8637 (p) REVERT: J 475 GLU cc_start: 0.7962 (tt0) cc_final: 0.7731 (mt-10) REVERT: J 500 VAL cc_start: 0.9065 (m) cc_final: 0.8531 (p) REVERT: K 49 THR cc_start: 0.9135 (m) cc_final: 0.8804 (p) REVERT: K 78 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7668 (mp) REVERT: K 123 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7909 (tt0) REVERT: K 224 MET cc_start: 0.7529 (tpt) cc_final: 0.7042 (tpp) REVERT: K 228 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: K 252 ARG cc_start: 0.8443 (ttm-80) cc_final: 0.8228 (ttm-80) REVERT: K 260 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: K 261 SER cc_start: 0.8797 (t) cc_final: 0.8584 (p) REVERT: K 291 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6538 (ttp80) REVERT: K 365 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7354 (t0) REVERT: K 481 ARG cc_start: 0.7189 (mtp180) cc_final: 0.6696 (mtp85) REVERT: K 500 VAL cc_start: 0.9075 (m) cc_final: 0.8530 (p) REVERT: L 49 THR cc_start: 0.9086 (m) cc_final: 0.8756 (p) REVERT: L 54 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6840 (mt-10) REVERT: L 78 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7608 (mp) REVERT: L 123 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7918 (tt0) REVERT: L 171 LYS cc_start: 0.7678 (mptt) cc_final: 0.7191 (mmmm) REVERT: L 224 MET cc_start: 0.7549 (tpt) cc_final: 0.7059 (tpp) REVERT: L 228 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: L 252 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: L 258 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6957 (tp30) REVERT: L 261 SER cc_start: 0.8831 (t) cc_final: 0.8471 (p) REVERT: L 329 ASN cc_start: 0.7400 (t0) cc_final: 0.6849 (t0) REVERT: L 481 ARG cc_start: 0.6912 (mtm-85) cc_final: 0.6100 (mtp85) REVERT: L 500 VAL cc_start: 0.9086 (m) cc_final: 0.8563 (p) REVERT: L 543 LEU cc_start: 0.8281 (tm) cc_final: 0.7957 (tt) outliers start: 66 outliers final: 30 residues processed: 400 average time/residue: 1.2116 time to fit residues: 547.6069 Evaluate side-chains 387 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 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 207 LEU Chi-restraints excluded: chain J residue 213 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 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 228 GLU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 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 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 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: 0.9990 chunk 214 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 287 ASN J 517 HIS K 333 ASN K 517 HIS L 287 ASN L 517 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119250 restraints weight = 54499.054| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.93 r_work: 0.3133 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18208 Z= 0.155 Angle : 0.602 6.845 24688 Z= 0.298 Chirality : 0.045 0.146 2748 Planarity : 0.005 0.058 3172 Dihedral : 11.888 160.549 2530 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.56 % Allowed : 15.82 % Favored : 80.62 % 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: 0.37 (0.18), residues: 2220 helix: 1.02 (0.18), residues: 920 sheet: -0.57 (0.25), residues: 348 loop : -0.04 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 389 TYR 0.011 0.001 TYR J 42 PHE 0.012 0.001 PHE L 163 TRP 0.011 0.002 TRP J 358 HIS 0.004 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00365 (18208) covalent geometry : angle 0.60166 (24688) hydrogen bonds : bond 0.03521 ( 731) hydrogen bonds : angle 4.48646 ( 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 413 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 344 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 49 THR cc_start: 0.9151 (m) cc_final: 0.8799 (p) REVERT: H 54 GLU cc_start: 0.7372 (mp0) cc_final: 0.7143 (mt-10) REVERT: H 78 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7659 (mp) REVERT: H 109 LYS cc_start: 0.8714 (mttm) cc_final: 0.8474 (mttm) REVERT: H 123 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7925 (tt0) REVERT: H 224 MET cc_start: 0.7659 (tpt) cc_final: 0.7151 (tpp) REVERT: H 228 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: H 252 