Starting phenix.real_space_refine on Mon Jul 6 09:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mif_23848/07_2026/7mif_23848.map" } resolution = 3.1 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= 0.208 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 10968 2.51 5 N 2944 2.21 5 O 3224 1.98 5 H 17036 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s 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: 34284 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "G" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "H" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "I" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8488 Classifications: {'peptide': 533} Modifications used: {'ACID-GLU': 4, 'NH2NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 504} Chain breaks: 4 Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 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: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN G 603 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'UTP': 1, 'ZG4': 1} Inner-chain residues flagged as termini: ['pdbres="GLN I 602 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Time building chain proxies: 5.67, per 1000 atoms: 0.17 Number of scatterers: 34284 At special positions: 0 Unit cell: (124.95, 133.35, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 96 16.00 P 12 15.00 Mg 4 11.99 O 3224 8.00 N 2944 7.00 C 10968 6.00 H 17036 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 243 " distance=2.05 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 243 " distance=2.05 Simple disulfide: pdb=" SG CYS H 218 " - pdb=" SG CYS H 243 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 243 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 919.1 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 46.3% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 68 through 78 removed outlier: 4.017A 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 103 Processing helix chain 'C' and resid 112 through 131 removed outlier: 7.220A pdb=" N THR C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 4.684A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 194 through 207 Processing helix chain 'C' and resid 223 through 234 Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' 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 270 Processing helix chain 'C' and resid 283 through 293 Processing helix chain 'C' and resid 314 through 329 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.693A pdb=" N GLU C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 364 Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 413 removed outlier: 3.684A pdb=" N GLN C 403 " --> pdb=" O CYS C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.723A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 526 through 531 removed outlier: 3.535A 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 555 Processing helix chain 'G' and resid 15 through 30 Processing helix chain 'G' and resid 68 through 78 removed outlier: 4.017A 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 131 removed outlier: 7.220A pdb=" N THR G 118 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE G 131 " --> pdb=" O ARG G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 170 removed outlier: 4.684A pdb=" N PHE G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 173 No H-bonds generated for 'chain 'G' and resid 171 through 173' Processing helix chain 'G' and resid 194 through 207 Processing helix chain 'G' and resid 223 through 234 Processing helix chain 'G' and resid 237 through 239 No H-bonds generated for 'chain 'G' and resid 237 through 239' 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 270 Processing helix chain 'G' and resid 283 through 293 Processing helix chain 'G' and resid 314 through 329 Processing helix chain 'G' and resid 345 through 350 removed outlier: 3.693A pdb=" N GLU G 349 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 364 Processing helix chain 'G' and resid 377 through 391 Processing helix chain 'G' and resid 399 through 413 removed outlier: 3.684A pdb=" N GLN G 403 " --> pdb=" O CYS G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.723A pdb=" N LYS G 466 " --> pdb=" O SER G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 526 through 531 removed outlier: 3.535A 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 555 Processing helix chain 'H' and resid 15 through 30 Processing helix chain 'H' and resid 68 through 78 removed outlier: 4.017A 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 103 Processing helix chain 'H' and resid 112 through 131 removed outlier: 7.219A pdb=" N THR H 118 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 130 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 170 removed outlier: 4.684A pdb=" N PHE H 168 " --> pdb=" O ARG H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 194 through 207 Processing helix chain 'H' and resid 223 through 234 Processing helix chain 'H' and resid 237 through 239 No H-bonds generated for 'chain 'H' and resid 237 through 239' Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 252 through 260 Processing helix chain 'H' and resid 261 through 270 Processing helix chain 'H' and resid 283 through 293 Processing helix chain 'H' and resid 314 through 329 Processing helix chain 'H' and resid 345 through 350 removed outlier: 3.693A pdb=" N GLU H 349 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 364 Processing helix chain 'H' and resid 377 through 391 Processing helix chain 'H' and resid 399 through 413 removed outlier: 3.685A pdb=" N GLN H 403 " --> pdb=" O CYS H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 468 removed outlier: 3.723A pdb=" N LYS H 466 " --> pdb=" O SER H 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 491 Processing helix chain 'H' and resid 526 through 531 removed outlier: 3.535A 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 555 Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 68 through 78 removed outlier: 4.017A pdb=" N GLY I 72 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 90 through 103 Processing helix chain 'I' and resid 112 through 131 removed outlier: 7.219A pdb=" N THR I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU I 130 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 170 removed outlier: 4.684A pdb=" N PHE I 168 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 194 through 207 Processing helix chain 'I' and resid 223 through 234 Processing helix chain 'I' and resid 237 through 239 No H-bonds generated for 'chain 'I' and resid 237 through 239' Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 252 through 260 Processing helix chain 'I' and resid 261 through 270 Processing helix chain 'I' and resid 283 through 293 Processing helix chain 'I' and resid 314 through 329 Processing helix chain 'I' and resid 345 through 350 removed outlier: 3.692A pdb=" N GLU I 349 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 364 Processing helix chain 'I' and resid 377 through 391 Processing helix chain 'I' and resid 399 through 413 removed outlier: 3.685A pdb=" N GLN I 403 " --> pdb=" O CYS I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 468 removed outlier: 3.723A pdb=" N LYS I 466 " --> pdb=" O SER I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 491 Processing helix chain 'I' and resid 526 through 531 removed outlier: 3.535A pdb=" N PHE I 529 " --> pdb=" O HIS I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 537 through 548 Processing helix chain 'I' and resid 550 through 555 Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.199A pdb=" N ILE C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU C 147 " --> pdb=" O ILE C 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 6 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 181 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'C' and resid 331 through 338 removed outlier: 6.691A pdb=" N CYS C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 301 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY C 366 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL C 398 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 369 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY C 501 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL C 512 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE C 499 " --> pdb=" O VAL C 512 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 420 through 421 removed outlier: 7.693A pdb=" N ASN C 420 " --> pdb=" O VAL C 432 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL