Starting phenix.real_space_refine on Sat Jul 4 02:07:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7miu_23865/07_2026/7miu_23865.cif" } resolution = 2.6 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= 0.263 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: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 100 5.16 5 C 11116 2.51 5 N 2960 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17412 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "C" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "H" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "G" Number of atoms: 4280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4280 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 513} Chain breaks: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.96, per 1000 atoms: 0.23 Number of scatterers: 17412 At special positions: 0 Unit cell: (122.85, 133.35, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 100 16.00 P 12 15.00 Mg 4 11.99 O 3220 8.00 N 2960 7.00 C 11116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 768.9 milliseconds 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4016 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 16 sheets defined 49.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'D' and resid 15 through 30 Processing helix chain 'D' and resid 46 through 50 removed outlier: 3.541A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 4.186A pdb=" N HIS D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.939A pdb=" N GLY D 72 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 112 through 130 removed outlier: 7.159A pdb=" N THR D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 156 through 167 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.837A pdb=" N ARG D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 338 through 342 Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.610A pdb=" N LYS D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 Processing helix chain 'D' and resid 377 through 391 Processing helix chain 'D' and resid 399 through 414 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.787A pdb=" N LYS D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 526 through 531 removed outlier: 3.713A pdb=" N PHE D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 550 through 557 Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 3.527A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.202A pdb=" N HIS C 55 " --> pdb=" O SER C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 78 removed outlier: 3.933A pdb=" N GLY C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 112 through 130 removed outlier: 7.159A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 282 through 294 removed outlier: 3.834A pdb=" N ARG C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.565A pdb=" N LYS C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 414 Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.737A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.737A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'H' and resid 15 through 30 Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.541A pdb=" N THR H 49 " --> pdb=" O ASP H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 56 removed outlier: 4.186A pdb=" N HIS H 55 " --> pdb=" O SER H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 removed outlier: 3.939A pdb=" N GLY H 72 " --> pdb=" O ASP H 68 " (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 112 through 130 removed outlier: 7.159A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 156 through 167 Processing helix chain 'H' and resid 194 through 207 Processing helix chain 'H' and resid 223 through 235 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 271 Processing helix chain 'H' and resid 282 through 294 removed outlier: 3.837A pdb=" N ARG H 294 " --> pdb=" O ASP H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'H' and resid 314 through 328 Processing helix chain 'H' and resid 338 through 342 Processing helix chain 'H' and resid 343 through 350 removed outlier: 3.610A pdb=" N LYS H 347 " --> pdb=" O GLU H 343 " (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 Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.788A pdb=" N LYS H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 492 Processing helix chain 'H' and resid 526 through 531 removed outlier: 3.713A pdb=" N PHE H 529 " --> pdb=" O HIS H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 537 through 548 Processing helix chain 'H' and resid 550 through 557 Processing helix chain 'G' and resid 15 through 30 Processing helix chain 'G' and resid 46 through 50 removed outlier: 3.527A pdb=" N THR G 49 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 56 removed outlier: 4.202A pdb=" N HIS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 removed outlier: 3.933A pdb=" N GLY G 72 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 90 through 103 Processing helix chain 'G' and resid 112 through 130 removed outlier: 7.159A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 156 through 167 Processing helix chain 'G' and resid 194 through 207 Processing helix chain 'G' and resid 223 through 235 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 252 through 260 Processing helix chain 'G' and resid 261 through 271 Processing helix chain 'G' and resid 282 through 294 removed outlier: 3.834A pdb=" N ARG G 294 " --> pdb=" O ASP G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'G' and resid 314 through 328 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 343 through 350 removed outlier: 3.565A pdb=" N LYS G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 363 Processing helix chain 'G' and resid 377 through 391 Processing helix chain 'G' and resid 399 through 414 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.738A pdb=" N LYS G 466 " --> pdb=" O SER G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 526 through 531 removed outlier: 3.737A pdb=" N PHE G 529 " --> pdb=" O HIS G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 548 Processing helix chain 'G' and resid 550 through 557 Processing sheet with id=AA1, first strand: chain 'D' and resid 87 through 89 removed outlier: 8.031A pdb=" N ILE D 88 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS D 38 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS D 2 " --> pdb=" O CYS D 143 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE D 145 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR D 3 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU D 213 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL D 215 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG D 217 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'D' and resid 330 through 337 removed outlier: 6.817A pdb=" N LYS D 297 " --> pdb=" O LYS D 331 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN D 333 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS D 299 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET D 335 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE D 301 " --> pdb=" O MET D 335 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLY D 366 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N SER D 300 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU D 368 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE D 367 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE D 398 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 369 " --> pdb=" O ILE D 398 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET D 509 " --> pdb=" O GLU D 502 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU D 502 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 419 through 421 removed outlier: 6.740A pdb=" N ASN D 420 