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8114 (ttm-80) REVERT: H 258 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6969 (tp30) REVERT: H 260 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: H 261 SER cc_start: 0.8863 (t) cc_final: 0.8553 (p) REVERT: H 389 ARG cc_start: 0.7213 (ttp-110) cc_final: 0.6951 (ttp-110) REVERT: H 500 VAL cc_start: 0.9069 (m) cc_final: 0.8535 (p) REVERT: H 543 LEU cc_start: 0.8314 (tm) cc_final: 0.7987 (tt) REVERT: J 49 THR cc_start: 0.9151 (m) cc_final: 0.8809 (p) REVERT: J 78 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7641 (mp) REVERT: J 172 ARG cc_start: 0.7851 (tpt90) cc_final: 0.7460 (tpt170) REVERT: J 224 MET cc_start: 0.7599 (tpt) cc_final: 0.7078 (tpp) REVERT: J 228 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: J 239 GLU cc_start: 0.7832 (mp0) cc_final: 0.7602 (mp0) REVERT: J 252 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8202 (ttm-80) REVERT: J 258 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7179 (tp30) REVERT: J 260 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: J 261 SER cc_start: 0.8884 (t) cc_final: 0.8632 (p) REVERT: J 475 GLU cc_start: 0.7852 (tt0) cc_final: 0.7595 (mt-10) REVERT: J 500 VAL cc_start: 0.9073 (m) cc_final: 0.8530 (p) REVERT: J 543 LEU cc_start: 0.8307 (tm) cc_final: 0.7979 (tt) REVERT: K 49 THR cc_start: 0.9150 (m) cc_final: 0.8816 (p) REVERT: K 78 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7655 (mp) REVERT: K 123 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7933 (tt0) REVERT: K 224 MET cc_start: 0.7605 (tpt) cc_final: 0.7099 (tpp) REVERT: K 228 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: K 260 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: K 261 SER cc_start: 0.8847 (t) cc_final: 0.8600 (p) REVERT: K 481 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6745 (mtp85) REVERT: K 500 VAL cc_start: 0.9070 (m) cc_final: 0.8507 (p) REVERT: K 543 LEU cc_start: 0.8303 (tm) cc_final: 0.7971 (tt) REVERT: K 544 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.8014 (mp) REVERT: L 54 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6820 (mt-10) REVERT: L 78 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7598 (mp) REVERT: L 123 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7927 (tt0) REVERT: L 224 MET cc_start: 0.7639 (tpt) cc_final: 0.7121 (tpp) REVERT: L 228 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: L 258 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: L 260 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: L 261 SER cc_start: 0.8841 (t) cc_final: 0.8511 (p) REVERT: L 329 ASN cc_start: 0.7357 (t0) cc_final: 0.6802 (t0) REVERT: L 465 ARG cc_start: 0.7433 (ttt-90) cc_final: 0.7113 (ttt-90) REVERT: L 481 ARG cc_start: 0.6879 (mtm-85) cc_final: 0.6050 (mtp85) REVERT: L 500 VAL cc_start: 0.9087 (m) cc_final: 0.8556 (p) REVERT: L 543 LEU cc_start: 0.8297 (tm) cc_final: 0.7964 (tt) outliers start: 69 outliers final: 35 residues processed: 392 average time/residue: 1.2343 time to fit residues: 545.4265 Evaluate side-chains 386 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 228 GLU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 367 ILE Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 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 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 367 ILE Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 228 GLU Chi-restraints excluded: chain L residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 168 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 287 ASN J 287 ASN L 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.164427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.118938 restraints weight = 54368.792| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.94 r_work: 0.3140 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18208 Z= 0.145 Angle : 0.588 6.839 24688 Z= 0.290 Chirality : 0.045 0.146 2748 Planarity : 0.005 0.055 3172 Dihedral : 11.577 157.349 2530 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.25 % Allowed : 17.06 % Favored : 79.69 % 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: 0.47 (0.18), residues: 2220 helix: 1.15 (0.18), residues: 920 sheet: -0.58 (0.26), residues: 348 loop : -0.01 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 389 TYR 0.012 0.001 TYR H 42 PHE 0.012 0.001 PHE J 163 TRP 0.008 0.001 TRP J 358 HIS 0.004 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00338 (18208) covalent geometry : angle 0.58831 (24688) hydrogen bonds : bond 0.03392 ( 731) hydrogen bonds : angle 4.40844 ( 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 400 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 0.743 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: 0.9149 (m) cc_final: 0.8811 (p) REVERT: H 54 GLU cc_start: 0.7373 (mp0) cc_final: 0.7144 (mt-10) REVERT: H 78 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7649 (mp) REVERT: H 109 LYS cc_start: 0.8748 (mttm) cc_final: 0.8507 (mttm) REVERT: H 224 MET cc_start: 0.7671 (tpt) cc_final: 0.7180 (tpp) REVERT: H 252 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8106 (ttm-80) REVERT: H 258 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: H 260 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: H 261 SER cc_start: 0.8863 (t) cc_final: 0.8560 (p) REVERT: H 286 ARG cc_start: 0.6970 (ttt90) cc_final: 0.6497 (ttp-110) REVERT: H 481 ARG cc_start: 0.6931 (mtm-85) cc_final: 0.6097 (mtp85) REVERT: H 500 VAL cc_start: 0.9052 (m) cc_final: 0.8509 (p) REVERT: H 543 LEU cc_start: 0.8389 (tm) cc_final: 0.8058 (tt) REVERT: J 78 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7620 (mp) REVERT: J 134 ASP cc_start: 0.7146 (t70) cc_final: 0.6495 (p0) REVERT: J 172 ARG cc_start: 0.7878 (tpt90) cc_final: 0.7473 (tpt170) REVERT: J 224 MET cc_start: 0.7590 (tpt) cc_final: 0.7073 (tpp) REVERT: J 239 GLU cc_start: 0.7832 (mp0) cc_final: 0.7601 (mp0) REVERT: J 260 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: J 261 SER cc_start: 0.8893 (t) cc_final: 0.8637 (p) REVERT: J 475 GLU cc_start: 0.7817 (tt0) cc_final: 0.7575 (mt-10) REVERT: J 481 ARG cc_start: 0.6882 (mtm-85) cc_final: 0.6433 (mtm110) REVERT: J 500 VAL cc_start: 0.9064 (m) cc_final: 0.8518 (p) REVERT: J 535 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7789 (pptt) REVERT: J 543 LEU cc_start: 0.8410 (tm) cc_final: 0.8082 (tt) REVERT: K 78 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7652 (mp) REVERT: K 123 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7880 (tt0) REVERT: K 224 MET cc_start: 0.7615 (tpt) cc_final: 0.7115 (tpp) REVERT: K 260 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8111 (mt0) REVERT: K 261 SER cc_start: 0.8826 (t) cc_final: 0.8573 (p) REVERT: K 481 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6757 (mtp85) REVERT: K 500 VAL cc_start: 0.9059 (m) cc_final: 0.8495 (p) REVERT: K 543 LEU cc_start: 0.8310 (tm) cc_final: 0.7986 (tt) REVERT: L 54 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6805 (mt-10) REVERT: L 78 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7622 (mp) REVERT: L 123 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7917 (tt0) REVERT: L 224 MET cc_start: 0.7655 (tpt) cc_final: 0.7149 (tpp) REVERT: L 258 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6911 (tp30) REVERT: L 260 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: L 261 SER cc_start: 0.8874 (t) cc_final: 0.8530 (p) REVERT: L 329 ASN cc_start: 0.7357 (t0) cc_final: 0.6798 (t0) REVERT: L 481 ARG cc_start: 0.6889 (mtm-85) cc_final: 0.6079 (mtp85) REVERT: L 500 VAL cc_start: 0.9082 (m) cc_final: 0.8549 (p) REVERT: L 535 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7770 (pptt) REVERT: L 543 LEU cc_start: 0.8391 (tm) cc_final: 0.8052 (tt) outliers start: 63 outliers final: 29 residues processed: 385 average time/residue: 1.2312 time to fit residues: 533.7681 Evaluate side-chains 375 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 334 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 424 PHE Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 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 Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 104 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 187 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 167 GLN J 167 GLN J 287 ASN L 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.165226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120303 