C 434 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 87 through 89 removed outlier: 6.199A pdb=" N ILE G 4 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU G 147 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G 6 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR G 3 " --> pdb=" O CYS G 176 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU G 213 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN G 177 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL G 215 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS G 179 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG G 217 " --> pdb=" O HIS G 179 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER G 181 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AA7, first strand: chain 'G' and resid 331 through 338 removed outlier: 6.692A pdb=" N CYS G 299 " --> pdb=" O GLU G 333 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS G 335 " --> pdb=" O CYS G 299 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE G 301 " --> pdb=" O LYS G 335 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE G 337 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU G 303 " --> pdb=" O ILE G 337 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 366 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL G 367 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL G 398 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL G 369 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE G 395 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL G 523 " --> pdb=" O PHE G 395 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY G 397 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY G 501 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL G 512 " --> pdb=" O PHE G 499 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE G 499 " --> pdb=" O VAL G 512 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 420 through 421 removed outlier: 7.693A pdb=" N ASN G 420 " --> pdb=" O VAL G 432 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL G 434 " --> pdb=" O ASN G 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 87 through 89 removed outlier: 6.199A pdb=" N ILE H 4 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU H 147 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL H 6 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR H 3 " --> pdb=" O CYS H 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE H 178 " --> pdb=" O TYR H 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU H 5 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL H 180 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR H 7 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N LEU H 182 " --> pdb=" O THR H 7 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU H 213 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN H 177 " --> pdb=" O LEU H 213 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL H 215 " --> pdb=" O ASN H 177 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS H 179 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG H 217 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 6.774A 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 331 through 338 removed outlier: 6.691A pdb=" N CYS H 299 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS H 335 " --> pdb=" O CYS H 299 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE H 301 " --> pdb=" O LYS H 335 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE H 337 " --> pdb=" O ILE H 301 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU H 303 " --> pdb=" O ILE H 337 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY H 366 " --> pdb=" O SER H 300 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL H 367 " --> pdb=" O LEU H 396 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL H 398 " --> pdb=" O VAL H 367 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL H 369 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE H 395 " --> pdb=" O VAL H 521 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL H 523 " --> pdb=" O PHE H 395 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY H 397 " --> pdb=" O VAL H 523 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY H 501 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL H 512 " --> pdb=" O PHE H 499 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE H 499 " --> pdb=" O VAL H 512 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 420 through 421 removed outlier: 7.693A pdb=" N ASN H 420 " --> pdb=" O VAL H 432 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL H 434 " --> pdb=" O ASN H 420 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 87 through 89 removed outlier: 6.199A pdb=" N ILE I 4 " --> pdb=" O ILE I 145 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU I 147 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL I 6 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N TYR I 3 " --> pdb=" O CYS I 176 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE I 178 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU I 5 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL I 180 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 7 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU I 182 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LEU I 213 " --> pdb=" O PHE I 175 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN I 177 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL I 215 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS I 179 " --> pdb=" O VAL I 215 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG I 217 " --> pdb=" O HIS I 179 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER I 181 " --> pdb=" O ARG I 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB6, first strand: chain 'I' and resid 331 through 338 removed outlier: 6.692A pdb=" N CYS I 299 " --> pdb=" O GLU I 333 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS I 335 " --> pdb=" O CYS I 299 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE I 301 " --> pdb=" O LYS I 335 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE I 337 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU I 303 " --> pdb=" O ILE I 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY I 366 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL I 367 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL I 398 " --> pdb=" O VAL I 367 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL I 369 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE I 395 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 523 " --> pdb=" O PHE I 395 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY I 397 " --> pdb=" O VAL I 523 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY I 501 " --> pdb=" O GLU I 510 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL I 512 " --> pdb=" O PHE I 499 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE I 499 " --> pdb=" O VAL I 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 420 through 421 removed outlier: 7.693A pdb=" N ASN I 420 " --> pdb=" O VAL I 432 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL I 434 " --> pdb=" O ASN I 420 " (cutoff:3.500A) 712 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.24: 19305 1.24 - 1.54: 10830 1.54 - 1.83: 4513 1.83 - 2.12: 4 2.12 - 2.42: 12 Bond restraints: 34664 Sorted by residual: bond pdb=" OE2 GLU G 203 " pdb=" HE2 GLU G 203 " ideal model delta sigma weight residual 0.948 2.419 -1.471 2.00e-02 2.50e+03 5.41e+03 bond pdb=" OE2 GLU I 203 " pdb=" HE2 GLU I 203 " ideal model delta sigma weight residual 0.948 2.418 -1.470 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU C 203 " pdb=" HE2 GLU C 203 " ideal model delta sigma weight residual 0.948 2.418 -1.470 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU H 203 " pdb=" HE2 GLU H 203 " ideal model delta sigma weight residual 0.948 2.417 -1.469 2.00e-02 2.50e+03 5.40e+03 bond pdb=" OE2 GLU H 476 " pdb=" HE2 GLU H 476 " ideal model delta sigma weight residual 0.948 2.401 -1.453 2.00e-02 2.50e+03 5.28e+03 ... (remaining 34659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.10: 62676 11.10 - 22.19: 28 22.19 - 33.29: 0 33.29 - 44.39: 0 44.39 - 55.49: 12 Bond angle restraints: 62716 Sorted by residual: angle pdb=" CD GLU I 203 " pdb=" OE2 GLU I 203 " pdb=" HE2 GLU I 203 " ideal model delta sigma weight residual 108.32 52.83 55.49 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU C 203 " pdb=" OE2 GLU C 203 " pdb=" HE2 GLU C 203 " ideal model delta sigma weight residual 108.32 52.84 