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP D 435 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 89 removed outlier: 8.038A pdb=" N ILE C 88 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS C 38 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS C 2 " --> pdb=" O CYS C 143 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR C 3 " --> pdb=" O TYR C 176 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'C' and resid 330 through 338 removed outlier: 6.819A pdb=" N LYS C 297 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN C 333 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS C 299 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE C 301 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY C 366 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE C 398 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 369 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET C 509 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 419 through 421 removed outlier: 6.614A pdb=" N ASN C 420 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ASP C 435 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 87 through 89 removed outlier: 8.031A pdb=" N ILE H 88 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS H 38 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS H 2 " --> pdb=" O CYS H 143 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE H 145 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE H 4 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU H 147 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 6 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR H 3 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N LEU H 213 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASN H 177 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL H 215 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS H 179 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG H 217 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER H 181 " --> pdb=" O ARG H 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AB2, first strand: chain 'H' and resid 330 through 337 removed outlier: 6.816A pdb=" N LYS H 297 " --> pdb=" O LYS H 331 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASN H 333 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS H 299 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N MET H 335 " --> pdb=" O CYS H 299 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE H 301 " --> pdb=" O MET H 335 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE H 337 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N LEU H 303 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N GLY H 366 " --> pdb=" O ILE H 298 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER H 300 " --> pdb=" O GLY H 366 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N LEU H 368 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA H 302 " --> pdb=" O LEU H 368 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE H 367 " --> pdb=" O LEU H 396 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE H 398 " --> pdb=" O ILE H 367 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL H 369 " --> pdb=" O ILE H 398 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE H 520 " --> pdb=" O LEU H 514 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET H 509 " --> pdb=" O GLU H 502 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU H 502 " --> pdb=" O MET H 509 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE H 511 " --> pdb=" O VAL H 500 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 419 through 421 removed outlier: 6.740A pdb=" N ASN H 420 " --> pdb=" O VAL H 433 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP H 435 " --> pdb=" O ASN H 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 87 through 89 removed outlier: 8.038A pdb=" N ILE G 88 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS G 38 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS G 2 " --> pdb=" O CYS G 143 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE G 145 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE G 4 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU G 147 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 6 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR G 3 " --> pdb=" O TYR G 176 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N LEU G 213 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN G 177 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL G 215 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS G 179 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG G 217 " --> pdb=" O HIS G 179 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER G 181 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'G' and resid 330 through 338 removed outlier: 6.818A pdb=" N LYS G 297 " --> pdb=" O LYS G 331 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ASN G 333 " --> pdb=" O LYS G 297 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N CYS G 299 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET G 335 " --> pdb=" O CYS G 299 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE G 301 " --> pdb=" O MET G 335 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE G 337 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU G 303 " --> pdb=" O ILE G 337 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY G 366 " --> pdb=" O ILE G 298 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER G 300 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU G 368 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ALA G 302 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE G 367 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE G 398 " --> pdb=" O ILE G 367 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 369 " --> pdb=" O ILE G 398 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE G 520 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N MET G 509 " --> pdb=" O GLU G 502 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU G 502 " --> pdb=" O MET G 509 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE G 511 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 419 through 421 removed outlier: 6.614A pdb=" N ASN G 420 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N ASP G 435 " --> pdb=" O ASN G 420 " (cutoff:3.500A) 763 hydrogen bonds defined for protein. 2169 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: 2.89 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 5644 1.36 - 1.49: 4257 1.49 - 1.63: 7707 1.63 - 1.77: 28 1.77 - 1.90: 144 Bond restraints: 17780 Sorted by residual: bond pdb=" C16 ZG4 H 602 " pdb=" S2 ZG4 H 602 " ideal model delta sigma weight residual 1.760 1.902 -0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C16 ZG4 D 602 " pdb=" S2 ZG4 D 602 " ideal model delta sigma weight residual 1.760 1.902 -0.142 2.00e-02 2.50e+03 5.02e+01 bond pdb=" C16 ZG4 C 604 " pdb=" S2 ZG4 C 604 " ideal model delta sigma weight residual 1.760 1.901 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C16 ZG4 G 604 " pdb=" S2 ZG4 G 604 " ideal model delta sigma weight residual 1.760 1.901 -0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" CD GLU H 146 " pdb=" OE2 GLU H 146 " ideal model delta sigma weight residual 1.249 1.358 -0.109 1.90e-02 2.77e+03 3.30e+01 ... (remaining 17775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 19287 2.32 - 4.63: 4067 4.63 - 6.95: 677 6.95 - 9.26: 55 9.26 - 11.58: 10 Bond angle restraints: 24096 Sorted by residual: angle pdb=" N PRO G 538 " pdb=" CA PRO G 538 " pdb=" C PRO G 538 " ideal model delta sigma weight residual 110.70 120.23 -9.53 1.22e+00 6.72e-01 6.10e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 120.22 -9.52 