Starting phenix.real_space_refine on Mon Jul 6 10:40:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mip_23859/07_2026/7mip_23859.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.263 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 11116 2.51 5 N 2976 2.21 5 O 3268 1.98 5 H 17328 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: 34800 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "D" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "G" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 Chain: "I" Number of atoms: 8617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8617 Classifications: {'peptide': 540} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 510} Chain breaks: 2 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: "D" 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: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" 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: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'UTP': 1, 'ZG4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" 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: "I" 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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ILE C 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE C 250 " occ=0.80 residue: pdb=" N ILE D 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE D 250 " occ=0.80 residue: pdb=" N ILE G 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE G 250 " occ=0.80 residue: pdb=" N ILE I 250 " occ=0.80 ... (17 atoms not shown) pdb="HD13 ILE I 250 " occ=0.80 Time building chain proxies: 6.45, per 1000 atoms: 0.19 Number of scatterers: 34800 At special positions: 0 Unit cell: (124.95, 129.15, 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 3268 8.00 N 2976 7.00 C 11116 6.00 H 17328 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=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 243 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 243 " distance=2.04 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 243 " distance=2.04 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: 3.31 Conformation dependent library (CDL) restraints added in 1.0 seconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 48.1% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'C' and resid 15 through 30 Processing helix chain 'C' and resid 46 through 50 removed outlier: 4.317A pdb=" N THR C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 79 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 115 through 130 removed outlier: 3.500A pdb=" N LEU C 130 " --> pdb=" O MET C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 170 removed outlier: 4.431A pdb=" N PHE C 168 " --> pdb=" O ARG C 164 " (cutoff:3.500A) 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 310 through 313 Processing helix chain 'C' and resid 314 through 328 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 350 Processing helix chain 'C' and resid 350 through 364 removed outlier: 3.565A pdb=" N TYR C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 391 Processing helix chain 'C' and resid 399 through 414 Processing helix chain 'C' and resid 462 through 468 removed outlier: 3.508A pdb=" N LYS C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 495 removed outlier: 3.983A pdb=" N GLN C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.558A pdb=" N PHE C 529 " --> pdb=" O HIS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 548 Processing helix chain 'C' and resid 550 through 557 Processing helix chain 'D' and resid 15 through 30 Processing helix chain 'D' and resid 46 through 50 removed outlier: 4.316A pdb=" N THR D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 90 through 103 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 153 through 155 No H-bonds generated for 'chain 'D' and resid 153 through 155' Processing helix chain 'D' and resid 156 through 170 removed outlier: 4.432A pdb=" N PHE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 314 through 328 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 350 Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.566A pdb=" N TYR D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 391 Processing helix chain 'D' and resid 399 through 414 Processing helix chain 'D' and resid 462 through 468 removed outlier: 3.509A pdb=" N LYS D 466 " --> pdb=" O SER D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 495 removed outlier: 3.983A pdb=" N GLN D 495 " --> pdb=" O CYS D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 530 removed outlier: 3.559A pdb=" N PHE D 529 " --> pdb=" O HIS D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 548 Processing helix chain 'D' and resid 550 through 557 Processing helix chain 'G' and resid 15 through 30 Processing helix chain 'G' and resid 46 through 50 removed outlier: 4.317A pdb=" N THR G 49 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 79 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 115 through 130 removed outlier: 3.500A pdb=" N LEU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 156 through 170 removed outlier: 4.431A pdb=" N PHE G 168 " --> pdb=" O ARG G 164 " (cutoff:3.500A) 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 310 through 313 Processing helix chain 'G' and resid 314 through 328 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 344 through 350 Processing helix chain 'G' and resid 350 through 364 removed outlier: 