restraints weight = 54485.066| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.92 r_work: 0.3152 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4466 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= 0.130 Angle : 0.575 6.785 24688 Z= 0.282 Chirality : 0.045 0.150 2748 Planarity : 0.005 0.069 3172 Dihedral : 11.167 153.369 2530 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.99 % Allowed : 17.47 % Favored : 79.54 % 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: -0.52 (0.26), residues: 348 loop : 0.02 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 389 TYR 0.011 0.001 TYR L 42 PHE 0.011 0.001 PHE J 409 TRP 0.008 0.001 TRP J 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00303 (18208) covalent geometry : angle 0.57539 (24688) hydrogen bonds : bond 0.03229 ( 731) hydrogen bonds : angle 4.31231 ( 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 392 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 ILE cc_start: 0.9304 (tp) cc_final: 0.9083 (tp) REVERT: H 54 GLU cc_start: 0.7377 (mp0) cc_final: 0.7111 (mt-10) REVERT: H 78 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7623 (mp) REVERT: H 109 LYS cc_start: 0.8740 (mttm) cc_final: 0.8499 (mttm) REVERT: H 224 MET cc_start: 0.7670 (tpt) cc_final: 0.7218 (tpp) REVERT: H 252 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.8083 (ttm-80) REVERT: H 258 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6917 (tp30) REVERT: H 260 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: H 261 SER cc_start: 0.8872 (t) cc_final: 0.8577 (p) REVERT: H 286 ARG cc_start: 0.6953 (ttt90) cc_final: 0.6469 (ttp-110) REVERT: H 500 VAL cc_start: 0.9059 (m) cc_final: 0.8509 (p) REVERT: H 543 LEU cc_start: 0.8381 (tm) cc_final: 0.8063 (tt) REVERT: J 18 ILE cc_start: 0.9328 (tp) cc_final: 0.9101 (tp) REVERT: J 78 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7602 (mp) REVERT: J 134 ASP cc_start: 0.7130 (t70) cc_final: 0.6545 (p0) REVERT: J 172 ARG cc_start: 0.7879 (tpt90) cc_final: 0.7446 (tpt170) REVERT: J 224 MET cc_start: 0.7608 (tpt) cc_final: 0.7118 (tpp) REVERT: J 239 GLU cc_start: 0.7824 (mp0) cc_final: 0.7599 (mp0) REVERT: J 260 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8148 (mt0) REVERT: J 261 SER cc_start: 0.8858 (t) cc_final: 0.8639 (p) REVERT: J 475 GLU cc_start: 0.7797 (tt0) cc_final: 0.7582 (mt-10) REVERT: J 481 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6453 (mtm110) REVERT: J 500 VAL cc_start: 0.9062 (m) cc_final: 0.8504 (p) REVERT: J 535 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7816 (pptt) REVERT: J 543 LEU cc_start: 0.8383 (tm) cc_final: 0.8068 (tt) REVERT: K 18 ILE cc_start: 0.9322 (tp) cc_final: 0.9097 (tp) REVERT: K 78 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7594 (mp) REVERT: K 123 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7895 (tt0) REVERT: K 224 MET cc_start: 0.7627 (tpt) cc_final: 0.7142 (tpp) REVERT: K 260 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: K 261 SER cc_start: 0.8826 (t) cc_final: 0.8584 (p) REVERT: K 481 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6699 (mtp85) REVERT: K 500 VAL cc_start: 0.9057 (m) cc_final: 0.8475 (p) REVERT: K 543 LEU cc_start: 0.8378 (tm) cc_final: 0.8065 (tt) REVERT: L 123 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7905 (tt0) REVERT: L 224 MET cc_start: 0.7668 (tpt) cc_final: 0.7205 (tpp) REVERT: L 258 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: L 260 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: L 261 SER cc_start: 0.8865 (t) cc_final: 0.8542 (p) REVERT: L 329 ASN cc_start: 0.7365 (t0) cc_final: 0.6808 (t0) REVERT: L 465 ARG cc_start: 0.7455 (ttt-90) cc_final: 0.7181 (ttt-90) REVERT: L 481 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6132 (mtp85) REVERT: L 500 VAL cc_start: 0.9077 (m) cc_final: 0.8531 (p) REVERT: L 535 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7808 (pptt) REVERT: L 543 LEU cc_start: 0.8368 (tm) cc_final: 0.8058 (tt) outliers start: 58 outliers final: 31 residues processed: 379 average time/residue: 1.2167 time to fit residues: 518.7935 Evaluate side-chains 375 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 332 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 