1.22e+00 6.72e-01 6.09e+01 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 120.18 -9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" N PRO H 538 " pdb=" CA PRO H 538 " pdb=" C PRO H 538 " ideal model delta sigma weight residual 110.70 120.18 -9.48 1.22e+00 6.72e-01 6.04e+01 angle pdb=" C GLY H 9 " pdb=" N VAL H 10 " pdb=" CA VAL H 10 " ideal model delta sigma weight residual 121.97 133.55 -11.58 1.80e+00 3.09e-01 4.14e+01 ... (remaining 24091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9988 17.95 - 35.90: 692 35.90 - 53.85: 88 53.85 - 71.80: 52 71.80 - 89.75: 44 Dihedral angle restraints: 10864 sinusoidal: 4616 harmonic: 6248 Sorted by residual: dihedral pdb=" CA PRO C 115 " pdb=" C PRO C 115 " pdb=" N HIS C 116 " pdb=" CA HIS C 116 " ideal model delta harmonic sigma weight residual -180.00 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PRO H 115 " pdb=" C PRO H 115 " pdb=" N HIS H 116 " pdb=" CA HIS H 116 " ideal model delta harmonic sigma weight residual 180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA PRO G 115 " pdb=" C PRO G 115 " pdb=" N HIS G 116 " pdb=" CA HIS G 116 " ideal model delta harmonic sigma weight residual 180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 10861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1423 0.082 - 0.164: 754 0.164 - 0.246: 359 0.246 - 0.327: 121 0.327 - 0.409: 35 Chirality restraints: 2692 Sorted by residual: chirality pdb=" CB THR H 89 " pdb=" CA THR H 89 " pdb=" OG1 THR H 89 " pdb=" CG2 THR H 89 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB THR D 89 " pdb=" CA THR D 89 " pdb=" OG1 THR D 89 " pdb=" CG2 THR D 89 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB THR C 89 " pdb=" CA THR C 89 " pdb=" OG1 THR C 89 " pdb=" CG2 THR C 89 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.18e+00 ... (remaining 2689 not shown) Planarity restraints: 3072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 336 " 0.107 2.00e-02 2.50e+03 5.73e-02 6.57e+01 pdb=" CG TYR H 336 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR H 336 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR H 336 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR H 336 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR H 336 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR H 336 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR H 336 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 336 " 0.107 2.00e-02 2.50e+03 5.73e-02 6.57e+01 pdb=" CG TYR D 336 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 336 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR D 336 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR D 336 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 336 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR D 336 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 336 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 74 " -0.090 2.00e-02 2.50e+03 5.58e-02 6.22e+01 pdb=" CG TYR C 74 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 74 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR C 74 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR C 74 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR C 74 " 0.051 2.00e-02 2.50e+03 pdb=" CZ TYR C 74 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 74 " -0.094 2.00e-02 2.50e+03 ... (remaining 3069 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 50 2.55 - 3.14: 12711 3.14 - 3.73: 29400 3.73 - 4.31: 43901 4.31 - 4.90: 70367 Nonbonded interactions: 156429 Sorted by model distance: nonbonded pdb="MG MG D 603 " pdb=" O1G UTP D 604 " model vdw 1.966 2.170 nonbonded pdb="MG MG H 603 " pdb=" O2G UTP H 604 " model vdw 1.966 2.170 nonbonded pdb=" O2G UTP C 602 " pdb="MG MG C 603 " model vdw 1.967 2.170 nonbonded pdb=" O1G UTP G 602 " pdb="MG MG G 603 " model vdw 1.967 2.170 nonbonded pdb=" CG2 THR C 49 " pdb=" OE2 GLU G 101 " model vdw 2.052 3.460 ... (remaining 156424 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 601 or resid 603)) selection = (chain 'D' and (resid 1 through 601 or resid 603)) selection = (chain 'G' and (resid 1 through 601 or resid 603)) selection = (chain 'H' and (resid 1 through 601 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.300 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.020 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 : 0.014 0.142 17780 Z= 0.820 Angle : 1.968 11.579 24096 Z= 1.323 Chirality : 0.123 0.409 2692 Planarity : 0.012 0.074 3072 Dihedral : 14.464 89.748 6848 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.29 % Favored : 95.06 % Rotamer: Outliers : 2.22 % Allowed : 3.28 % Favored : 94.50 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 3.57 % 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: -1.19 (0.17), residues: 2144 helix: -0.54 (0.15), residues: 908 sheet: -0.61 (0.27), residues: 316 loop : -0.95 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 252 TYR 0.107 0.023 TYR H 336 PHE 0.071 0.018 PHE C 318 TRP 0.045 0.015 TRP D 387 HIS 0.024 0.005 HIS H 480 Details of bonding type rmsd/Z covalent geometry : bond 0.01435 / 0.82 (17780) covalent geometry : angle 1.96806 / 1.32 (24096) hydrogen bonds : bond 0.15217 / 10.23 ( 763) hydrogen bonds : angle 7.57670 / 5.38 ( 2169) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 536 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 176 TYR cc_start: 0.7577 (m-80) cc_final: 0.7290 (m-80) REVERT: D 268 GLU cc_start: 0.6704 (mt-10) cc_final: 0.6371 (mt-10) REVERT: D 338 ASP cc_start: 0.7325 (t0) cc_final: 0.7100 (t0) REVERT: D 341 ASP cc_start: 0.7990 (m-30) cc_final: 0.7775 (m-30) REVERT: D 390 THR cc_start: 0.8429 (p) cc_final: 0.8205 (p) REVERT: C 176 TYR cc_start: 0.7535 (m-80) cc_final: 0.7277 (m-80) REVERT: C 268 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6241 (mt-10) REVERT: C 390 THR cc_start: 0.8411 (p) cc_final: 0.8139 (p) REVERT: H 54 GLU cc_start: 0.7984 (tp30) cc_final: 0.7741 (tp30) REVERT: H 176 TYR cc_start: 0.7568 (m-80) cc_final: 0.7297 (m-80) REVERT: H 268 GLU cc_start: 0.6721 (mt-10) cc_final: 0.6381 (mt-10) REVERT: H 338 ASP cc_start: 0.7366 (t0) cc_final: 0.7128 (t0) REVERT: H 341 ASP cc_start: 0.8013 (m-30) cc_final: 0.7741 (m-30) REVERT: H 390 THR cc_start: 0.8357 (p) cc_final: 0.8129 (p) REVERT: G 126 MET cc_start: 0.7187 (mmm) cc_final: 0.6930 (tpt) REVERT: G 176 TYR cc_start: 0.7556 (m-80) cc_final: 0.7276 (m-80) REVERT: G 284 LYS cc_start: 0.7817 (mmtm) cc_final: 0.7612 (mmtm) REVERT: G 390 THR cc_start: 0.8389 (p) cc_final: 0.8109 (p) outliers start: 42 outliers final: 2 residues processed: 556 average time/residue: 0.5764 time to fit residues: 358.8407 Evaluate side-chains 392 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 390 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain H residue 378 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 HIS D 415 ASN ** D 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN D 556 GLN C 55 HIS C 412 ASN C 415 ASN C 556 GLN H 55 HIS H 415 ASN ** H 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN H 556 GLN G 55 HIS G 412 ASN G 415 ASN G 556 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.156937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.128129 restraints weight = 18192.319| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.58 r_work: 0.3229 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17780 Z= 0.169 Angle : 0.625 8.720 24096 Z= 0.325 Chirality : 0.048 0.176 2692 Planarity : 0.004 0.035 3072 Dihedral : 7.321 45.016 2598 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.68 % Favored : 98.13 % Rotamer: Outliers : 1.74 % Allowed : 12.05 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.12 (0.18), residues: 2144 helix: 0.83 (0.16), residues: 936 sheet: -0.72 (0.27), residues: 348 