3.565A pdb=" N TYR G 354 " --> pdb=" O GLU G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 391 Processing helix chain 'G' and resid 399 through 414 Processing helix chain 'G' and resid 462 through 468 removed outlier: 3.509A pdb=" N LYS G 466 " --> pdb=" O SER G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 488 through 495 removed outlier: 3.983A pdb=" N GLN G 495 " --> pdb=" O CYS G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 526 through 530 removed outlier: 3.559A pdb=" N PHE G 529 " --> pdb=" O HIS G 526 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 548 Processing helix chain 'G' and resid 550 through 557 Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 46 through 50 removed outlier: 4.316A pdb=" N THR I 49 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 79 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 115 through 130 Processing helix chain 'I' and resid 153 through 155 No H-bonds generated for 'chain 'I' and resid 153 through 155' Processing helix chain 'I' and resid 156 through 170 removed outlier: 4.432A pdb=" N PHE I 168 " --> pdb=" O ARG I 164 " (cutoff:3.500A) 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 310 through 313 Processing helix chain 'I' and resid 314 through 328 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 344 through 350 Processing helix chain 'I' and resid 350 through 364 removed outlier: 3.565A pdb=" N TYR I 354 " --> pdb=" O GLU I 350 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 391 Processing helix chain 'I' and resid 399 through 414 Processing helix chain 'I' and resid 462 through 468 removed outlier: 3.509A pdb=" N LYS I 466 " --> pdb=" O SER I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 488 through 495 removed outlier: 3.983A pdb=" N GLN I 495 " --> pdb=" O CYS I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 530 removed outlier: 3.559A 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 557 Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 89 removed outlier: 3.927A pdb=" N GLY C 8 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR C 3 " --> pdb=" O CYS C 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 178 " --> pdb=" O TYR C 3 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU C 5 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL C 180 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR C 7 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU C 182 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU C 213 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN C 177 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL C 215 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS C 179 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG C 217 " --> pdb=" O HIS C 179 " (cutoff:3.500A) removed outlier: 6.553A 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: 6.768A pdb=" N CYS C 299 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS C 335 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 301 " --> pdb=" O LYS C 335 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE C 337 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU C 303 " --> pdb=" O ILE C 337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY C 366 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER C 300 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU C 368 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA C 302 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL C 367 " --> pdb=" O LEU C 396 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL C 398 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 369 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C 395 " --> pdb=" O VAL C 521 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL C 523 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY C 397 " --> pdb=" O VAL C 523 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 520 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET C 509 " --> pdb=" O GLN C 502 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN C 502 " --> pdb=" O MET C 509 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE C 511 " --> pdb=" O VAL C 500 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG C 481 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN C 420 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP C 435 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 87 through 89 removed outlier: 3.927A pdb=" N GLY D 8 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU D 213 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL D 215 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N HIS D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG D 217 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AA6, first strand: chain 'D' and resid 331 through 338 removed outlier: 6.768A pdb=" N CYS D 299 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS D 335 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE D 301 " --> pdb=" O LYS D 335 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE D 337 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU D 303 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY D 366 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER D 300 " --> pdb=" O GLY D 366 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU D 368 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL D 367 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 398 