55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU G 203 " pdb=" OE2 GLU G 203 " pdb=" HE2 GLU G 203 " ideal model delta sigma weight residual 108.32 52.84 55.48 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU H 203 " pdb=" OE2 GLU H 203 " pdb=" HE2 GLU H 203 " ideal model delta sigma weight residual 108.32 52.85 55.47 3.00e+00 1.11e-01 3.42e+02 angle pdb=" CD GLU C 476 " pdb=" OE2 GLU C 476 " pdb=" HE2 GLU C 476 " ideal model delta sigma weight residual 108.32 53.52 54.80 3.00e+00 1.11e-01 3.34e+02 ... (remaining 62711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 14462 17.48 - 34.96: 1138 34.96 - 52.44: 547 52.44 - 69.92: 197 69.92 - 87.39: 52 Dihedral angle restraints: 16396 sinusoidal: 9156 harmonic: 7240 Sorted by residual: dihedral pdb=" CB CYS I 218 " pdb=" SG CYS I 218 " pdb=" SG CYS I 243 " pdb=" CB CYS I 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS C 218 " pdb=" SG CYS C 218 " pdb=" SG CYS C 243 " pdb=" CB CYS C 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS H 218 " pdb=" SG CYS H 218 " pdb=" SG CYS H 243 " pdb=" CB CYS H 243 " ideal model delta sinusoidal sigma weight residual -86.00 -173.39 87.39 1 1.00e+01 1.00e-02 9.16e+01 ... (remaining 16393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1474 0.090 - 0.180: 752 0.180 - 0.271: 329 0.271 - 0.361: 69 0.361 - 0.451: 16 Chirality restraints: 2640 Sorted by residual: chirality pdb=" CA PRO I 538 " pdb=" N PRO I 538 " pdb=" C PRO I 538 " pdb=" CB PRO I 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PRO C 538 " pdb=" N PRO C 538 " pdb=" C PRO C 538 " pdb=" CB PRO C 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PRO H 538 " pdb=" N PRO H 538 " pdb=" C PRO H 538 " pdb=" CB PRO H 538 " both_signs ideal model delta sigma weight residual False 2.72 2.27 0.45 2.00e-01 2.50e+01 5.06e+00 ... (remaining 2637 not shown) Planarity restraints: 5064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 387 " 0.152 2.00e-02 2.50e+03 6.05e-02 1.47e+02 pdb=" CG TRP G 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP G 387 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP G 387 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 387 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP G 387 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP G 387 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 387 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 387 " -0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP G 387 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP G 387 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP G 387 " -0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP G 387 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 387 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 387 " -0.058 2.00e-02 2.50e+03 pdb=" HH2 TRP G 387 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 387 " 0.152 2.00e-02 2.50e+03 6.05e-02 1.47e+02 pdb=" CG TRP I 387 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP I 387 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP I 387 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 387 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP I 387 " 0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP I 387 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 387 " 0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 387 " -0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP I 387 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP I 387 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP I 387 " -0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP I 387 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP I 387 " 0.112 2.00e-02 2.50e+03 pdb=" HZ3 TRP I 387 " -0.058 2.00e-02 2.50e+03 pdb=" HH2 TRP I 387 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 387 " -0.152 2.00e-02 2.50e+03 6.05e-02 1.46e+02 pdb=" CG TRP H 387 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP H 387 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP H 387 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 387 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP H 387 " -0.017 2.00e-02 2.50e+03 pdb=" CE3 TRP H 387 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 387 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 387 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP H 387 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP H 387 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 TRP H 387 " 0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP H 387 " 0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 387 " -0.111 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 387 " 0.059 2.00e-02 2.50e+03 pdb=" HH2 TRP H 387 " -0.014 2.00e-02 2.50e+03 ... (remaining 5061 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 51 1.69 - 2.42: 12354 2.42 - 3.14: 114055 3.14 - 3.87: 158927 3.87 - 4.60: 244891 Warning: very small nonbonded interaction distances. Nonbonded interactions: 530278 Sorted by model distance: nonbonded pdb=" OE1 GLU I 483 " pdb=" HE2 GLU I 483 " model vdw 0.959 1.960 nonbonded pdb=" OE1 GLU C 476 " pdb=" HE2 GLU C 476 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU G 483 " pdb=" HE2 GLU G 483 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU I 476 " pdb=" HE2 GLU I 476 " model vdw 0.960 1.960 nonbonded pdb=" OE1 GLU H 476 " pdb=" HE2 GLU H 476 " model vdw 0.960 1.960 ... (remaining 530273 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 556) selection = (chain 'G' and resid 1 through 556) selection = (chain 'H' and resid 1 through 556) selection = (chain 'I' and resid 1 through 556) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 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: 0.250 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.910 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.015 0.179 17632 Z= 0.840 Angle : 1.987 9.283 23904 Z= 1.325 Chirality : 0.124 0.451 2640 Planarity : 0.014 0.096 3064 Dihedral : 15.505 85.910 6784 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.72 % Allowed : 3.68 % Favored : 95.60 % Rotamer: Outliers : 1.48 % Allowed : 5.92 % Favored : 92.60 % Cbeta Deviations : 0.66 % 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: -1.46 (0.18), residues: 2092 helix: -1.12 (0.16), residues: 864 sheet: -0.81 (0.27), residues: 344 loop : -0.62 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 202 TYR 0.070 0.012 TYR I 74 PHE 0.101 0.020 PHE H 163 TRP 0.098 0.017 TRP I 387 HIS 0.021 0.006 HIS H 439 Details of bonding type rmsd/Z covalent geometry : bond 0.01463 / 0.84 (17628) covalent geometry : angle 1.98746 / 1.33 (23896) SS BOND : bond 0.01575 / 0.79 ( 4) SS BOND : angle 1.66123 / 0.82 ( 8) hydrogen bonds : bond 0.16295 / 10.99 ( 712) hydrogen bonds : angle 6.98540 / 4.86 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 530 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 502 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 CYS cc_start: 0.7143 (t) cc_final: 0.6907 (t) REVERT: C 240 GLN cc_start: 0.6664 (mt0) cc_final: 0.6106 (mt0) REVERT: C 330 HIS cc_start: 0.7772 (m-70) cc_final: 0.7562 (m170) REVERT: C 402 MET cc_start: 0.6892 (ttt) cc_final: 0.6604 (ttt) REVERT: G 103 LYS cc_start: 0.7013 (mmmm) cc_final: 0.6806 (mtpt) REVERT: G 240 GLN cc_start: 0.7515 (mt0) cc_final: 0.7236 (mt0) REVERT: G 393 LYS cc_start: 0.7148 (mmtt) cc_final: 0.6902 (mmtt) REVERT: G 452 LYS cc_start: 0.7806 (tttt) cc_final: 0.7270 (ttpt) REVERT: G 466 LYS cc_start: 0.7969 (mttt) cc_final: 0.7701 (mtpt) REVERT: H 84 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7392 (mttt) REVERT: H 240 GLN cc_start: 0.7475 (mt0) cc_final: 0.7206 (mt0) REVERT: H 393 LYS cc_start: 0.7130 (mmtt) cc_final: 0.6872 (mmtt) REVERT: H 452 LYS cc_start: 0.7792 (tttt) cc_final: 0.7419 (ttpt) REVERT: H 466 LYS cc_start: 0.7981 (mttt) cc_final: 0.7730 (mtpt) REVERT: I 103 LYS cc_start: 0.7039 (mmmm) cc_final: 0.6837 (mtpt) REVERT: I 240 GLN cc_start: 0.7515 (mt0) cc_final: 0.7247 (mt0) REVERT: I 393 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6882 (mmtt) REVERT: I 466 LYS cc_start: 0.7982 (mttt) cc_final: 0.7715 (mtpt) outliers start: 28 outliers final: 10 residues processed: 524 average time/residue: 0.3635 time to fit residues: 273.9293 Evaluate side-chains 405 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 395 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 264 ASP Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 89 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 ASN C 185 GLN C 220 ASN C 412 ASN C 556 GLN G 