loop : -0.24 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 376 TYR 0.019 0.002 TYR D 336 PHE 0.015 0.002 PHE G 354 TRP 0.011 0.002 TRP G 358 HIS 0.005 0.002 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17780) covalent geometry : angle 0.62460 / 0.33 (24096) hydrogen bonds : bond 0.03990 / 2.64 ( 763) hydrogen bonds : angle 5.38509 / 3.80 ( 2169) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 407 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8258 (tttp) cc_final: 0.7880 (tttt) REVERT: D 55 HIS cc_start: 0.8637 (m-70) cc_final: 0.8376 (m-70) REVERT: D 176 TYR cc_start: 0.8072 (m-80) cc_final: 0.7657 (m-80) REVERT: D 224 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6961 (mmm) REVERT: D 391 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7664 (mttm) REVERT: D 425 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6144 (mm-30) REVERT: D 481 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7328 (mtp85) REVERT: D 511 ILE cc_start: 0.8801 (mt) cc_final: 0.8594 (mt) REVERT: C 53 TYR cc_start: 0.8305 (m-80) cc_final: 0.8078 (m-80) REVERT: C 55 HIS cc_start: 0.8668 (m-70) cc_final: 0.8392 (m-70) REVERT: C 176 TYR cc_start: 0.8056 (m-80) cc_final: 0.7666 (m-80) REVERT: C 224 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.7035 (mmm) REVERT: C 456 VAL cc_start: 0.8219 (t) cc_final: 0.7930 (m) REVERT: H 28 LYS cc_start: 0.8271 (tttm) cc_final: 0.8048 (tttt) REVERT: H 54 GLU cc_start: 0.8210 (tp30) cc_final: 0.7968 (tp30) REVERT: H 132 SER cc_start: 0.8497 (p) cc_final: 0.8050 (t) REVERT: H 176 TYR cc_start: 0.8072 (m-80) cc_final: 0.7654 (m-80) REVERT: H 224 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6999 (mmm) REVERT: H 331 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7771 (mtmt) REVERT: H 409 PHE cc_start: 0.7946 (t80) cc_final: 0.7676 (t80) REVERT: G 55 HIS cc_start: 0.8641 (m-70) cc_final: 0.8427 (m-70) REVERT: G 176 TYR cc_start: 0.8070 (m-80) cc_final: 0.7647 (m-80) REVERT: G 224 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7065 (mmm) REVERT: G 268 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6766 (mt-10) REVERT: G 288 MET cc_start: 0.8332 (mtm) cc_final: 0.7965 (mtt) REVERT: G 389 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7527 (ttp80) REVERT: G 390 THR cc_start: 0.8412 (p) cc_final: 0.8177 (p) REVERT: G 409 PHE cc_start: 0.7995 (t80) cc_final: 0.7715 (t80) REVERT: G 425 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.6035 (mm-30) REVERT: G 456 VAL cc_start: 0.8263 (t) cc_final: 0.7985 (m) outliers start: 33 outliers final: 6 residues processed: 427 average time/residue: 0.5411 time to fit residues: 259.7308 Evaluate side-chains 394 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 382 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 425 GLU Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 425 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 145 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 196 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 ASN D 552 ASN H 552 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.150546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123148 restraints weight = 19158.332| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.56 r_work: 0.3208 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17780 Z= 0.167 Angle : 0.601 7.753 24096 Z= 0.309 Chirality : 0.048 0.156 2692 Planarity : 0.005 0.043 3072 Dihedral : 7.473 57.939 2596 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.05 % Favored : 97.76 % Rotamer: Outliers : 3.44 % Allowed : 14.64 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.46 (0.18), residues: 2144 helix: 1.17 (0.17), residues: 932 sheet: -0.66 (0.27), residues: 348 loop : -0.08 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 376 TYR 0.015 0.002 TYR H 42 PHE 0.017 0.002 PHE H 354 TRP 0.018 0.002 TRP H 387 HIS 0.006 0.002 HIS H 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (17780) covalent geometry : angle 0.60114 / 0.31 (24096) hydrogen bonds : bond 0.03788 / 2.51 ( 763) hydrogen bonds : angle 4.96195 / 3.50 ( 2169) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8335 (tttp) cc_final: 0.8065 (tttt) REVERT: D 53 TYR cc_start: 0.8214 (m-80) cc_final: 0.7983 (m-80) REVERT: D 123 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: D 132 SER cc_start: 0.8613 (p) cc_final: 0.8128 (t) REVERT: D 157 MET cc_start: 0.8428 (mmp) cc_final: 0.8124 (mmt) REVERT: D 176 TYR cc_start: 0.8109 (m-80) cc_final: 0.7599 (m-80) REVERT: D 292 TYR cc_start: 0.8536 (t80) cc_final: 0.8292 (t80) REVERT: D 375 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7535 (pp) REVERT: D 466 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7957 (mtmm) REVERT: D 481 ARG cc_start: 0.7820 (mtt90) cc_final: 0.7364 (mtt-85) REVERT: C 28 LYS cc_start: 0.8308 (tttp) cc_final: 0.7972 (tttt) REVERT: C 53 TYR cc_start: 0.8385 (m-80) cc_final: 0.8081 (m-80) REVERT: C 123 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8107 (tp30) REVERT: C 132 SER cc_start: 0.8612 (p) cc_final: 0.8135 (t) REVERT: C 157 MET cc_start: 0.8317 (mmp) cc_final: 0.8041 (mmt) REVERT: C 176 TYR cc_start: 0.8115 (m-80) cc_final: 0.7591 (m-80) REVERT: C 292 TYR cc_start: 0.8531 (t80) cc_final: 0.8267 (t80) REVERT: C 329 ASN cc_start: 0.8203 (m-40) cc_final: 0.7891 (t0) REVERT: C 466 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8065 (mtmm) REVERT: H 53 TYR cc_start: 0.8412 (m-80) cc_final: 0.8048 (m-80) REVERT: H 123 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: H 132 SER cc_start: 0.8616 (p) cc_final: 0.8148 (t) REVERT: H 157 MET cc_start: 0.8344 (mmp) cc_final: 0.8085 (mmt) REVERT: H 176 TYR cc_start: 0.8100 (m-80) cc_final: 0.7644 (m-80) REVERT: H 228 GLU cc_start: 0.7393 (pp20) cc_final: 0.7121 (pp20) REVERT: H 341 ASP cc_start: 0.8288 (m-30) cc_final: 0.8051 (m-30) REVERT: H 356 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7019 (mt-10) REVERT: H 375 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7596 (pp) REVERT: G 28 LYS cc_start: 0.8343 (tttp) cc_final: 0.7989 (tttt) REVERT: G 123 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: G 132 SER cc_start: 0.8586 (p) cc_final: 0.8130 (t) REVERT: G 157 MET cc_start: 0.8425 (mmp) cc_final: 0.8124 (mmt) REVERT: G 229 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: G 268 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6882 (mt-10) REVERT: G 333 ASN cc_start: 0.8716 (t0) cc_final: 0.8478 (t0) REVERT: G 389 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7602 (ttp80) REVERT: G 466 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8050 (mtmm) outliers start: 65 outliers final: 19 residues processed: 433 average time/residue: 0.5674 time to fit residues: 275.1346 Evaluate side-chains 406 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 377 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 466 LYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 466 LYS Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 ASN D 552 ASN H 552 ASN G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120488 restraints weight = 18724.222| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.57 r_work: 0.3177 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17780 Z= 0.166 Angle : 0.566 7.462 24096 Z= 0.289 Chirality : 0.047 0.144 2692 Planarity : 0.005 0.047 3072 Dihedral : 7.356 56.482 2596 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.96 % Favored : 97.85 % Rotamer: Outliers : 2.33 % Allowed : 16.49 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.66 (0.18), residues: 2144 helix: 1.40 (0.17), residues: 912 sheet: -0.73 (0.26), residues: 352 loop : 0.07 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 205 TYR 0.015 0.001 TYR H 42 PHE 0.014 0.002 PHE G 354 TRP 0.025 0.002 TRP