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 369 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 523 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY D 397 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET D 509 " --> pdb=" O GLN D 502 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN D 502 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE D 511 " --> pdb=" O VAL D 500 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG D 481 " --> pdb=" O MET D 436 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN D 420 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP D 435 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 87 through 89 removed outlier: 3.928A pdb=" N GLY G 8 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR G 3 " --> pdb=" O CYS G 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE G 178 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU G 5 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL G 180 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR G 7 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU G 182 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU G 213 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN G 177 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL G 215 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS G 179 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ARG G 217 " --> pdb=" O HIS G 179 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER G 181 " --> pdb=" O ARG G 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'G' and resid 331 through 338 removed outlier: 6.769A pdb=" N CYS G 299 " --> pdb=" O GLU G 333 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS G 335 " --> pdb=" O CYS G 299 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE G 301 " --> pdb=" O LYS G 335 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE G 337 " --> pdb=" O ILE G 301 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU G 303 " --> pdb=" O ILE G 337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY G 366 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER G 300 " --> pdb=" O GLY G 366 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU G 368 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA G 302 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 367 " --> pdb=" O LEU G 396 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL G 398 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 369 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE G 395 " --> pdb=" O VAL G 521 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL G 523 " --> pdb=" O PHE G 395 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY G 397 " --> pdb=" O VAL G 523 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE G 520 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET G 509 " --> pdb=" O GLN G 502 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLN G 502 " --> pdb=" O MET G 509 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE G 511 " --> pdb=" O VAL G 500 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG G 481 " --> pdb=" O MET G 436 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN G 420 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP G 435 " --> pdb=" O ASN G 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 87 through 89 removed outlier: 3.927A pdb=" N GLY I 8 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR I 3 " --> pdb=" O CYS I 176 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE I 178 " --> pdb=" O TYR I 3 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU I 5 " --> pdb=" O ILE I 178 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL I 180 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 7 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N LEU I 182 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LEU I 213 " --> pdb=" O PHE I 175 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN I 177 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL I 215 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N HIS I 179 " --> pdb=" O VAL I 215 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG I 217 " --> pdb=" O HIS I 179 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER I 181 " --> pdb=" O ARG I 217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'I' and resid 331 through 338 removed outlier: 6.768A pdb=" N CYS I 299 " --> pdb=" O GLU I 333 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LYS I 335 " --> pdb=" O CYS I 299 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE I 301 " --> pdb=" O LYS I 335 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE I 337 " --> pdb=" O ILE I 301 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU I 303 " --> pdb=" O ILE I 337 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY I 366 " --> pdb=" O THR I 298 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N SER I 300 " --> pdb=" O GLY I 366 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU I 368 " --> pdb=" O SER I 300 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ALA I 302 " --> pdb=" O LEU I 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL I 367 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL I 398 " --> pdb=" O VAL I 367 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL I 369 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE I 395 " --> pdb=" O VAL I 521 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL I 523 " --> pdb=" O PHE I 395 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLY I 397 " --> pdb=" O VAL I 523 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE I 520 " --> pdb=" O LEU I 514 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET I 509 " --> pdb=" O GLN I 502 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN I 502 " --> pdb=" O MET I 509 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE I 511 " --> pdb=" O VAL I 500 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ARG I 481 " --> pdb=" O MET I 436 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 420 " --> pdb=" O VAL I 433 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP I 435 " --> pdb=" O ASN I 420 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.15 Time building geometry restraints manager: 4.