87 ASN G 185 GLN G 412 ASN G 556 GLN H 87 ASN H 185 GLN H 220 ASN H 412 ASN H 556 GLN I 87 ASN I 185 GLN I 220 ASN I 412 ASN I 556 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.178448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.150145 restraints weight = 54645.322| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.94 r_work: 0.3430 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17632 Z= 0.171 Angle : 0.660 6.950 23904 Z= 0.349 Chirality : 0.046 0.173 2640 Planarity : 0.005 0.048 3064 Dihedral : 8.465 53.332 2601 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.01 % Favored : 96.80 % Rotamer: Outliers : 1.22 % Allowed : 7.56 % Favored : 91.23 % 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: -0.29 (0.18), residues: 2092 helix: 0.49 (0.17), residues: 904 sheet: -1.02 (0.26), residues: 348 loop : -0.39 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 81 TYR 0.012 0.002 TYR I 265 PHE 0.020 0.002 PHE C 163 TRP 0.013 0.001 TRP G 387 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (17628) covalent geometry : angle 0.65310 / 0.35 (23896) SS BOND : bond 0.01393 / 0.69 ( 4) SS BOND : angle 5.10408 / 2.45 ( 8) hydrogen bonds : bond 0.04415 / 3.00 ( 712) hydrogen bonds : angle 5.05373 / 3.50 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 462 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 439 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7629 (mttt) REVERT: C 139 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6965 (tp30) REVERT: C 176 CYS cc_start: 0.8333 (t) cc_final: 0.8101 (t) REVERT: C 232 MET cc_start: 0.8421 (ttp) cc_final: 0.8126 (ttt) REVERT: C 234 CYS cc_start: 0.7004 (m) cc_final: 0.6791 (t) REVERT: C 265 TYR cc_start: 0.7394 (t80) cc_final: 0.7105 (t80) REVERT: C 271 ASP cc_start: 0.7098 (t0) cc_final: 0.6759 (t0) REVERT: C 293 ASP cc_start: 0.6545 (m-30) cc_final: 0.6329 (m-30) REVERT: C 391 GLN cc_start: 0.6262 (mm-40) cc_final: 0.5554 (mm-40) REVERT: G 223 ASP cc_start: 0.6561 (t0) cc_final: 0.6287 (t0) REVERT: G 265 TYR cc_start: 0.7759 (t80) cc_final: 0.7166 (t80) REVERT: G 354 TYR cc_start: 0.6833 (t80) cc_final: 0.6348 (t80) REVERT: G 383 GLN cc_start: 0.7656 (mt0) cc_final: 0.7224 (mt0) REVERT: G 393 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7101 (mmtt) REVERT: G 466 LYS cc_start: 0.7817 (mttt) cc_final: 0.7495 (mtpt) REVERT: G 550 ARG cc_start: 0.7813 (mmt90) cc_final: 0.7356 (mmt90) REVERT: H 84 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7691 (mttt) REVERT: H 157 MET cc_start: 0.7522 (mtp) cc_final: 0.6967 (mmp) REVERT: H 223 ASP cc_start: 0.6571 (t0) cc_final: 0.6272 (t0) REVERT: H 265 TYR cc_start: 0.7779 (t80) cc_final: 0.7143 (t80) REVERT: H 354 TYR cc_start: 0.6830 (t80) cc_final: 0.6353 (t80) REVERT: H 379 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7185 (mm-30) REVERT: H 383 GLN cc_start: 0.7538 (mt0) cc_final: 0.6976 (mt0) REVERT: H 393 LYS cc_start: 0.7362 (mmtt) cc_final: 0.7085 (mmtt) REVERT: H 412 ASN cc_start: 0.6928 (m110) cc_final: 0.6361 (m110) REVERT: H 466 LYS cc_start: 0.7775 (mttt) cc_final: 0.7462 (mtpt) REVERT: I 103 LYS cc_start: 0.7778 (mmmm) cc_final: 0.7381 (mtmt) REVERT: I 223 ASP cc_start: 0.6590 (t0) cc_final: 0.6276 (t0) REVERT: I 265 TYR cc_start: 0.7736 (t80) cc_final: 0.7104 (t80) REVERT: I 354 TYR cc_start: 0.6797 (t80) cc_final: 0.6330 (t80) REVERT: I 393 LYS cc_start: 0.7403 (mmtt) cc_final: 0.7118 (mmtt) REVERT: I 466 LYS cc_start: 0.7765 (mttt) cc_final: 0.7441 (mtpt) outliers start: 23 outliers final: 15 residues processed: 453 average time/residue: 0.3433 time to fit residues: 223.9413 Evaluate side-chains 407 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 391 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 467 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 GLN C 220 ASN C 329 ASN C 524 GLN G 329 ASN ** G 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN I 329 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.165670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135161 restraints weight = 54200.400| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.98 r_work: 0.3307 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17632 Z= 0.161 Angle : 0.615 6.483 23904 Z= 0.318 Chirality : 0.045 0.203 2640 Planarity : 0.006 0.067 3064 Dihedral : 6.898 53.042 2591 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 1.59 % Allowed : 10.20 % Favored : 88.21 % 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: 0.14 (0.19), residues: 2092 helix: 0.97 (0.17), residues: 900 sheet: -1.02 (0.26), residues: 348 loop : -0.21 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 81 TYR 0.013 0.001 TYR G 42 PHE 0.021 0.002 PHE C 163 TRP 0.027 0.002 TRP G 387 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (17628) covalent geometry : angle 0.60895 / 0.32 (23896) SS BOND : bond 0.00718 / 0.35 ( 4) SS BOND : angle 4.64897 / 2.27 ( 8) hydrogen bonds : bond 0.03794 / 2.58 ( 712) hydrogen bonds : angle 4.60708 / 3.21 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 433 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7803 (mttt) REVERT: C 139 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: C 153 ASP cc_start: 0.7754 (m-30) cc_final: 0.7430 (m-30) REVERT: C 157 MET cc_start: 0.7277 (mtp) cc_final: 0.6718 (mmp) REVERT: C 232 MET cc_start: 0.8513 (ttp) cc_final: 0.8259 (ttt) REVERT: C 259 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7610 (tp30) REVERT: C 271 ASP cc_start: 0.7413 (t0) cc_final: 0.7009 (t0) REVERT: C 293 ASP cc_start: 0.6726 (m-30) cc_final: 0.6496 (m-30) REVERT: C 391 GLN cc_start: 0.6603 (mm-40) cc_final: 0.5959 (mm-40) REVERT: C 393 LYS cc_start: 0.6816 (mmtt) cc_final: 0.6546 (mmtt) REVERT: G 103 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7853 (tppp) REVERT: G 139 GLU cc_start: 0.8061 (tt0) cc_final: 0.7607 (tt0) REVERT: G 157 MET cc_start: 0.7810 (mtp) cc_final: 0.7158 (mmp) REVERT: G 223 ASP cc_start: 0.6736 (t0) cc_final: 0.6302 (m-30) REVERT: G 232 MET cc_start: 0.7216 (mtp) cc_final: 0.6943 (mmp) REVERT: G 265 TYR cc_start: 0.7901 (t80) cc_final: 0.7221 (t80) REVERT: G 292 TYR cc_start: 0.8402 (t80) cc_final: 0.8144 (t80) REVERT: G 365 HIS cc_start: 0.8431 (m170) cc_final: 0.8196 (m-70) REVERT: G 383 GLN cc_start: 0.7699 (mt0) cc_final: 0.7419 (mm-40) REVERT: G 393 LYS cc_start: 0.7375 (mmtt) cc_final: 0.7120 (mmtt) REVERT: G 448 MET cc_start: 0.8324 (ttt) cc_final: 0.7942 (ttt) REVERT: G 452 LYS cc_start: 0.8425 (tttt) cc_final: 0.7761 (ttpt) REVERT: G 466 LYS cc_start: 0.7966 (mttt) cc_final: 0.7619 (mtpt) REVERT: G 475 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: G 525 TYR cc_start: 0.8701 (p90) cc_final: 0.8398 (p90) REVERT: H 46 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8166 (p0) REVERT: H 84 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7682 (mttt) REVERT: H 103 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7832 (tppp) REVERT: H 157 MET cc_start: 0.7780 (mtp) cc_final: 0.7161 (mmp) REVERT: H 223 ASP cc_start: 0.6711 (t0) cc_final: 0.6325 (t0) REVERT: H 232 MET cc_start: 0.7224 (mtp) cc_final: 0.6868 (mmt) REVERT: H 292 TYR cc_start: 0.8404 (t80) cc_final: 0.8112 (t80) REVERT: H 331 LYS cc_start: 0.7857 (mtpp) cc_final: 0.7466 (mtpp) REVERT: H 365 HIS cc_start: 0.8439 (m170) cc_final: 0.8160 (m-70) REVERT: H 383 GLN cc_start: 0.7677 (mt0) cc_final: 0.7076 (mt0) REVERT: H 393 LYS cc_start: 0.7379 (mmtt) cc_final: 0.7164 (mmtt) REVERT: H 466 LYS cc_start: 0.7975 (mttt) cc_final: 0.7643 (mtpt) REVERT: H 525 TYR cc_start: 0.8681 (p90) cc_final: 0.8325 (p90) REVERT: I 103 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7480 (mtmm) REVERT: I 157 MET cc_start: 0.7794 (mtp) cc_final: 0.7183 (mmp) REVERT: I 223 ASP cc_start: 0.6782 (t0) cc_final: 0.6445 (t0) REVERT: I 232 MET cc_start: 0.7277 (mtp) cc_final: 0.6967 (mmp) REVERT: I 265 TYR cc_start: 0.7891 (t80) cc_final: 0.7241 (t80) REVERT: I 292 TYR cc_start: 0.8420 (t80) cc_final: 0.8140 (t80) REVERT: I 331 LYS cc_start: 0.7929 (mtpp) cc_final: 0.7518 (mtpp) REVERT: I 365 HIS cc_start: 0.8443 (m170) cc_final: 0.8144 (m-70) REVERT: I 393 LYS cc_start: 0.7399 (mmtt) cc_final: 0.7171 (mmtt) REVERT: I 466 LYS cc_start: 0.7949 (mttt) cc_final: 0.7603 (mtpt) REVERT: I 475 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: I 525 TYR cc_start: 0.8691 (p90) cc_final: 0.8374 (p90) outliers start: 30 outliers final: 15 residues processed: 455 average time/residue: 0.3380 time to fit residues: 222.9580 Evaluate side-chains 414 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 394 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 