G 387 HIS 0.005 0.002 HIS G 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (17780) covalent geometry : angle 0.56648 / 0.29 (24096) hydrogen bonds : bond 0.03522 / 2.33 ( 763) hydrogen bonds : angle 4.83957 / 3.42 ( 2169) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8328 (tttp) cc_final: 0.8089 (tttt) REVERT: D 53 TYR cc_start: 0.8316 (m-80) cc_final: 0.8051 (m-80) REVERT: D 123 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: D 132 SER cc_start: 0.8562 (p) cc_final: 0.8087 (t) REVERT: D 146 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: D 157 MET cc_start: 0.8515 (mmp) cc_final: 0.8170 (mmt) REVERT: D 176 TYR cc_start: 0.8065 (m-80) cc_final: 0.7478 (m-80) REVERT: D 232 MET cc_start: 0.8107 (mtp) cc_final: 0.7879 (mtm) REVERT: D 341 ASP cc_start: 0.8077 (m-30) cc_final: 0.7846 (m-30) REVERT: D 375 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7630 (pp) REVERT: D 391 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7341 (mttm) REVERT: D 402 MET cc_start: 0.8944 (tmm) cc_final: 0.8553 (ttt) REVERT: D 466 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7997 (mtmm) REVERT: D 481 ARG cc_start: 0.7807 (mtt90) cc_final: 0.7382 (mtt-85) REVERT: D 483 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6876 (mm-30) REVERT: C 28 LYS cc_start: 0.8361 (tttp) cc_final: 0.8042 (tttt) REVERT: C 53 TYR cc_start: 0.8388 (m-80) cc_final: 0.8113 (m-80) REVERT: C 123 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: C 146 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: C 157 MET cc_start: 0.8479 (mmp) cc_final: 0.8125 (mmt) REVERT: C 176 TYR cc_start: 0.8073 (m-80) cc_final: 0.7465 (m-80) REVERT: C 375 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7664 (pp) REVERT: H 53 TYR cc_start: 0.8367 (m-80) cc_final: 0.7969 (m-80) REVERT: H 123 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: H 132 SER cc_start: 0.8599 (p) cc_final: 0.8157 (t) REVERT: H 157 MET cc_start: 0.8514 (mmp) cc_final: 0.8182 (mmt) REVERT: H 176 TYR cc_start: 0.8069 (m-80) cc_final: 0.7492 (m-80) REVERT: H 333 ASN cc_start: 0.8767 (t0) cc_final: 0.8558 (t0) REVERT: H 341 ASP cc_start: 0.8252 (m-30) cc_final: 0.8022 (m-30) REVERT: H 375 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7557 (pp) REVERT: H 483 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6834 (mm-30) REVERT: G 28 LYS cc_start: 0.8389 (tttp) cc_final: 0.8057 (tttt) REVERT: G 123 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8026 (tp30) REVERT: G 132 SER cc_start: 0.8594 (p) cc_final: 0.8135 (t) REVERT: G 146 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8211 (tt0) REVERT: G 157 MET cc_start: 0.8505 (mmp) cc_final: 0.8162 (mmt) REVERT: G 229 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8414 (ttpt) REVERT: G 268 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7006 (mt-10) REVERT: G 375 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7602 (pp) REVERT: G 389 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7539 (ttp80) outliers start: 44 outliers final: 18 residues processed: 415 average time/residue: 0.5612 time to fit residues: 261.4331 Evaluate side-chains 421 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 390 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 229 LYS Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 375 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 105 optimal weight: 0.0970 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 ASN D 552 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN G 177 ASN ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.150909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.123155 restraints weight = 18639.614| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.58 r_work: 0.3206 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17780 Z= 0.118 Angle : 0.522 7.174 24096 Z= 0.266 Chirality : 0.045 0.156 2692 Planarity : 0.005 0.049 3072 Dihedral : 7.196 59.115 2596 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.70 % Allowed : 17.23 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.97 (0.19), residues: 2144 helix: 1.74 (0.17), residues: 916 sheet: -0.73 (0.26), residues: 352 loop : 0.21 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.014 0.001 TYR C 473 PHE 0.015 0.001 PHE D 318 TRP 0.013 0.002 TRP G 387 HIS 0.003 0.001 HIS H 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17780) covalent geometry : angle 0.52200 / 0.27 (24096) hydrogen bonds : bond 0.03144 / 2.10 ( 763) hydrogen bonds : angle 4.59313 / 3.26 ( 2169) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 393 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8334 (tttp) cc_final: 0.8103 (tttt) REVERT: D 53 TYR cc_start: 0.8321 (m-80) cc_final: 0.8103 (m-80) REVERT: D 123 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8063 (tp30) REVERT: D 132 SER cc_start: 0.8519 (p) cc_final: 0.8132 (t) REVERT: D 146 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: D 157 MET cc_start: 0.8448 (mmp) cc_final: 0.8094 (mmt) REVERT: D 176 TYR cc_start: 0.7981 (m-80) cc_final: 0.7437 (m-80) REVERT: D 232 MET cc_start: 0.8258 (mtp) cc_final: 0.8037 (mtm) REVERT: D 265 TYR cc_start: 0.8176 (t80) cc_final: 0.7946 (t80) REVERT: D 286 LYS cc_start: 0.7923 (ttpt) cc_final: 0.7372 (tmmt) REVERT: D 333 ASN cc_start: 0.8446 (t0) cc_final: 0.8220 (t0) REVERT: D 335 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8276 (mtp) REVERT: D 341 ASP cc_start: 0.7998 (m-30) cc_final: 0.7786 (m-30) REVERT: D 375 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7413 (pp) REVERT: D 391 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7281 (mttm) REVERT: D 402 MET cc_start: 0.8969 (tmm) cc_final: 0.8576 (ttt) REVERT: D 430 VAL cc_start: 0.7253 (OUTLIER) cc_final: 0.6921 (t) REVERT: D 466 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7967 (mtmm) REVERT: D 481 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7533 (mtt-85) REVERT: C 28 LYS cc_start: 0.8346 (tttp) cc_final: 0.8048 (tttt) REVERT: C 53 TYR cc_start: 0.8359 (m-80) cc_final: 0.8042 (m-80) REVERT: C 123 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: C 157 MET cc_start: 0.8373 (mmp) cc_final: 0.8018 (mmt) REVERT: C 293 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7177 (mm-30) REVERT: C 329 ASN cc_start: 0.8260 (t0) cc_final: 0.7972 (t0) REVERT: C 375 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7458 (pp) REVERT: H 53 TYR cc_start: 0.8344 (m-80) cc_final: 0.7848 (m-80) REVERT: H 123 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8100 (tp30) REVERT: H 132 SER cc_start: 0.8568 (p) cc_final: 0.8210 (t) REVERT: H 157 MET cc_start: 0.8422 (mmp) cc_final: 0.8085 (mmt) REVERT: H 176 TYR cc_start: 0.7987 (m-80) cc_final: 0.7422 (m-80) REVERT: H 212 ASP cc_start: 0.8826 (m-30) cc_final: 0.8619 (m-30) REVERT: H 265 TYR cc_start: 0.8160 (t80) cc_final: 0.7947 (t80) REVERT: H 293 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7149 (mm-30) REVERT: H 333 ASN cc_start: 0.8529 (t0) cc_final: 0.8316 (t0) REVERT: H 375 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7413 (pp) REVERT: G 28 LYS cc_start: 0.8398 (tttp) cc_final: 0.8087 (tttt) REVERT: G 123 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8050 (tp30) REVERT: G 132 SER cc_start: 0.8610 (p) cc_final: 0.8226 (t) REVERT: G 146 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: G 157 MET cc_start: 0.8418 (mmp) cc_final: 0.8054 (mmt) REVERT: G 268 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7051 (mt-10) REVERT: G 335 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: G 375 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7373 (pp) REVERT: G 389 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7533 (ttp80) REVERT: G 430 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6884 (t) outliers