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.14: 17292 1.14 - 1.33: 3228 1.33 - 1.51: 7089 1.51 - 1.70: 7423 1.70 - 1.88: 152 Bond restraints: 35184 Sorted by residual: bond pdb=" ND1 HIS G 526 " pdb=" CE1 HIS G 526 " ideal model delta sigma weight residual 1.321 1.456 -0.135 1.00e-02 1.00e+04 1.81e+02 bond pdb=" ND1 HIS C 526 " pdb=" CE1 HIS C 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" ND1 HIS D 526 " pdb=" CE1 HIS D 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" ND1 HIS I 526 " pdb=" CE1 HIS I 526 " ideal model delta sigma weight residual 1.321 1.455 -0.134 1.00e-02 1.00e+04 1.80e+02 bond pdb=" N VAL G 548 " pdb=" H VAL G 548 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 35179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 49783 1.89 - 3.78: 9198 3.78 - 5.68: 2708 5.68 - 7.57: 1771 7.57 - 9.46: 288 Bond angle restraints: 63748 Sorted by residual: angle pdb=" N PRO G 538 " pdb=" CA PRO G 538 " pdb=" C PRO G 538 " ideal model delta sigma weight residual 110.70 120.16 -9.46 1.22e+00 6.72e-01 6.01e+01 angle pdb=" N PRO C 538 " pdb=" CA PRO C 538 " pdb=" C PRO C 538 " ideal model delta sigma weight residual 110.70 120.16 -9.46 1.22e+00 6.72e-01 6.01e+01 angle pdb=" N PRO I 538 " pdb=" CA PRO I 538 " pdb=" C PRO I 538 " ideal model delta sigma weight residual 110.70 120.09 -9.39 1.22e+00 6.72e-01 5.92e+01 angle pdb=" N PRO D 538 " pdb=" CA PRO D 538 " pdb=" C PRO D 538 " ideal model delta sigma weight residual 110.70 120.08 -9.38 1.22e+00 6.72e-01 5.92e+01 angle pdb=" CG HIS G 526 " pdb=" CD2 HIS G 526 " pdb=" NE2 HIS G 526 " ideal model delta sigma weight residual 107.20 114.59 -7.39 1.00e+00 1.00e+00 5.47e+01 ... (remaining 63743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14637 17.91 - 35.82: 1080 35.82 - 53.73: 517 53.73 - 71.64: 322 71.64 - 89.55: 60 Dihedral angle restraints: 16616 sinusoidal: 9328 harmonic: 7288 Sorted by residual: dihedral pdb=" CA PRO I 115 " pdb=" C PRO I 115 " pdb=" N HIS I 116 " pdb=" CA HIS I 116 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO D 115 " pdb=" C PRO D 115 " pdb=" N HIS D 116 " pdb=" CA HIS D 116 " ideal model delta harmonic sigma weight residual -180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PRO C 115 " pdb=" C PRO C 115 " pdb=" N HIS C 116 " pdb=" CA HIS C 116 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 16613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1448 0.089 - 0.178: 820 0.178 - 0.267: 332 0.267 - 0.356: 48 0.356 - 0.445: 28 Chirality restraints: 2676 Sorted by residual: chirality pdb=" CA PHE C 163 " pdb=" N PHE C 163 " pdb=" C PHE C 163 " pdb=" CB PHE C 163 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA PHE G 163 " pdb=" N PHE G 163 " pdb=" C PHE G 163 " pdb=" CB PHE G 163 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" CA PHE I 163 " pdb=" N PHE I 163 " pdb=" C PHE I 163 " pdb=" CB PHE I 163 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 2673 not shown) Planarity restraints: 5120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 265 " -0.155 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR D 265 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR D 265 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 265 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR D 265 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 265 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR D 265 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR D 265 " -0.122 2.00e-02 2.50e+03 pdb=" HD1 TYR D 265 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR D 265 " 0.070 2.00e-02 2.50e+03 pdb=" HE1 TYR D 265 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR D 265 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 265 " 0.155 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR I 265 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR I 265 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR I 265 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR I 265 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR I 265 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR I 265 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR I 265 " 0.122 2.00e-02 2.50e+03 pdb=" HD1 TYR I 265 " -0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR I 265 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 TYR I 265 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR I 265 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 265 " 0.155 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG TYR C 265 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR C 265 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 265 