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 481 ARG Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 424 PHE Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.164302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.119054 restraints weight = 54222.517| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.93 r_work: 0.3139 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.004 0.037 18208 Z= 0.159 Angle : 0.594 6.881 24688 Z= 0.291 Chirality : 0.045 0.151 2748 Planarity : 0.005 0.064 3172 Dihedral : 11.307 159.796 2530 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.04 % Allowed : 17.73 % 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: 0.64 (0.18), residues: 2220 helix: 1.29 (0.18), residues: 920 sheet: -0.45 (0.26), residues: 348 loop : 0.04 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 389 TYR 0.012 0.002 TYR H 42 PHE 0.013 0.001 PHE J 424 TRP 0.007 0.001 TRP K 358 HIS 0.005 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00373 (18208) covalent geometry : angle 0.59361 (24688) hydrogen bonds : bond 0.03341 ( 731) hydrogen bonds : angle 4.32030 ( 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 399 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 340 time to evaluate : 0.783 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: H 54 GLU cc_start: 0.7393 (mp0) cc_final: 0.7128 (mt-10) REVERT: H 78 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7607 (mp) REVERT: H 109 LYS cc_start: 0.8776 (mttm) cc_final: 0.8541 (mttm) REVERT: H 224 MET cc_start: 0.7657 (tpt) cc_final: 0.7191 (tpp) REVERT: H 252 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8120 (ttm-80) REVERT: H 258 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: H 260 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: H 261 SER cc_start: 0.8867 (t) cc_final: 0.8562 (p) REVERT: H 286 ARG cc_start: 0.6962 (ttt90) cc_final: 0.6489 (ttp-110) REVERT: H 365 ASP cc_start: 0.7700 (t0) cc_final: 0.7356 (t0) REVERT: H 376 ARG cc_start: 0.6823 (ttm-80) cc_final: 0.6294 (tmm-80) REVERT: H 500 VAL cc_start: 0.9058 (m) cc_final: 0.8497 (p) REVERT: H 535 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7802 (pptt) REVERT: H 543 LEU cc_start: 0.8387 (tm) cc_final: 0.8092 (tt) REVERT: J 78 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7637 (mp) REVERT: J 134 ASP cc_start: 0.7193 (t70) cc_final: 0.6784 (p0) REVERT: J 172 ARG cc_start: 0.7899 (tpt90) cc_final: 0.7436 (tpt170) REVERT: J 224 MET cc_start: 0.7581 (tpt) cc_final: 0.7100 (tpp) REVERT: J 239 GLU cc_start: 0.7880 (mp0) cc_final: 0.7556 (mp0) REVERT: J 260 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: J 261 SER cc_start: 0.8871 (t) cc_final: 0.8630 (p) REVERT: J 475 GLU cc_start: 0.7824 (tt0) cc_final: 0.7609 (mt-10) REVERT: J 500 VAL cc_start: 0.9059 (m) cc_final: 0.8489 (p) REVERT: J 535 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7933 (pptt) REVERT: J 543 LEU cc_start: 0.8380 (tm) cc_final: 0.8079 (tt) REVERT: K 78 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (mp) REVERT: K 123 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7887 (tt0) REVERT: K 224 MET cc_start: 0.7672 (tpt) cc_final: 0.7210 (tpp) REVERT: K 228 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: K 260 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: K 261 SER cc_start: 0.8815 (t) cc_final: 0.8574 (p) REVERT: K 481 ARG cc_start: 0.7270 (mtp180) cc_final: 0.6733 (mtp85) REVERT: K 543 LEU cc_start: 0.8383 (tm) cc_final: 0.8075 (tt) REVERT: L 123 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7905 (tt0) REVERT: L 134 ASP cc_start: 0.7124 (t70) cc_final: 0.6528 (p0) REVERT: L 224 MET cc_start: 0.7664 (tpt) cc_final: 0.7196 (tpp) REVERT: L 258 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: L 260 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: L 261 SER cc_start: 0.8866 (t) cc_final: 0.8518 (p) REVERT: L 329 ASN cc_start: 0.7366 (t0) cc_final: 0.6805 (t0) REVERT: L 465 ARG cc_start: 0.7426 (ttt-90) cc_final: 0.7183 (ttt-90) REVERT: L 481 ARG cc_start: 0.6902 (mtm-85) cc_final: 0.6129 (mtp85) REVERT: L 500 VAL cc_start: 0.9072 (m) cc_final: 0.8509 (p) REVERT: L 535 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7933 (pptt) REVERT: L 543 LEU