475 GLU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 219 SER Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 475 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 198 GLN ** G 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.134153 restraints weight = 54338.076| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.94 r_work: 0.3267 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17632 Z= 0.161 Angle : 0.571 5.838 23904 Z= 0.292 Chirality : 0.044 0.175 2640 Planarity : 0.005 0.060 3064 Dihedral : 6.423 53.401 2590 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.72 % Favored : 97.08 % Rotamer: Outliers : 1.43 % Allowed : 11.79 % Favored : 86.79 % 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: 0.34 (0.19), residues: 2092 helix: 1.21 (0.17), residues: 904 sheet: -1.21 (0.25), residues: 356 loop : -0.04 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 81 TYR 0.020 0.002 TYR G 468 PHE 0.017 0.002 PHE I 163 TRP 0.008 0.001 TRP C 358 HIS 0.008 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (17628) covalent geometry : angle 0.56553 / 0.29 (23896) SS BOND : bond 0.00538 / 0.27 ( 4) SS BOND : angle 4.27419 / 2.07 ( 8) hydrogen bonds : bond 0.03410 / 2.34 ( 712) hydrogen bonds : angle 4.51768 / 3.16 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 407 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7805 (mttt) REVERT: C 157 MET cc_start: 0.7588 (mtp) cc_final: 0.7012 (mmp) REVERT: C 240 GLN cc_start: 0.7653 (mt0) cc_final: 0.7226 (mt0) REVERT: C 259 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7510 (tp30) REVERT: C 271 ASP cc_start: 0.7685 (t0) cc_final: 0.7308 (t0) REVERT: C 293 ASP cc_start: 0.6753 (m-30) cc_final: 0.6411 (m-30) REVERT: C 391 GLN cc_start: 0.6654 (mm-40) cc_final: 0.6009 (mm-40) REVERT: C 393 LYS cc_start: 0.6928 (mmtt) cc_final: 0.6605 (mmtt) REVERT: C 510 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6648 (mt-10) REVERT: C 541 PHE cc_start: 0.8221 (t80) cc_final: 0.8001 (t80) REVERT: C 550 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7341 (mmt90) REVERT: G 46 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8161 (p0) REVERT: G 103 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7845 (tppp) REVERT: G 157 MET cc_start: 0.7945 (mtp) cc_final: 0.7290 (mmp) REVERT: G 161 GLU cc_start: 0.8123 (tp30) cc_final: 0.7739 (tp30) REVERT: G 223 ASP cc_start: 0.6764 (t0) cc_final: 0.6283 (t0) REVERT: G 232 MET cc_start: 0.7155 (mtp) cc_final: 0.6887 (mmp) REVERT: G 265 TYR cc_start: 0.7977 (t80) cc_final: 0.7365 (t80) REVERT: G 292 TYR cc_start: 0.8517 (t80) cc_final: 0.8231 (t80) REVERT: G 383 GLN cc_start: 0.7704 (mt0) cc_final: 0.7417 (mm-40) REVERT: G 393 LYS cc_start: 0.7211 (mmtt) cc_final: 0.7002 (mmtt) REVERT: G 466 LYS cc_start: 0.8029 (mttt) cc_final: 0.7667 (mtpt) REVERT: G 481 ARG cc_start: 0.6259 (mtt180) cc_final: 0.5722 (mtt90) REVERT: G 525 TYR cc_start: 0.8630 (p90) cc_final: 0.8428 (p90) REVERT: G 550 ARG cc_start: 0.7788 (mmt90) cc_final: 0.7194 (mmt-90) REVERT: H 46 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8232 (p0) REVERT: H 84 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7852 (mttt) REVERT: H 103 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7812 (tppp) REVERT: H 139 GLU cc_start: 0.7959 (tt0) cc_final: 0.7625 (tt0) REVERT: H 157 MET cc_start: 0.7860 (mtp) cc_final: 0.7208 (mmp) REVERT: H 223 ASP cc_start: 0.6784 (t0) cc_final: 0.6345 (m-30) REVERT: H 232 MET cc_start: 0.7180 (mtp) cc_final: 0.6845 (mmp) REVERT: H 265 TYR cc_start: 0.7945 (t80) cc_final: 0.7320 (t80) REVERT: H 292 TYR cc_start: 0.8532 (t80) cc_final: 0.8227 (t80) REVERT: H 331 LYS cc_start: 0.7774 (mtpp) cc_final: 0.7434 (mtpp) REVERT: H 393 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6977 (mmtt) REVERT: H 466 LYS cc_start: 0.8064 (mttt) cc_final: 0.7715 (mtpt) REVERT: I 103 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7792 (tppp) REVERT: I 157 MET cc_start: 0.7970 (mtp) cc_final: 0.7330 (mmp) REVERT: I 161 GLU cc_start: 0.8156 (tp30) cc_final: 0.7657 (tp30) REVERT: I 223 ASP cc_start: 0.6751 (t0) cc_final: 0.6221 (t0) REVERT: I 232 MET cc_start: 0.7220 (mtp) cc_final: 0.6924 (mmp) REVERT: I 265 TYR cc_start: 0.7933 (t80) cc_final: 0.7287 (t80) REVERT: I 292 TYR cc_start: 0.8504 (t80) cc_final: 0.8208 (t80) REVERT: I 331 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7476 (mtpp) REVERT: I 383 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7279 (mt0) REVERT: I 393 LYS cc_start: 0.7215 (mmtt) cc_final: 0.6999 (mmtt) REVERT: I 466 LYS cc_start: 0.8000 (mttt) cc_final: 0.7641 (mtpt) outliers start: 27 outliers final: 16 residues processed: 424 average time/residue: 0.3645 time to fit residues: 219.9346 Evaluate side-chains 418 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 398 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 1 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 ASN G 524 GLN I 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130483 restraints weight = 54026.543| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.98 r_work: 0.3227 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17632 Z= 0.181 Angle : 0.578 5.638 23904 Z= 0.297 Chirality : 0.044 0.182 2640 Planarity : 0.005 0.052 3064 Dihedral : 6.611 54.262 2590 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % Rotamer: Outliers : 1.74 % Allowed : 12.00 % Favored : 86.26 % 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: 0.38 (0.19), residues: 2092 helix: 1.33 (0.17), residues: 892 sheet: -1.21 (0.26), residues: 344 loop : -0.13 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 81 TYR 0.017 0.002 TYR C 292 PHE 0.020 0.002 PHE I 163 TRP 0.008 0.001 TRP H 124 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (17628) covalent geometry : angle 0.57366 / 0.29 (23896) SS BOND : bond 0.00721 / 0.35 ( 4) SS BOND : angle 4.00497 / 1.99 ( 8) hydrogen bonds : bond 0.03521 / 2.39 ( 712) hydrogen bonds : angle 4.48832 / 3.15 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 409 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7841 (mttt) REVERT: C 157 MET cc_start: 0.7851 (mtp) cc_final: 0.7254 (mmp) REVERT: C 265 TYR cc_start: 0.7962 (t80) cc_final: 0.7624 (t80) REVERT: C 271 ASP cc_start: 0.7939 (t0) cc_final: 0.7640 (t0) REVERT: C 292 TYR cc_start: 0.8364 (t80) cc_final: 0.8041 (t80) REVERT: C 293 ASP cc_start: 0.6904 (m-30) cc_final: 0.6534 (m-30) REVERT: C 525 TYR cc_start: 0.8554 (p90) cc_final: 0.8322 (p90) REVERT: C 550 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7196 (mmt90) REVERT: G 46 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8181 (p0) REVERT: G 103 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7900 (tppp) REVERT: G 157 MET cc_start: 0.7977 (mtp) cc_final: 0.7285 (mmp) REVERT: G 161 GLU cc_start: 0.8178 (tp30) cc_final: 0.7921 (tp30) REVERT: G 223 ASP cc_start: 0.6749 (t0) cc_final: 0.6294 (m-30) REVERT: G 232 MET cc_start: 0.7156 (mtp) cc_final: 0.6918 (mmp) REVERT: G 265 TYR cc_start: 0.8003 (t80) cc_final: 0.7641 (t80) REVERT: G 283 MET cc_start: 0.6816 (tpp) cc_final: 0.6545 (tpp) REVERT: G 292 TYR cc_start: 0.8512 (t80) cc_final: 0.8185 (t80) REVERT: G 383 GLN cc_start: 0.7774 (mt0) cc_final: 0.7457 (mm-40) REVERT: G 393 LYS cc_start: 0.7307 (mmtt) cc_final: 0.7054 (mmtt) REVERT: G 466 LYS cc_start: 0.8035 (mttt) cc_final: 0.7662 (mtpt) REVERT: G 481 ARG cc_start: 0.6317 (mtt180) cc_final: 0.6000 (mtm180) REVERT: G 525 TYR cc_start: 0.8629 (p90) cc_final: 0.8345 (p90) REVERT: H 46 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8163 (p0) REVERT: H 84 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7691 (mttt) REVERT: H 103 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (tppp) REVERT: H 155 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: H 157 MET cc_start: 0.7967 (mtp) cc_final: 0.7318 (mmp) REVERT: H 223 ASP cc_start: 0.6802 (t0) cc_final: 0.6379 (t0) REVERT: H 232 MET cc_start: 0.7136 (mtp) cc_final: 0.6849 (mmp) REVERT: H 265 TYR cc_start: 0.7980 (t80) cc_final: 0.7508 (t80) REVERT: H 283 MET cc_start: 0.5700 (pmm) cc_final: 0.5182 (pmm) REVERT: H 292 TYR cc_start: 0.8539 (t80) cc_final: 0.8189 (t80) REVERT: H 331 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7483 (mtpp) REVERT: H 393 LYS cc_start: 0.7269 (mmtt) cc_final: 0.7016 (mmtt) REVERT: H 466 LYS cc_start: 0.8058 (mttt) cc_final: 0.7700 (mtpt) REVERT: H 525 TYR cc_start: 0.8612 (p90) cc_final: 0.8273 (p90) REVERT: I 103 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7675 (mtmm) REVERT: I 155 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: I 157 MET cc_start: 0.8000 (mtp) cc_final: 0.7327 (mmp) REVERT: I 223 ASP cc_start: 0.6718 (t0) cc_final: 0.6319 (t0) REVERT: I 232 MET cc_start: 0.7263 (mtp) cc_final: 0.6940 (mmp) REVERT: I 265 TYR cc_start: 0.7989 (t80) cc_final: 0.7540 (t80) REVERT: I 331 LYS cc_start: 0.7810 (mtpp) cc_final: 0.7502 (mtpp) REVERT: I 393 LYS cc_start: 0.7275 (mmtt) cc_final: 0.7007 (mmtt) REVERT: I 466 LYS cc_start: 0.8024 (mttt) cc_final: 0.7660 (mtpt) REVERT: I 525 TYR cc_start: 0.8560 (p90) cc_final: 0.8256 (p90) outliers start: 33 outliers final: 23 residues processed: 425 average time/residue: 0.3597 time to fit residues: 219.9465 Evaluate side-chains 420 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 391 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 458 GLN Chi-restraints excluded: chain G residue 467 LEU Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 155 GLU Chi-restraints excluded: chain H residue 189 THR Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain H residue 467 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 155 GLU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 467 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 43 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 ASN H 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.162986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132370 restraints weight = 53522.467| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.96 r_work: 0.3255 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17632 Z= 0.125 Angle : 0.525 5.410 23904 Z= 0.267 Chirality : 0.042 0.179 2640 Planarity : 0.005 0.060 3064 Dihedral : 6.040 54.184 2590 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.48 % Allowed : 11.95 % Favored : 86.58 % 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: 0.67 (0.19), residues: 2092 helix: 1.61 (0.18), residues: 900 sheet: -1.21 (0.26), residues: 344 loop : 0.05 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.015 0.001 TYR G 468 PHE 0.012 0.001 PHE G 163 TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17628) covalent geometry : angle 0.51876 / 0.26 (23896) SS BOND : bond 0.00603 / 0.30 ( 4) SS BOND : angle 4.45447 / 2.18 ( 8) hydrogen bonds : bond 0.03099 / 2.13 ( 712) hydrogen bonds : angle 4.31676 / 3.02 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 420 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.7798 (mtp) cc_final: 0.7247 (mmp) REVERT: C 217 ARG cc_start: 0.8976 (tpt90) cc_final: 0.8727 (tpt90) REVERT: C 265 TYR cc_start: 0.7945 (t80) cc_final: 0.7585 (t80) REVERT: C 292 TYR cc_start: 0.8439 (t80) cc_final: 0.8136 (t80) REVERT: C 293 ASP cc_start: 0.6996 (m-30) cc_final: 0.6639 (m-30) REVERT: C 393 LYS cc_start: 0.7503 (mmtt) cc_final: 0.7168 (mmtt) REVERT: C 550 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7220 (mmt90) REVERT: G 46 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8134 (p0) REVERT: G 103 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7854 (tppp) REVERT: G 161 GLU cc_start: 0.8146 (tp30) cc_final: 0.7771 (tp30) REVERT: G 223 ASP cc_start: 0.6720 (t0) cc_final: 0.6347 (t0) REVERT: G 265 TYR cc_start: 0.7947 (t80) cc_final: 0.7621 (t80) REVERT: G 283 MET cc_start: 0.6913 (tpp) cc_final: 0.6630 (tpp) REVERT: G 383 GLN cc_start: 0.7811 (mt0) cc_final: 0.7494 (mm-40) REVERT: G 393 LYS cc_start: 0.7292 (mmtt) cc_final: 0.7044 (mmtt) REVERT: G 466 LYS cc_start: 0.8019 (mttt) cc_final: 0.7639 (mtpt) REVERT: G 481 ARG cc_start: 0.6285 (mtt180) cc_final: 0.5964 (mtm180) REVERT: G 525 TYR cc_start: 0.8628 (p90) cc_final: 0.8377 (p90) REVERT: G 550 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7155 (mmt-90) REVERT: H 46 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8157 (p0) REVERT: H 66 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7764 (mt-10) REVERT: H 84 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7824 (mttt) REVERT: H 103 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7839 (tppp) REVERT: H 157 MET cc_start: 0.7927 (mtp) cc_final: 0.7298 (mmp) REVERT: H 223 ASP cc_start: 0.6816 (t0) cc_final: 0.6385 (t0) REVERT: H 232 MET cc_start: 0.7055 (mtp) cc_final: 0.6792 (mmp) REVERT: H 265 TYR cc_start: 0.7926 (t80) cc_final: 0.7646 (t80) REVERT: H 331 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7533 (mtpp) REVERT: H 393 LYS cc_start: 0.7286 (mmtt) cc_final: 0.7034 (mmtt) REVERT: H 406 VAL cc_start: 0.7872 (t) cc_final: 0.7602 (p) REVERT: H 466 LYS cc_start: 0.8054 (mttt) cc_final: 0.7686 (mtpt) REVERT: H 525 TYR cc_start: 0.8528 (p90) cc_final: 0.8306 (p90) REVERT: H 550 ARG cc_start: 0.7751 (mmt90) cc_final: 0.7206 (mmt-90) REVERT: I 49 THR cc_start: 0.7916 (t) cc_final: 0.7705 (p) REVERT: I 103 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7691 (mtmm) REVERT: I 157 MET cc_start: 0.7955 (mtp) cc_final: 0.7351 (mmp) REVERT: I 223 ASP cc_start: 0.6718 (t0) cc_final: 0.6318 (t0) REVERT: I 232 MET cc_start: 0.7153 (mtp) cc_final: 0.6910 (mmp) REVERT: I 265 TYR cc_start: 0.7933 (t80) cc_final: 0.7632 (t80) REVERT: I 331 LYS cc_start: 0.7830 (mtpp) cc_final: 0.7513 (mtpp) REVERT: I 393 LYS cc_start: 0.7261 (mmtt) cc_final: 0.6993 (mmtt) REVERT: I 466 LYS cc_start: 0.8036 (mttt) cc_final: 0.7670 (mtpt) REVERT: I 525 TYR cc_start: 0.8547 (p90) cc_final: 0.8331 (p90) outliers start: 28 outliers final: 19 residues processed: 434 average time/residue: 0.3745 time to fit residues: 233.7375 Evaluate side-chains 426 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 403 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 458 GLN Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 104 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 GLN C 174 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133954 restraints weight = 53510.601| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.96 r_work: 0.3242 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17632 Z= 0.139 Angle : 0.536 5.600 23904 Z= 0.273 Chirality : 0.043 0.185 2640 Planarity : 0.005 0.059 3064 Dihedral : 5.952 53.735 2587 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.80 % Allowed : 11.15 % Favored : 87.05 % 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: 0.74 (0.19), residues: 2092 helix: 1.65 (0.18), residues: 900 sheet: -1.12 (0.26), residues: 340 loop : 0.07 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 465 TYR 0.020 0.002 TYR H 468 PHE 0.014 0.001 PHE G 163 TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17628) covalent geometry : angle 0.53071 / 0.27 (23896) SS BOND : bond 0.00688 / 0.34 ( 4) SS BOND : angle 4.31531 / 2.12 ( 8) hydrogen bonds : bond 0.03183 / 2.19 ( 712) hydrogen bonds : angle 4.27103 / 2.99 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 440 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 406 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 157 MET cc_start: 0.7833 (mtp) cc_final: 0.7266 (mmp) REVERT: C 240 GLN cc_start: 0.7870 (mt0) cc_final: 0.7520 (mt0) REVERT: C 265 TYR cc_start: 0.7952 (t80) cc_final: 0.7663 (t80) REVERT: C 292 TYR cc_start: 0.8458 (t80) cc_final: 0.8153 (t80) REVERT: C 293 ASP cc_start: 0.7016 (m-30) cc_final: 0.6656 (m-30) REVERT: C 392 LYS cc_start: 0.7262 (mmtm) cc_final: 0.6997 (tppt) REVERT: C 393 LYS cc_start: 0.7489 (mmtt) cc_final: 0.7179 (mmtt) REVERT: C 467 LEU cc_start: 0.7943 (mt) cc_final: 0.7681 (mt) REVERT: C 550 ARG cc_start: 0.7539 (tpp80) cc_final: 0.7262 (mmt90) REVERT: G 46 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8119 (p0) REVERT: G 103 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7917 (tppp) REVERT: G 157 MET cc_start: 0.7965 (mtp) cc_final: 0.7370 (mmp) REVERT: G 161 GLU cc_start: 0.8155 (tp30) cc_final: 0.7888 (tp30) REVERT: G 223 ASP cc_start: 0.6748 (t0) cc_final: 0.6361 (t0) REVERT: G 283 MET cc_start: 0.7002 (tpp) cc_final: 0.6792 (mmm) REVERT: G 383 GLN cc_start: 0.7814 (mt0) cc_final: 0.7492 (mm-40) REVERT: G 393 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7046 (mmtt) REVERT: G 466 LYS cc_start: 0.8007 (mttt) cc_final: 0.7627 (mtpt) REVERT: G 481 ARG cc_start: 0.6304 (mtt180) cc_final: 0.5977 (mtm180) REVERT: G 525 TYR cc_start: 0.8641 (p90) cc_final: 0.8384 (p90) REVERT: H 84 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7865 (mttt) REVERT: H 103 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7875 (tppp) REVERT: H 157 MET cc_start: 0.7957 (mtp) cc_final: 0.7324 (mmp) REVERT: H 161 GLU cc_start: 0.8189 (tp30) cc_final: 0.7833 (tp30) REVERT: H 223 ASP cc_start: 0.6811 (t0) cc_final: 0.6383 (t0) REVERT: H 232 MET cc_start: 0.7076 (mtp) cc_final: 0.6814 (mmp) REVERT: H 265 TYR