start: 51 outliers final: 16 residues processed: 419 average time/residue: 0.5503 time to fit residues: 258.9153 Evaluate side-chains 410 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 379 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 335 MET Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 132 optimal weight: 0.1980 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 ASN D 552 ASN C 177 ASN C 412 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.149721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.121693 restraints weight = 18591.314| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.59 r_work: 0.3188 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17780 Z= 0.123 Angle : 0.529 8.969 24096 Z= 0.268 Chirality : 0.045 0.153 2692 Planarity : 0.005 0.048 3072 Dihedral : 7.136 58.861 2596 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.01 % Allowed : 16.75 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.03 (0.19), residues: 2144 helix: 1.81 (0.17), residues: 920 sheet: -0.65 (0.25), residues: 372 loop : 0.20 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 291 TYR 0.014 0.001 TYR D 42 PHE 0.016 0.001 PHE H 318 TRP 0.009 0.002 TRP C 387 HIS 0.004 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (17780) covalent geometry : angle 0.52892 / 0.27 (24096) hydrogen bonds : bond 0.03144 / 2.10 ( 763) hydrogen bonds : angle 4.54176 / 3.23 ( 2169) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 392 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 LYS cc_start: 0.8361 (tttp) cc_final: 0.8160 (tttt) REVERT: D 123 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: D 132 SER cc_start: 0.8492 (p) cc_final: 0.8128 (t) REVERT: D 146 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: D 157 MET cc_start: 0.8489 (mmp) cc_final: 0.8176 (mmt) REVERT: D 176 TYR cc_start: 0.7980 (m-80) cc_final: 0.7428 (m-80) REVERT: D 265 TYR cc_start: 0.8181 (t80) cc_final: 0.7944 (t80) REVERT: D 286 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7417 (tmmt) REVERT: D 335 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: D 375 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7444 (pp) REVERT: D 391 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7258 (mttm) REVERT: D 430 VAL cc_start: 0.7294 (OUTLIER) cc_final: 0.6974 (t) REVERT: D 466 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7972 (mtmm) REVERT: D 481 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7559 (mtt-85) REVERT: C 28 LYS cc_start: 0.8338 (tttp) cc_final: 0.8063 (tttt) REVERT: C 53 TYR cc_start: 0.8348 (m-80) cc_final: 0.8039 (m-80) REVERT: C 123 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: C 157 MET cc_start: 0.8423 (mmp) cc_final: 0.8061 (mmt) REVERT: C 212 ASP cc_start: 0.8702 (m-30) cc_final: 0.8430 (m-30) REVERT: C 293 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 329 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7947 (t0) REVERT: C 375 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7400 (pp) REVERT: C 412 ASN cc_start: 0.7738 (m-40) cc_final: 0.7471 (m-40) REVERT: H 123 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8129 (tp30) REVERT: H 132 SER cc_start: 0.8560 (p) cc_final: 0.8212 (t) REVERT: H 146 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: H 157 MET cc_start: 0.8473 (mmp) cc_final: 0.8193 (mmt) REVERT: H 176 TYR cc_start: 0.8002 (m-80) cc_final: 0.7390 (m-80) REVERT: H 293 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7222 (mm-30) REVERT: H 333 ASN cc_start: 0.8602 (t0) cc_final: 0.8390 (t0) REVERT: H 375 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7402 (pp) REVERT: G 28 LYS cc_start: 0.8381 (tttp) cc_final: 0.8093 (tttt) REVERT: G 53 TYR cc_start: 0.8334 (m-80) cc_final: 0.7826 (m-80) REVERT: G 123 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8064 (tp30) REVERT: G 132 SER cc_start: 0.8554 (p) cc_final: 0.8201 (t) REVERT: G 146 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: G 157 MET cc_start: 0.8458 (mmp) cc_final: 0.8127 (mmt) REVERT: G 232 MET cc_start: 0.8081 (mtp) cc_final: 0.7578 (OUTLIER) REVERT: G 268 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7068 (mt-10) REVERT: G 293 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7170 (mm-30) REVERT: G 335 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8153 (mtp) REVERT: G 375 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7386 (pp) REVERT: G 389 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7460 (ttp80) REVERT: G 430 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6923 (t) outliers start: 57 outliers final: 23 residues processed: 419 average time/residue: 0.5617 time to fit residues: 264.5491 Evaluate side-chains 416 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 378 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 335 MET Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 185 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 94 optimal weight: 0.0010 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 177 ASN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 ASN H 552 ASN G 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121949 restraints weight = 18710.331| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.59 r_work: 0.3193 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17780 Z= 0.127 Angle : 0.531 9.860 24096 Z= 0.267 Chirality : 0.045 0.151 2692 Planarity : 0.005 0.048 3072 Dihedral : 7.145 58.340 2596 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.22 % Allowed : 16.97 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.06 (0.19), residues: 2144 helix: 1.81 (0.17), residues: 920 sheet: -0.71 (0.26), residues: 348 loop : 0.26 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 291 TYR 0.014 0.001 TYR C 42 PHE 0.014 0.001 PHE G 318 TRP 0.008 0.001 TRP D 358 HIS 0.004 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17780) covalent geometry : angle 0.53104 / 0.27 (24096) hydrogen bonds : bond 0.03196 / 2.13 ( 763) hydrogen bonds : angle 4.52853 / 3.22 ( 2169) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 390 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8073 (tp30) REVERT: D 132 SER cc_start: 0.8462 (p) cc_final: 0.8106 (t) REVERT: D 157 MET cc_start: 0.8458 (mmp) cc_final: 0.8256 (mmt) REVERT: D 176 TYR cc_start: 0.7941 (m-80) cc_final: 0.7391 (m-80) REVERT: D 212 ASP cc_start: 0.8826 (m-30) cc_final: 0.8615 (m-30) REVERT: D 265 TYR cc_start: 0.8177 (t80) cc_final: 0.7953 (t80) REVERT: D 286 LYS cc_start: 0.7958 (ttpt) cc_final: 0.7379 (tmmt) REVERT: D 293 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7172 (mm-30) REVERT: D 335 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8296 (mtp) REVERT: D 375 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7558 (pp) REVERT: D 391 LYS cc_start: 0.7610 (mtpp) cc_final: 0.7296 (mttm) REVERT: D 430 VAL cc_start: 0.7283 (OUTLIER) cc_final: 0.6979 (t) REVERT: D 466 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7946 (mtmm) REVERT: D 481 ARG cc_start: 0.7834 (mtt90) cc_final: 0.7580 (mtt-85) REVERT: C 28 LYS cc_start: 0.8324 (tttp) cc_final: 0.8051 (tttt) REVERT: C 53 TYR cc_start: 0.8351 (m-80) cc_final: 0.8038 (m-80) REVERT: C 123 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8077 (tp30) REVERT: C 146 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8194 (tt0) REVERT: C 157 MET cc_start: 0.8439 (mmp) cc_final: 0.8162 (mmt) REVERT: C 212 ASP cc_start: 0.8613 (m-30) cc_final: 0.8390 (m-30) REVERT: C 293 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7205 (mm-30) REVERT: C 329 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7936 (t0) REVERT: C 331 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7667 (mttp) REVERT: C 375 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7395 (pp) REVERT: C 412 ASN cc_start: 0.7735 (m-40) cc_final: 0.7460 (m-40) REVERT: H 53 TYR cc_start: 0.7997 (m-80) cc_final: 0.7737 (m-80) REVERT: H 123 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: H 132 SER cc_start: 0.8526 (p) cc_final: 0.8189 (t) REVERT: H 176 TYR cc_start: 0.7981 (m-80) cc_final: 0.7421 (m-80) REVERT: H 293 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7215 (mm-30) REVERT: H 375 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7421 (pp) REVERT: G 28 LYS cc_start: 0.8397 (tttp) cc_final: 0.8100 (tttt) REVERT: G 123 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: G 132 SER cc_start: 0.8480 (p) cc_final: 0.8150 (t) REVERT: G 157 MET cc_start: 0.8502 (mmp) cc_final: 0.8209 (mmt) REVERT: G 232 MET cc_start: 0.8088 (mtp) cc_final: 0.7589 (tmm) REVERT: G 268 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7060 (mt-10) REVERT: G 293 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7195 (mm-30) REVERT: G 375 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7357 (pp) REVERT: G 389 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7419 (ttp80) REVERT: G 434 ILE cc_start: 0.8324 (pt) cc_final: 0.8098 (pt) outliers start: 61 outliers final: 29 residues processed: 419 average time/residue: 0.5332 time to fit residues: 252.1242 Evaluate side-chains 413 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 335 MET Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 39 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 99 optimal weight: 0.0670 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.150036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.122012 restraints weight = 18741.263| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.60 r_work: 0.3198 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17780 Z= 0.122 Angle : 0.536 9.773 24096 Z= 0.270 Chirality : 0.045 0.173 2692 Planarity : 0.005 0.048 3072 Dihedral : 7.119 58.608 2596 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.75 % Allowed : 17.60 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.09 (0.19), residues: 2144 helix: 1.89 (0.17), residues: 912 sheet: -0.63 (0.25), residues: 368 loop : 0.21 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 291 TYR 0.014 0.001 TYR D 42 PHE 0.013 0.001 PHE H 354 TRP 0.014 0.002 TRP G 387 HIS 0.004 0.001 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (17780) covalent geometry : angle 0.53571 / 0.27 (24096) hydrogen bonds : bond 0.03164 / 2.10 ( 763) hydrogen bonds : angle 4.48870 / 3.19 ( 2169) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 383 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 123 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: D 132 SER cc_start: 0.8427 (p) cc_final: 0.8087 (t) REVERT: D 146 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: D 157 MET cc_start: 0.8438 (mmp) cc_final: 0.8230 (mmt) REVERT: D 176 TYR cc_start: 0.7953 (m-80) cc_final: 0.7401 (m-80) REVERT: D 212 ASP cc_start: 0.8827 (m-30) cc_final: 0.8614 (m-30) REVERT: D 265 TYR cc_start: 0.8148 (t80) cc_final: 0.7934 (t80) REVERT: D 286 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7425 (tmmt) REVERT: D 293 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 375 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7520 (pp) REVERT: D 391 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7295 (mttm) REVERT: D 430 VAL cc_start: 0.7276 (OUTLIER) cc_final: 0.6983 (t) REVERT: D 466 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7952 (mtmm) REVERT: D 481 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7592 (mtt-85) REVERT: C 28 LYS cc_start: 0.8351 (tttp) cc_final: 0.8055 (tttt) REVERT: C 53 TYR cc_start: 0.8363 (m-80) cc_final: 0.8038 (m-80) REVERT: C 123 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8060 (tp30) REVERT: C 146 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: C 157 MET cc_start: 0.8427 (mmp) cc_final: 0.8221 (mmt) REVERT: C 212 ASP cc_start: 0.8560 (m-30) cc_final: 0.8350 (m-30) REVERT: C 329 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 331 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7668 (mttp) REVERT: C 375 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7343 (pp) REVERT: H 123 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: H 132 SER cc_start: 0.8469 (p) cc_final: 0.8135 (t) REVERT: H 146 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: H 176 TYR cc_start: 0.7958 (m-80) cc_final: 0.7395 (m-80) REVERT: H 293 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7268 (mm-30) REVERT: H 375 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7411 (pp) REVERT: G 28 LYS cc_start: 0.8407 (tttp) cc_final: 0.8102 (tttt) REVERT: G 123 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: G 132 SER cc_start: 0.8498 (p) cc_final: 0.8179 (t) REVERT: G 146 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: G 157 MET cc_start: 0.8458 (mmp) cc_final: 0.8246 (mmt) REVERT: G 232 MET cc_start: 0.8099 (mtp) cc_final: 0.7609 (tmm) REVERT: G 268 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7094 (mt-10) REVERT: G 329 ASN cc_start: 0.8316 (OUTLIER) cc_final: 0.8107 (t0) REVERT: G 375 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7358 (pp) REVERT: G 389 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7474 (ttp80) outliers start: 52 outliers final: 26 residues processed: 406 average time/residue: 0.5308 time to fit residues: 241.9999 Evaluate side-chains 413 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 371 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 329 ASN Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 214 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN H 552 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.121715 restraints weight = 18687.828| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.58 r_work: 0.3172 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17780 Z= 0.144 Angle : 0.558 10.314 24096 Z= 0.281 Chirality : 0.046 0.178 2692 Planarity : 0.005 0.048 3072 Dihedral : 7.168 56.428 2596 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.54 % Allowed : 17.92 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.02 (0.19), residues: 2144 helix: 1.79 (0.17), residues: 912 sheet: -0.77 (0.26), residues: 352 loop : 0.27 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 291 TYR 0.015 0.001 TYR C 176 PHE 0.016 0.001 PHE D 318 TRP 0.012 0.001 TRP C 387 HIS 0.005 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (17780) covalent geometry : angle 0.55805 / 0.28 (24096) hydrogen bonds : bond 0.03316 / 2.21 ( 763) hydrogen bonds : angle 4.52560 / 3.21 ( 2169) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8145 (tpp) cc_final: 0.6872 (tpp) REVERT: D 123 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8075 (tp30) REVERT: D 132 SER cc_start: 0.8442 (p) cc_final: 0.8105 (t) REVERT: D 139 ASP cc_start: 0.7570 (m-30) cc_final: 0.7303 (m-30) REVERT: D 146 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8181 (tt0) REVERT: D 176 TYR cc_start: 0.7980 (m-80) cc_final: 0.7389 (m-80) REVERT: D 212 ASP cc_start: 0.8850 (m-30) cc_final: 0.8633 (m-30) REVERT: D 265 TYR cc_start: 0.8179 (t80) cc_final: 0.7962 (t80) REVERT: D 286 LYS cc_start: 0.8047 (ttpt) cc_final: 0.7478 (tmmt) REVERT: D 293 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7141 (mm-30) REVERT: D 375 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7398 (pp) REVERT: D 391 LYS cc_start: 0.7622 (mtpp) cc_final: 0.7239 (mmmm) REVERT: D 402 MET cc_start: 0.8963 (ttp) cc_final: 0.8297 (ttt) REVERT: D 466 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.8007 (mtmm) REVERT: D 481 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7548 (mtt-85) REVERT: D 485 ASN cc_start: 0.8587 (t0) cc_final: 0.8379 (t0) REVERT: C 28 LYS cc_start: 