cc_start: 0.8357 (tm) cc_final: 0.8061 (tt) outliers start: 59 outliers final: 33 residues processed: 384 average time/residue: 1.2797 time to fit residues: 553.4226 Evaluate side-chains 386 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 260 GLN Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 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 481 ARG Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 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 268 GLU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 424 PHE Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 155 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 154 optimal weight: 0.0170 chunk 70 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 167 GLN K 323 HIS L 44 ASN L 167 GLN L 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.165704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.121118 restraints weight = 54337.644| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.91 r_work: 0.3164 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18208 Z= 0.119 Angle : 0.567 6.715 24688 Z= 0.277 Chirality : 0.044 0.147 2748 Planarity : 0.005 0.067 3172 Dihedral : 10.757 149.643 2530 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.47 % Allowed : 18.81 % Favored : 78.71 % 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: 0.77 (0.18), residues: 2220 helix: 1.45 (0.18), residues: 920 sheet: -0.44 (0.27), residues: 348 loop : 0.08 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 389 TYR 0.013 0.001 TYR L 42 PHE 0.013 0.001 PHE L 424 TRP 0.008 0.001 TRP K 358 HIS 0.004 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00276 (18208) covalent geometry : angle 0.56671 (24688) hydrogen bonds : bond 0.03081 ( 731) hydrogen bonds : angle 4.24184 ( 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 392 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 344 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 54 GLU cc_start: 0.7314 (mp0) cc_final: 0.7082 (mt-10) REVERT: H 78 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7637 (mp) REVERT: H 109 LYS cc_start: 0.8753 (mttm) cc_final: 0.8501 (mttm) REVERT: H 224 MET cc_start: 0.7665 (tpt) cc_final: 0.7212 (tpp) REVERT: H 252 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8089 (ttm-80) REVERT: H 258 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: H 260 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: H 261 SER cc_start: 0.8855 (t) cc_final: 0.8563 (p) REVERT: H 286 ARG cc_start: 0.6938 (ttt90) cc_final: 0.6466 (ttp-110) REVERT: H 365 ASP cc_start: 0.7696 (t0) cc_final: 0.7381 (t0) REVERT: H 376 ARG cc_start: 0.6841 (ttm-80) cc_final: 0.6269 (tmm-80) REVERT: H 500 VAL cc_start: 0.9048 (m) cc_final: 0.8486 (p) REVERT: H 535 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7809 (pptt) REVERT: H 543 LEU cc_start: 0.8370 (tm) cc_final: 0.8080 (tt) REVERT: J 78 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7610 (mp) REVERT: J 134 ASP cc_start: 0.7065 (t70) cc_final: 0.6517 (p0) REVERT: J 172 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7402 (tpt170) REVERT: J 224 MET cc_start: 0.7606 (tpt) cc_final: 0.7138 (tpp) REVERT: J 239 GLU cc_start: 0.7896 (mp0) cc_final: 0.7591 (mp0) REVERT: J 260 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: J 261 SER cc_start: 0.8858 (t) cc_final: 0.8620 (p) REVERT: J 465 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7228 (ttt-90) REVERT: J 473 PHE cc_start: 0.8180 (p90) cc_final: 0.7966 (p90) REVERT: J 475 GLU cc_start: 0.7810 (tt0) cc_final: 0.7595 (mt-10) REVERT: J 481 ARG cc_start: 0.6900 (mtm-85) cc_final: 0.6489 (mtm110) REVERT: J 500 VAL cc_start: 0.9054 (m) cc_final: 0.8489 (p) REVERT: J 535 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7900 (pptt) REVERT: J 543 LEU cc_start: 0.8358 (tm) cc_final: 0.8074 (tt) REVERT: K 78 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7646 (mp) REVERT: K 123 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7885 (tt0) REVERT: K 224 MET cc_start: 0.7652 (tpt) cc_final: 0.7195 (tpp) REVERT: K 260 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: K 261 SER cc_start: 0.8819 (t) cc_final: 0.8586 (p) REVERT: K 481 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6724 (mtp85) REVERT: K 508 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7409 (mtt-85) REVERT: K 543 LEU cc_start: 0.8361 (tm) cc_final: 0.8082 (tt) REVERT: L 123 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7918 (tt0) REVERT: L 134 ASP cc_start: 0.7010 (t70) cc_final: 0.6403 (p0) REVERT: L 224 MET cc_start: 0.7667 (tpt) cc_final: 0.7212 (tpp) REVERT: L 258 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6886 (tp30) REVERT: L 260 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: L 261 SER cc_start: 0.8873 (t) cc_final: 0.8544 (p) REVERT: L 329 ASN cc_start: 0.7368 (t0) cc_final: 0.6837 (t0) REVERT: L 389 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.7059 (ttp-110) REVERT: L 465 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.7168 (ttt-90) REVERT: L 481 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6121 (mtp85) REVERT: L 500 VAL cc_start: 0.9069 (m) cc_final: 0.8513 (p) REVERT: L 535 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: L 543 LEU cc_start: 0.8344 (tm) cc_final: 0.8052 (tt) outliers start: 48 outliers final: 32 residues processed: 381 average time/residue: 1.2728 time to fit residues: 544.9697 Evaluate side-chains 378 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 334 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 240 GLN 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 207 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain K residue 260 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 324 SER Chi-restraints excluded: chain K residue 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 217 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 44 ASN K 44 ASN L 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.165318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.120242 restraints weight = 54352.222| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.94 r_work: 0.3146 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18208 Z= 0.142 Angle : 0.581 6.772 24688 Z= 0.284 Chirality : 0.045 0.146 2748 Planarity : 0.005 0.067 3172 Dihedral : 10.831 154.453 2530 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.68 % Allowed : 19.12 % Favored : 78.20 % 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: 0.80 (0.18), residues: 2220 helix: 1.47 (0.18), residues: 920 sheet: -0.41 (0.27), residues: 348 loop : 0.11 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 389 TYR 0.012 0.001 TYR K 42 PHE 0.013 0.001 PHE J 409 TRP 0.007 0.001 TRP K 358 HIS 0.005 0.001 HIS J 96 Details of bonding type rmsd covalent geometry : bond 0.00333 (18208) covalent geometry : angle 0.58149 (24688) hydrogen bonds : bond 0.03184 ( 731) hydrogen bonds : angle 4.24820 ( 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 384 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 332 time to evaluate : 0.899 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: 0.9151 (m) cc_final: 0.8883 (p) REVERT: H 54 GLU cc_start: 0.7313 (mp0) cc_final: 0.7074 (mt-10) REVERT: H 78 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7635 (mp) REVERT: H 109 LYS cc_start: 0.8756 (mttm) cc_final: 0.8527 (mttm) REVERT: H 224 MET cc_start: 0.7670 (tpt) cc_final: 0.7203 (tpp) REVERT: H 258 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: H 261 SER cc_start: 0.8857 (t) cc_final: 0.8560 (p) REVERT: H 286 ARG cc_start: 0.7009 (ttt90) cc_final: 0.6483 (ttp-110) REVERT: H 365 ASP cc_start: 0.7714 (t0) cc_final: 0.7413 (t0) REVERT: H 376 ARG cc_start: 0.6858 (ttm-80) cc_final: 0.6282 (tmm-80) REVERT: H 500 VAL cc_start: 0.9040 (m) cc_final: 0.8476 (p) REVERT: H 535 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7926 (pptt) REVERT: H 543 LEU cc_start: 0.8379 (tm) cc_final: 0.8095 (tt) REVERT: J 78 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (mp) REVERT: J 134 ASP cc_start: 0.7161 (t70) cc_final: 0.6590 (p0) REVERT: J 172 ARG cc_start: 0.7900 (tpt90) cc_final: 0.7415 (tpt170) REVERT: J 224 MET cc_start: 0.7618 (tpt) cc_final: 0.7147 (tpp) REVERT: J 239 GLU cc_start: 0.7874 (mp0) cc_final: 0.7554 (mp0) REVERT: J 260 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8182 (mt0) REVERT: J 261 SER cc_start: 0.8876 (t) cc_final: 0.8632 (p) REVERT: J 286 ARG cc_start: 0.7009 (ttt90) cc_final: 0.6522 (ttp-110) REVERT: J 475 GLU cc_start: 0.7786 (tt0) cc_final: 0.7575 (mt-10) REVERT: J 500 VAL cc_start: 0.9038 (m) cc_final: 0.8463 (p) REVERT: J 535 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7929 (pptt) REVERT: J 543 LEU cc_start: 0.8362 (tm) cc_final: 0.8077 (tt) REVERT: K 78 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7644 (mp) REVERT: K 123 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7879 (tt0) REVERT: K 224 MET cc_start: 0.7663 (tpt) cc_final: 0.7172 (tpp) REVERT: K 260 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: K 261 SER cc_start: 0.8836 (t) cc_final: 0.8602 (p) REVERT: K 481 ARG cc_start: 0.7300 (mtp180) cc_final: 0.7012 (mtm110) REVERT: K 543 LEU cc_start: 0.8363 (tm) cc_final: 0.8087 (tt) REVERT: L 123 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7906 (tt0) REVERT: L 224 MET cc_start: 0.7678 (tpt) cc_final: 0.7204 (tpp) REVERT: L 258 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: L 260 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: L 261 SER cc_start: 0.8892 (t) cc_final: 0.8548 (p) REVERT: L 286 ARG cc_start: 0.6960 (ttt90) cc_final: 0.6417 (ttp-110) REVERT: L 329 ASN cc_start: 0.7360 (t0) cc_final: 0.6847 (t0) REVERT: L 389 ARG cc_start: 0.7375 (ttp-110) cc_final: 0.7153 (ttp-110) REVERT: L 465 ARG cc_start: 0.7556 (ttt-90) cc_final: 0.7228 (ttt-90) REVERT: L 473 PHE cc_start: 0.8180 (p90) cc_final: 0.7965 (p90) REVERT: L 481 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6181 (mtp85) REVERT: L 500 VAL cc_start: 0.9055 (m) cc_final: 0.8490 (p) REVERT: L 535 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7923 (pptt) REVERT: L 543 LEU cc_start: 0.8361 (tm) cc_final: 0.8071 (tt) outliers start: 52 outliers final: 29 residues processed: 372 average time/residue: 1.2865 time to fit residues: 536.1064 Evaluate side-chains 371 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 331 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 240 GLN Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 258 GLU Chi-restraints excluded: chain H residue 268 GLU Chi-restraints excluded: chain H residue 324 SER Chi-restraints excluded: chain H residue 424 PHE Chi-restraints excluded: chain H residue 475 GLU Chi-restraints excluded: chain H residue 535 LYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 244 ILE Chi-restraints excluded: chain J residue 260 GLN Chi-restraints excluded: chain J residue 268 GLU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 324 SER Chi-restraints excluded: chain J residue 535 LYS Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 213 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 544 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 244 ILE Chi-restraints excluded: chain L residue 258 GLU Chi-restraints excluded: chain L residue 260 GLN Chi-restraints excluded: chain L residue 268 GLU Chi-restraints excluded: chain L residue 324 SER Chi-restraints excluded: chain L residue 535 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 170 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 181 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 323 HIS L 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.119031 restraints weight = 54182.280| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.93 r_work: 0.3136 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18208 Z= 0.157 Angle : 0.591 6.786 24688 Z= 0.290 Chirality : 0.045 0.146 2748 Planarity : 0.006 0.119 3172 Dihedral : 11.031 160.211 2530 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.22 % Allowed : 19.90 % Favored : 77.89 % 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: 0.77 (0.18), residues: 2220 helix: 1.39 (0.18), residues: 924 sheet: -0.42 (0.27), residues: 348 loop : 0.14 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG H 252 TYR 0.013 0.002 TYR L 307 PHE 0.013 0.001 PHE J 409 TRP 0.007 0.001 TRP K 358 HIS 0.004 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00369 (18208) covalent geometry : angle 0.59107 (24688) hydrogen bonds : bond 0.03264 ( 731) hydrogen bonds : angle 4.27437 ( 2073) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14225.15 seconds wall clock time: 240 minutes 28.95 seconds (14428.95 seconds total)