cc_start: 0.7935 (t80) cc_final: 0.7703 (t80) REVERT: H 331 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7561 (mtpp) REVERT: H 383 GLN cc_start: 0.7739 (mt0) cc_final: 0.7526 (mm-40) REVERT: H 393 LYS cc_start: 0.7304 (mmtt) cc_final: 0.7044 (mmtt) REVERT: H 406 VAL cc_start: 0.8024 (t) cc_final: 0.7770 (p) REVERT: H 466 LYS cc_start: 0.8053 (mttt) cc_final: 0.7709 (mtpt) REVERT: H 525 TYR cc_start: 0.8509 (p90) cc_final: 0.8236 (p90) REVERT: H 550 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7450 (mmt90) REVERT: I 103 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7579 (mtmm) REVERT: I 157 MET cc_start: 0.7973 (mtp) cc_final: 0.7402 (mmp) REVERT: I 161 GLU cc_start: 0.8198 (tp30) cc_final: 0.7924 (tp30) REVERT: I 223 ASP cc_start: 0.6740 (t0) cc_final: 0.6332 (t0) REVERT: I 232 MET cc_start: 0.7178 (mtp) cc_final: 0.6935 (mmp) REVERT: I 331 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7522 (mtpp) REVERT: I 393 LYS cc_start: 0.7231 (mmtt) cc_final: 0.6947 (mmtt) REVERT: I 466 LYS cc_start: 0.8013 (mttt) cc_final: 0.7611 (mttp) REVERT: I 550 ARG cc_start: 0.7822 (mmt90) cc_final: 0.7187 (mmt-90) outliers start: 34 outliers final: 23 residues processed: 417 average time/residue: 0.3604 time to fit residues: 216.5518 Evaluate side-chains 429 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 403 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 168 optimal weight: 0.4980 chunk 200 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.161669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.130893 restraints weight = 53584.700| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.96 r_work: 0.3237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17632 Z= 0.139 Angle : 0.535 7.056 23904 Z= 0.273 Chirality : 0.043 0.170 2640 Planarity : 0.005 0.063 3064 Dihedral : 5.710 43.095 2584 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.69 % Allowed : 11.79 % Favored : 86.52 % 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: 0.78 (0.19), residues: 2092 helix: 1.71 (0.18), residues: 900 sheet: -1.17 (0.26), residues: 344 loop : 0.10 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 81 TYR 0.020 0.002 TYR G 468 PHE 0.015 0.001 PHE H 163 TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17628) covalent geometry : angle 0.52939 / 0.27 (23896) SS BOND : bond 0.00639 / 0.31 ( 4) SS BOND : angle 4.28395 / 2.12 ( 8) hydrogen bonds : bond 0.03204 / 2.21 ( 712) hydrogen bonds : angle 4.24926 / 2.97 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 438 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 406 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 THR cc_start: 0.8127 (m) cc_final: 0.7649 (p) REVERT: C 157 MET cc_start: 0.7846 (mtp) cc_final: 0.7273 (mmp) REVERT: C 240 GLN cc_start: 0.7910 (mt0) cc_final: 0.7560 (mt0) REVERT: C 265 TYR cc_start: 0.7984 (t80) cc_final: 0.7712 (t80) REVERT: C 292 TYR cc_start: 0.8486 (t80) cc_final: 0.8183 (t80) REVERT: C 293 ASP cc_start: 0.7041 (m-30) cc_final: 0.6688 (m-30) REVERT: C 392 LYS cc_start: 0.7270 (mmtm) cc_final: 0.6979 (tppt) REVERT: C 393 LYS cc_start: 0.7424 (mmtt) cc_final: 0.7158 (mmtt) REVERT: C 467 LEU cc_start: 0.8026 (mt) cc_final: 0.7768 (mt) REVERT: C 550 ARG cc_start: 0.7505 (tpp80) cc_final: 0.7235 (mmt90) REVERT: G 46 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8076 (p0) REVERT: G 103 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7931 (tppp) REVERT: G 157 MET cc_start: 0.7999 (mtp) cc_final: 0.7458 (mmp) REVERT: G 161 GLU cc_start: 0.8159 (tp30) cc_final: 0.7886 (tp30) REVERT: G 223 ASP cc_start: 0.6729 (t0) cc_final: 0.6337 (t0) REVERT: G 240 GLN cc_start: 0.7891 (mt0) cc_final: 0.7256 (mt0) REVERT: G 283 MET cc_start: 0.7007 (tpp) cc_final: 0.6800 (mmm) REVERT: G 383 GLN cc_start: 0.7848 (mt0) cc_final: 0.7523 (mm-40) REVERT: G 393 LYS cc_start: 0.7288 (mmtt) cc_final: 0.7025 (mmtt) REVERT: G 466 LYS cc_start: 0.8004 (mttt) cc_final: 0.7617 (mtpt) REVERT: G 481 ARG cc_start: 0.6309 (mtt180) cc_final: 0.5984 (mtm180) REVERT: G 525 TYR cc_start: 0.8535 (p90) cc_final: 0.8319 (p90) REVERT: G 550 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7146 (mmt-90) REVERT: H 84 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7872 (mttt) REVERT: H 103 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7889 (tppp) REVERT: H 157 MET cc_start: 0.7959 (mtp) cc_final: 0.7387 (mmp) REVERT: H 161 GLU cc_start: 0.8172 (tp30) cc_final: 0.7743 (tp30) REVERT: H 223 ASP cc_start: 0.6770 (t0) cc_final: 0.6333 (t0) REVERT: H 232 MET cc_start: 0.7048 (mtp) cc_final: 0.6805 (mmp) REVERT: H 331 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7544 (mtpp) REVERT: H 335 LYS cc_start: 0.7980 (mttm) cc_final: 0.7603 (mttm) REVERT: H 393 LYS cc_start: 0.7284 (mmtt) cc_final: 0.7019 (mmtt) REVERT: H 406 VAL cc_start: 0.8017 (t) cc_final: 0.7773 (p) REVERT: H 466 LYS cc_start: 0.8027 (mttt) cc_final: 0.7672 (mtpt) REVERT: H 550 ARG cc_start: 0.7792 (mmt90) cc_final: 0.7490 (mmt90) REVERT: I 103 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7691 (mtmm) REVERT: I 157 MET cc_start: 0.7974 (mtp) cc_final: 0.7400 (mmp) REVERT: I 161 GLU cc_start: 0.8181 (tp30) cc_final: 0.7904 (tp30) REVERT: I 223 ASP cc_start: 0.6733 (t0) cc_final: 0.6326 (t0) REVERT: I 232 MET cc_start: 0.7127 (mtp) cc_final: 0.6897 (mmp) REVERT: I 331 LYS cc_start: 0.7817 (mtpp) cc_final: 0.7527 (mtpp) REVERT: I 335 LYS cc_start: 0.7974 (mttm) cc_final: 0.7610 (mttm) REVERT: I 393 LYS cc_start: 0.7246 (mmtt) cc_final: 0.6885 (mmtt) REVERT: I 466 LYS cc_start: 0.7989 (mttt) cc_final: 0.7587 (mttp) outliers start: 32 outliers final: 26 residues processed: 414 average time/residue: 0.3941 time to fit residues: 235.2870 Evaluate side-chains 430 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 401 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.161853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.131180 restraints weight = 53429.106| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.95 r_work: 0.3235 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17632 Z= 0.138 Angle : 0.537 7.410 23904 Z= 0.274 Chirality : 0.043 0.170 2640 Planarity : 0.005 0.062 3064 Dihedral : 5.669 43.437 2584 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.74 % Allowed : 11.84 % Favored : 86.42 % 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: 0.84 (0.19), residues: 2092 helix: 1.75 (0.18), residues: 900 sheet: -1.11 (0.26), residues: 344 loop : 0.13 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 81 TYR 0.017 0.002 TYR G 468 PHE 0.014 0.001 PHE I 163 TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS H 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17628) covalent geometry : angle 0.53174 / 0.27 (23896) SS BOND : bond 0.00654 / 0.32 ( 4) SS BOND : angle 4.26924 / 2.10 ( 8) hydrogen bonds : bond 0.03216 / 2.21 ( 712) hydrogen bonds : angle 4.22844 / 2.95 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. 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 : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 THR cc_start: 0.8086 (m) cc_final: 0.7652 (p) REVERT: C 157 MET cc_start: 0.7898 (mtp) cc_final: 0.7303 (mmp) REVERT: C 259 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7498 (tp30) REVERT: C 265 TYR cc_start: 0.7959 (t80) cc_final: 0.7639 (t80) REVERT: C 292 TYR cc_start: 0.8491 (t80) cc_final: 0.8187 (t80) REVERT: C 293 ASP cc_start: 0.7056 (m-30) cc_final: 0.6695 (m-30) REVERT: C 335 LYS cc_start: 0.7882 (mttm) cc_final: 0.7460 (mttm) REVERT: C 354 TYR cc_start: 0.7474 (t80) cc_final: 0.7176 (t80) REVERT: C 392 LYS cc_start: 0.7267 (mmtm) cc_final: 0.7008 (tppt) REVERT: C 393 LYS cc_start: 0.7396 (mmtt) cc_final: 0.7110 (mmtt) REVERT: C 550 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7252 (mmt90) REVERT: G 46 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8071 (p0) REVERT: G 103 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7923 (tppp) REVERT: G 155 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7505 (pm20) REVERT: G 157 MET cc_start: 0.8050 (mtp) cc_final: 0.7477 (mmp) REVERT: G 161 GLU cc_start: 0.8158 (tp30) cc_final: 0.7880 (tp30) REVERT: G 223 ASP cc_start: 0.6726 (t0) cc_final: 0.6268 (m-30) REVERT: G 239 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7464 (tm-30) REVERT: G 283 MET cc_start: 0.7031 (tpp) cc_final: 0.6811 (mmm) REVERT: G 335 LYS cc_start: 0.8005 (mttm) cc_final: 0.7735 (mttm) REVERT: G 383 GLN cc_start: 0.7857 (mt0) cc_final: 0.7530 (mm-40) REVERT: G 393 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6964 (mmtt) REVERT: G 466 LYS cc_start: 