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 265 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 265 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR C 265 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR C 265 " 0.121 2.00e-02 2.50e+03 pdb=" HD1 TYR C 265 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 TYR C 265 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 TYR C 265 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 TYR C 265 " -0.036 2.00e-02 2.50e+03 ... (remaining 5117 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1643 2.07 - 2.71: 49644 2.71 - 3.34: 112819 3.34 - 3.97: 151118 3.97 - 4.60: 220208 Nonbonded interactions: 535432 Sorted by model distance: nonbonded pdb="HE21 GLN C 95 " pdb=" OE1 GLN G 95 " model vdw 1.443 2.450 nonbonded pdb=" OE1 GLN D 95 " pdb="HE22 GLN I 95 " model vdw 1.445 2.450 nonbonded pdb=" OE1 GLN C 95 " pdb="HE22 GLN G 95 " model vdw 1.459 2.450 nonbonded pdb="HE22 GLN D 95 " pdb=" OE1 GLN I 95 " model vdw 1.461 2.450 nonbonded pdb=" HA THR D 110 " pdb=" HE1 PHE I 50 " model vdw 1.553 2.270 ... (remaining 535427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 601) selection = (chain 'D' and resid 1 through 601) selection = (chain 'G' and resid 1 through 601) selection = (chain 'I' and resid 1 through 601) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 1.990 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 34.830 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.135 17860 Z= 0.809 Angle : 1.989 9.533 24204 Z= 1.333 Chirality : 0.124 0.445 2676 Planarity : 0.013 0.091 3088 Dihedral : 14.454 88.560 6920 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.37 % Favored : 96.44 % Rotamer: Outliers : 1.04 % Allowed : 5.87 % Favored : 93.09 % Cbeta Deviations : 0.40 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2136 helix: -0.94 (0.15), residues: 900 sheet: -0.74 (0.28), residues: 340 loop : -0.47 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 252 TYR 0.120 0.020 TYR C 265 PHE 0.071 0.019 PHE G 482 TRP 0.067 0.018 TRP D 387 HIS 0.028 0.006 HIS I 526 Details of bonding type rmsd/Z covalent geometry : bond 0.01370 / 0.81 (17856) covalent geometry : angle 1.98443 / 1.33 (24196) SS BOND : bond 0.01038 / 0.51 ( 4) SS BOND : angle 7.66341 / 3.94 ( 8) hydrogen bonds : bond 0.15337 / 9.98 ( 758) hydrogen bonds : angle 7.01102 / 5.08 ( 2226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 506 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 486 time to evaluate : 0.913 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: C 71 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8598 (mp) REVERT: C 420 ASN cc_start: 0.6778 (t0) cc_final: 0.6462 (t0) REVERT: C 514 LEU cc_start: 0.7562 (tp) cc_final: 0.6995 (tt) REVERT: D 514 LEU cc_start: 0.7714 (tp) cc_final: 0.7153 (tt) REVERT: G 246 ASP cc_start: 0.8249 (m-30) cc_final: 0.8028 (m-30) REVERT: G 420 ASN cc_start: 0.6718 (t0) cc_final: 0.6378 (t0) REVERT: G 456 LEU cc_start: 0.8365 (mt) cc_final: 0.8121 (mp) REVERT: G 514 LEU cc_start: 0.7554 (tp) cc_final: 0.6996 (tt) REVERT: I 246 ASP cc_start: 0.8230 (m-30) cc_final: 0.8024 (m-30) REVERT: I 456 LEU cc_start: 0.8387 (mt) cc_final: 0.8148 (mp) REVERT: D 601 GLN cc_start: 0.8436 (pt0) cc_final: 0.8174 (pt0) REVERT: G 601 GLN cc_start: 0.8437 (pt0) cc_final: 0.8197 (pt0) outliers start: 20 outliers final: 4 residues processed: 494 average time/residue: 1.1126 time to fit residues: 632.2620 Evaluate side-chains 382 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 377 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain D residue 461 ASN Chi-restraints excluded: chain G residue 461 ASN Chi-restraints excluded: chain I residue 461 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 87 ASN C 348 GLN C 359 GLN C 412 ASN D 87 ASN D 348 GLN D 359 GLN D 412 ASN G 87 ASN G 348 GLN G 412 ASN I 87 ASN I 348 GLN I 359 GLN I 412 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124528 restraints weight = 51441.327| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.62 r_work: 0.3290 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17860 Z= 0.174 Angle : 0.692 5.312 24204 Z= 0.364 Chirality : 0.047 0.158 2676 Planarity : 0.005 0.066 3088 Dihedral : 7.434 40.947 2630 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.11 % Favored : 97.71 % Rotamer: Outliers : 2.03 % Allowed : 12.11 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2136 helix: 0.37 (0.16), residues: 900 sheet: -1.33 (0.25), residues: 404 loop : -0.12 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 481 TYR 0.017 0.002 TYR C 42 PHE 0.021 0.002 PHE I 163 TRP 0.007 0.001 TRP G 358 HIS 0.005 0.002 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (17856) covalent geometry : angle 0.68922 / 0.36 (24196) SS BOND : bond 0.00171 / 0.08 ( 4) SS BOND : angle 3.57602 / 1.81 ( 8) hydrogen bonds : bond 0.04938 / 3.25 ( 758) hydrogen bonds : angle 5.27314 / 3.81 ( 2226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 441 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 0.904 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 173 GLU cc_start: 0.7954 (pm20) cc_final: 0.7507 (pm20) REVERT: C 202 ARG cc_start: 0.8307 (tmm-80) cc_final: 0.7987 (ttm-80) REVERT: C 260 GLN cc_start: 0.8904 (mt0) cc_final: 0.8658 (mt0) REVERT: C 294 ARG cc_start: 0.7630 (ptp90) cc_final: 0.7245 (mtm-85) REVERT: C 333 GLU cc_start: 0.7415 (tt0) cc_final: 0.7091 (tt0) REVERT: C 535 LYS cc_start: 