0.8346 (tttp) cc_final: 0.8081 (tttt) REVERT: C 53 TYR cc_start: 0.8355 (m-80) cc_final: 0.8042 (m-80) REVERT: C 123 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: C 146 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: C 212 ASP cc_start: 0.8582 (m-30) cc_final: 0.8364 (m-30) REVERT: C 268 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7033 (mt-10) REVERT: C 293 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7144 (mm-30) REVERT: C 329 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (t0) REVERT: C 375 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7425 (pp) REVERT: C 485 ASN cc_start: 0.8590 (t0) cc_final: 0.8334 (t0) REVERT: H 123 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (tp30) REVERT: H 132 SER cc_start: 0.8486 (p) cc_final: 0.8148 (t) REVERT: H 146 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: H 176 TYR cc_start: 0.7964 (m-80) cc_final: 0.7352 (m-80) REVERT: H 177 ASN cc_start: 0.8623 (t160) cc_final: 0.8310 (t0) REVERT: H 375 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7457 (pp) REVERT: G 28 LYS cc_start: 0.8362 (tttp) cc_final: 0.8096 (tttt) REVERT: G 123 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8052 (tp30) REVERT: G 132 SER cc_start: 0.8470 (p) cc_final: 0.8159 (t) REVERT: G 146 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: G 232 MET cc_start: 0.8142 (mtp) cc_final: 0.7641 (tmm) REVERT: G 268 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7170 (mt-10) REVERT: G 329 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.8080 (t0) REVERT: G 375 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7386 (pp) REVERT: G 389 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7483 (ttp80) outliers start: 48 outliers final: 27 residues processed: 406 average time/residue: 0.5040 time to fit residues: 231.2675 Evaluate side-chains 419 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 377 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 466 LYS Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 329 ASN Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 168 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN H 260 GLN G 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.117683 restraints weight = 18454.763| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.57 r_work: 0.3153 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17780 Z= 0.198 Angle : 0.607 10.490 24096 Z= 0.304 Chirality : 0.048 0.178 2692 Planarity : 0.005 0.047 3072 Dihedral : 7.367 50.326 2596 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.64 % Allowed : 17.97 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.18), residues: 2144 helix: 1.59 (0.17), residues: 912 sheet: -0.85 (0.25), residues: 352 loop : 0.24 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 291 TYR 0.016 0.002 TYR H 176 PHE 0.019 0.002 PHE D 318 TRP 0.007 0.001 TRP D 358 HIS 0.006 0.002 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (17780) covalent geometry : angle 0.60687 / 0.30 (24096) hydrogen bonds : bond 0.03663 / 2.43 ( 763) hydrogen bonds : angle 4.68907 / 3.33 ( 2169) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4288 Ramachandran restraints generated. 2144 Oldfield, 0 Emsley, 2144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 400 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.8124 (tpp) cc_final: 0.6963 (tpp) REVERT: D 123 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: D 132 SER cc_start: 0.8538 (p) cc_final: 0.8185 (t) REVERT: D 139 ASP cc_start: 0.7519 (m-30) cc_final: 0.7231 (m-30) REVERT: D 176 TYR cc_start: 0.8019 (m-80) cc_final: 0.7293 (m-80) REVERT: D 259 GLU cc_start: 0.7425 (tp30) cc_final: 0.7139 (mt-10) REVERT: D 286 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7393 (tmmt) REVERT: D 293 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 375 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7613 (pp) REVERT: D 391 LYS cc_start: 0.7635 (mtpp) cc_final: 0.7238 (mmmm) REVERT: D 402 MET cc_start: 0.8958 (ttp) cc_final: 0.8272 (ttt) REVERT: D 481 ARG cc_start: 0.7778 (mtt90) cc_final: 0.7424 (mtt-85) REVERT: C 28 LYS cc_start: 0.8340 (tttp) cc_final: 0.8061 (tttt) REVERT: C 53 TYR cc_start: 0.8362 (m-80) cc_final: 0.8075 (m-80) REVERT: C 123 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8138 (tp30) REVERT: C 212 ASP cc_start: 0.8689 (m-30) cc_final: 0.8417 (m-30) REVERT: C 293 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7163 (mm-30) REVERT: C 341 ASP cc_start: 0.8147 (m-30) cc_final: 0.7872 (m-30) REVERT: C 375 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7581 (pp) REVERT: C 391 LYS cc_start: 0.7798 (ptpp) cc_final: 0.7404 (ptmt) REVERT: C 485 ASN cc_start: 0.8613 (t0) cc_final: 0.8392 (t0) REVERT: H 123 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: H 132 SER cc_start: 0.8589 (p) cc_final: 0.8242 (t) REVERT: H 176 TYR cc_start: 0.8017 (m-80) cc_final: 0.7245 (m-80) REVERT: H 177 ASN cc_start: 0.8608 (t160) cc_final: 0.8285 (t0) REVERT: H 341 ASP cc_start: 0.8172 (m-30) cc_final: 0.7926 (m-30) REVERT: H 375 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7676 (pp) REVERT: H 485 ASN cc_start: 0.8642 (t0) cc_final: 0.8415 (t0) REVERT: G 28 LYS cc_start: 0.8361 (tttp) cc_final: 0.8070 (tttt) REVERT: G 123 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8057 (tp30) REVERT: G 232 MET cc_start: 0.8133 (mtp) cc_final: 0.7643 (tmm) REVERT: G 268 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7052 (mt-10) REVERT: G 375 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7571 (pp) REVERT: G 389 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7475 (ttp80) outliers start: 50 outliers final: 26 residues processed: 423 average time/residue: 0.5152 time to fit residues: 246.4890 Evaluate side-chains 427 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 393 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 316 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 THR Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 428 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 231 SER Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 378 THR Chi-restraints excluded: chain H residue 428 THR Chi-restraints excluded: chain H residue 481 ARG Chi-restraints excluded: chain H residue 512 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 231 SER Chi-restraints excluded: chain G residue 316 SER Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 59 optimal weight: 0.0030 chunk 196 optimal weight: 0.9980 chunk 51 optimal weight: 0.0870 chunk 201 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.3168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 ASN ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.149628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.121940 restraints weight = 18837.203| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.59 r_work: 0.3198 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17780 Z= 0.112 Angle : 0.537 10.405 24096 Z= 0.271 Chirality : 0.045 0.164 2692 Planarity : 0.005 0.047 3072 Dihedral : 7.085 57.443 2596 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.69 % Allowed : 19.19 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.08 (0.19), residues: 2144 helix: 1.89 (0.17), residues: 912 sheet: -0.69 (0.25), residues: 372 loop : 0.22 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 291 TYR 0.013 0.001 TYR C 42 PHE 0.014 0.001 PHE D 318 TRP 0.010 0.001 TRP G 124 HIS 0.003 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (17780) covalent geometry : angle 0.53670 / 0.27 (24096) hydrogen bonds : bond 0.03199 / 2.15 ( 763) hydrogen bonds : angle 4.48604 / 3.19 ( 2169) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6729.89 seconds wall clock time: 115 minutes 22.71 seconds (6922.71 seconds total)