0.7965 (mttt) cc_final: 0.7592 (mtpt) REVERT: G 481 ARG cc_start: 0.6295 (mtt180) cc_final: 0.5978 (mtm180) REVERT: G 525 TYR cc_start: 0.8489 (p90) cc_final: 0.8232 (p90) REVERT: G 550 ARG cc_start: 0.7733 (mmt90) cc_final: 0.7129 (mmt-90) REVERT: H 84 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7863 (mttt) REVERT: H 103 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (tppp) REVERT: H 157 MET cc_start: 0.7968 (mtp) cc_final: 0.7386 (mmp) REVERT: H 161 GLU cc_start: 0.8152 (tp30) cc_final: 0.7773 (tp30) REVERT: H 223 ASP cc_start: 0.6749 (t0) cc_final: 0.6310 (t0) REVERT: H 232 MET cc_start: 0.7017 (mtp) cc_final: 0.6792 (mmp) REVERT: H 331 LYS cc_start: 0.7860 (mtpp) cc_final: 0.7584 (mtpp) REVERT: H 335 LYS cc_start: 0.8006 (mttm) cc_final: 0.7596 (mttm) REVERT: H 383 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7126 (mt0) REVERT: H 393 LYS cc_start: 0.7269 (mmtt) cc_final: 0.7002 (mmtt) REVERT: H 406 VAL cc_start: 0.8024 (t) cc_final: 0.7779 (p) REVERT: H 466 LYS cc_start: 0.7982 (mttt) cc_final: 0.7649 (mtpt) REVERT: H 507 GLU cc_start: 0.6981 (tt0) cc_final: 0.6717 (tp30) REVERT: H 550 ARG cc_start: 0.7794 (mmt90) cc_final: 0.7509 (mmt90) REVERT: I 53 TYR cc_start: 0.8059 (m-80) cc_final: 0.7813 (m-10) REVERT: I 103 LYS cc_start: 0.8120 (mmmm) cc_final: 0.7688 (mtmm) REVERT: I 157 MET cc_start: 0.8034 (mtp) cc_final: 0.7400 (mmp) REVERT: I 161 GLU cc_start: 0.8172 (tp30) cc_final: 0.7898 (tp30) REVERT: I 223 ASP cc_start: 0.6727 (t0) cc_final: 0.6321 (t0) REVERT: I 232 MET cc_start: 0.7271 (mtp) cc_final: 0.7042 (mmp) REVERT: I 240 GLN cc_start: 0.7900 (mt0) cc_final: 0.7204 (mt0) REVERT: I 331 LYS cc_start: 0.7816 (mtpp) cc_final: 0.7529 (mtpp) REVERT: I 335 LYS cc_start: 0.7978 (mttm) cc_final: 0.7571 (mttm) REVERT: I 393 LYS cc_start: 0.7289 (mmtt) cc_final: 0.6938 (mmtt) REVERT: I 466 LYS cc_start: 0.7964 (mttt) cc_final: 0.7580 (mttp) REVERT: I 507 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7167 (mt-10) outliers start: 33 outliers final: 28 residues processed: 418 average time/residue: 0.3780 time to fit residues: 229.1171 Evaluate side-chains 434 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 402 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 160 optimal weight: 0.2980 chunk 175 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.163761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.133510 restraints weight = 53457.954| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.94 r_work: 0.3250 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17632 Z= 0.120 Angle : 0.527 8.310 23904 Z= 0.267 Chirality : 0.042 0.165 2640 Planarity : 0.005 0.063 3064 Dihedral : 5.477 42.509 2584 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.48 % Allowed : 12.42 % Favored : 86.10 % 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: 0.94 (0.19), residues: 2092 helix: 1.85 (0.18), residues: 900 sheet: -1.07 (0.26), residues: 344 loop : 0.17 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 81 TYR 0.025 0.001 TYR H 468 PHE 0.011 0.001 PHE H 163 TRP 0.008 0.001 TRP G 124 HIS 0.005 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17628) covalent geometry : angle 0.52096 / 0.26 (23896) SS BOND : bond 0.00584 / 0.29 ( 4) SS BOND : angle 4.34520 / 2.14 ( 8) hydrogen bonds : bond 0.03086 / 2.14 ( 712) hydrogen bonds : angle 4.18412 / 2.92 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Residue LYS 381 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 408 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 THR cc_start: 0.8081 (m) cc_final: 0.7678 (p) REVERT: C 157 MET cc_start: 0.7880 (mtp) cc_final: 0.7291 (mmp) REVERT: C 240 GLN cc_start: 0.7950 (mt0) cc_final: 0.7611 (mt0) REVERT: C 265 TYR cc_start: 0.7929 (t80) cc_final: 0.7701 (t80) REVERT: C 292 TYR cc_start: 0.8486 (t80) cc_final: 0.8175 (t80) REVERT: C 293 ASP cc_start: 0.7078 (m-30) cc_final: 0.6720 (m-30) REVERT: C 335 LYS cc_start: 0.7929 (mttm) cc_final: 0.7536 (mttm) REVERT: C 354 TYR cc_start: 0.7345 (t80) cc_final: 0.7115 (t80) REVERT: C 392 LYS cc_start: 0.7381 (mmtm) cc_final: 0.7121 (tppt) REVERT: C 393 LYS cc_start: 0.7330 (mmtt) cc_final: 0.7091 (mmtt) REVERT: C 466 LYS cc_start: 0.7790 (mttt) cc_final: 0.7497 (mttp) REVERT: C 550 ARG cc_start: 0.7525 (tpp80) cc_final: 0.7269 (mmt90) REVERT: G 46 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.7992 (p0) REVERT: G 103 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7922 (tppp) REVERT: G 157 MET cc_start: 0.8038 (mtp) cc_final: 0.7451 (mmp) REVERT: G 161 GLU cc_start: 0.8146 (tp30) cc_final: 0.7870 (tp30) REVERT: G 223 ASP cc_start: 0.6707 (t0) cc_final: 0.6259 (m-30) REVERT: G 283 MET cc_start: 0.7065 (tpp) cc_final: 0.6847 (mmm) REVERT: G 330 HIS cc_start: 0.8047 (m-70) cc_final: 0.7797 (m-70) REVERT: G 335 LYS cc_start: 0.7965 (mttm) cc_final: 0.7720 (mttm) REVERT: G 383 GLN cc_start: 0.7834 (mt0) cc_final: 0.7521 (mm-40) REVERT: G 393 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6900 (mmtt) REVERT: G 466 LYS cc_start: 0.7967 (mttt) cc_final: 0.7730 (mttm) REVERT: G 481 ARG cc_start: 0.6263 (mtt180) cc_final: 0.5951 (mtm180) REVERT: G 550 ARG cc_start: 0.7737 (mmt90) cc_final: 0.7140 (mmt-90) REVERT: H 84 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7848 (mttt) REVERT: H 103 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7919 (tppp) REVERT: H 157 MET cc_start: 0.7963 (mtp) cc_final: 0.7384 (mmp) REVERT: H 161 GLU cc_start: 0.8138 (tp30) cc_final: 0.7758 (tp30) REVERT: H 223 ASP cc_start: 0.6757 (t0) cc_final: 0.6302 (m-30) REVERT: H 331 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7606 (mtpp) REVERT: H 335 LYS cc_start: 0.7981 (mttm) cc_final: 0.7722 (mttm) REVERT: H 393 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6953 (mmtt) REVERT: H 466 LYS cc_start: 0.8034 (mttt) cc_final: 0.7690 (mtpt) REVERT: H 468 TYR cc_start: 0.7381 (m-80) cc_final: 0.7107 (m-80) REVERT: H 507 GLU cc_start: 0.6914 (tt0) cc_final: 0.6684 (tp30) REVERT: H 550 ARG cc_start: 0.7749 (mmt90) cc_final: 0.7464 (mmt90) REVERT: I 53 TYR cc_start: 0.8038 (m-80) cc_final: 0.7789 (m-10) REVERT: I 103 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7695 (mtmm) REVERT: I 157 MET cc_start: 0.8028 (mtp) cc_final: 0.7406 (mmp) REVERT: I 161 GLU cc_start: 0.8166 (tp30) cc_final: 0.7914 (tp30) REVERT: I 223 ASP cc_start: 0.6715 (t0) cc_final: 0.6323 (t0) REVERT: I 232 MET cc_start: 0.7145 (mtp) cc_final: 0.6932 (mmp) REVERT: I 240 GLN cc_start: 0.7871 (mt0) cc_final: 0.7206 (mt0) REVERT: I 331 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7576 (mtpp) REVERT: I 335 LYS cc_start: 0.7979 (mttm) cc_final: 0.7749 (mttm) REVERT: I 393 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6930 (mmtt) REVERT: I 466 LYS cc_start: 0.7977 (mttt) cc_final: 0.7593 (mttp) REVERT: I 468 TYR cc_start: 0.7450 (m-80) cc_final: 0.7050 (m-80) REVERT: I 525 TYR cc_start: 0.8480 (p90) cc_final: 0.8170 (p90) REVERT: I 550 ARG cc_start: 0.7831 (mmt90) cc_final: 0.7204 (mmt-90) outliers start: 28 outliers final: 25 residues processed: 416 average time/residue: 0.3870 time to fit residues: 233.2669 Evaluate side-chains 432 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 404 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 103 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 243 CYS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 134 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 39 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.131984 restraints weight = 53876.325| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.95 r_work: 0.3242 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17632 Z= 0.130 Angle : 0.532 8.900 23904 Z= 0.270 Chirality : 0.042 0.164 2640 Planarity : 0.005 0.061 3064 Dihedral : 5.517 43.099 2584 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.69 % Allowed : 12.16 % Favored : 86.15 % 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: 0.96 (0.19), residues: 2092 helix: 1.84 (0.18), residues: 900 sheet: -1.04 (0.26), residues: 344 loop : 0.19 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 81 TYR 0.023 0.001 TYR H 468 PHE 0.013 0.001 PHE I 163 TRP 0.007 0.001 TRP C 358 HIS 0.006 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (17628) covalent geometry : angle 0.52654 / 0.27 (23896) SS BOND : bond 0.00675 / 0.33 ( 4) SS BOND : angle 4.25579 / 2.10 ( 8) hydrogen bonds : bond 0.03111 / 2.14 ( 712) hydrogen bonds : angle 4.17500 / 2.92 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9150.22 seconds wall clock time: 155 minutes 49.51 seconds (9349.51 seconds total)