0.7843 (tmtm) cc_final: 0.7599 (tttm) REVERT: C 550 ARG cc_start: 0.7215 (ttp-170) cc_final: 0.6981 (ttm-80) REVERT: D 203 GLU cc_start: 0.8372 (tp30) cc_final: 0.8094 (tm-30) REVERT: D 260 GLN cc_start: 0.8892 (mt0) cc_final: 0.8632 (mt0) REVERT: D 294 ARG cc_start: 0.7641 (ptp90) cc_final: 0.7239 (mtm-85) REVERT: D 333 GLU cc_start: 0.7382 (tt0) cc_final: 0.7069 (tt0) REVERT: D 356 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6723 (tt0) REVERT: D 392 LYS cc_start: 0.7487 (mttt) cc_final: 0.7178 (mptp) REVERT: D 535 LYS cc_start: 0.7775 (tmtm) cc_final: 0.7542 (tmtm) REVERT: D 550 ARG cc_start: 0.7219 (ttp-170) cc_final: 0.6984 (ttm-80) REVERT: G 202 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8001 (ttm-80) REVERT: G 259 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7272 (tm-30) REVERT: G 260 GLN cc_start: 0.8933 (mt0) cc_final: 0.8655 (mt0) REVERT: G 294 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7198 (mtm-85) REVERT: G 356 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6695 (mt-10) REVERT: G 456 LEU cc_start: 0.8072 (mt) cc_final: 0.7850 (mp) REVERT: G 514 LEU cc_start: 0.7927 (tp) cc_final: 0.7431 (tt) REVERT: G 535 LYS cc_start: 0.7906 (tmtm) cc_final: 0.7673 (tttm) REVERT: G 550 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.7022 (ttm-80) REVERT: I 157 MET cc_start: 0.8557 (mtt) cc_final: 0.8271 (mtp) REVERT: I 202 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8003 (ttm-80) REVERT: I 294 ARG cc_start: 0.7642 (ptp90) cc_final: 0.7217 (mtm-85) REVERT: I 306 LYS cc_start: 0.7748 (tttm) cc_final: 0.7512 (tttt) REVERT: I 333 GLU cc_start: 0.7351 (tt0) cc_final: 0.7067 (tt0) REVERT: I 456 LEU cc_start: 0.8096 (mt) cc_final: 0.7816 (mp) REVERT: I 550 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6969 (ttm-80) REVERT: D 601 GLN cc_start: 0.8578 (pt0) cc_final: 0.8194 (pt0) REVERT: G 601 GLN cc_start: 0.8589 (pt0) cc_final: 0.8140 (pt0) outliers start: 39 outliers final: 14 residues processed: 416 average time/residue: 1.2150 time to fit residues: 573.6664 Evaluate side-chains 390 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 374 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 461 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 232 MET Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 232 MET Chi-restraints excluded: chain I residue 461 ASN Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 151 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 180 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 GLN D 165 GLN D 359 GLN I 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119028 restraints weight = 51218.563| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.64 r_work: 0.3219 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 17860 Z= 0.195 Angle : 0.634 6.374 24204 Z= 0.325 Chirality : 0.046 0.158 2676 Planarity : 0.005 0.036 3088 Dihedral : 6.904 40.147 2626 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.15 % Favored : 97.66 % Rotamer: Outliers : 1.82 % Allowed : 13.51 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2136 helix: 0.47 (0.16), residues: 928 sheet: -1.20 (0.25), residues: 404 loop : 0.24 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 481 TYR 0.015 0.002 TYR G 42 PHE 0.019 0.002 PHE G 163 TRP 0.010 0.001 TRP C 358 HIS 0.008 0.002 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (17856) covalent geometry : angle 0.62948 / 0.32 (24196) SS BOND : bond 0.00818 / 0.40 ( 4) SS BOND : angle 4.14011 / 2.08 ( 8) hydrogen bonds : bond 0.04258 / 2.80 ( 758) hydrogen bonds : angle 4.98810 / 3.59 ( 2226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 388 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 173 GLU cc_start: 0.8123 (pm20) cc_final: 0.7617 (pm20) REVERT: C 202 ARG cc_start: 0.8381 (tmm-80) cc_final: 0.8006 (ttm-80) REVERT: C 243 CYS cc_start: 0.7602 (t) cc_final: 0.7271 (t) REVERT: C 331 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7799 (mtpp) REVERT: C 333 GLU cc_start: 0.7654 (tt0) cc_final: 0.7363 (tt0) REVERT: C 356 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6781 (mt-10) REVERT: C 483 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7228 (tt0) REVERT: C 550 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7009 (ttm-80) REVERT: D 173 GLU cc_start: 0.8075 (pm20) cc_final: 0.7738 (pm20) REVERT: D 202 ARG cc_start: 0.8363 (tmm-80) cc_final: 0.7980 (ttm-80) REVERT: D 203 GLU cc_start: 0.8401 (tp30) cc_final: 0.8099 (tm-30) REVERT: D 243 CYS cc_start: 0.7596 (t) cc_final: 0.7250 (t) REVERT: D 308 THR cc_start: 0.8464 (m) cc_final: 0.8227 (m) REVERT: D 333 GLU cc_start: 0.7583 (tt0) cc_final: 0.7314 (tt0) REVERT: D 356 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6935 (tt0) REVERT: D 483 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: D 550 ARG cc_start: 0.7387 (ttp-170) cc_final: 0.7005 (ttm-80) REVERT: G 173 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: G 243 CYS cc_start: 0.7475 (t) cc_final: 0.7076 (t) REVERT: G 259 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7406 (tm-30) REVERT: G 356 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6850 (mt-10) REVERT: G 456 LEU cc_start: 0.8152 (mt) cc_final: 0.7859 (mp) REVERT: G 550 ARG cc_start: 0.7351 (ttp-170) cc_final: 0.7039 (ttm-80) REVERT: I 157 MET cc_start: 0.8549 (mtt) cc_final: 0.8248 (mtp) REVERT: I 173 GLU cc_start: 0.8100 (pt0) cc_final: 0.7602 (pm20) REVERT: I 243 CYS cc_start: 0.7507 (t) cc_final: 0.7120 (t) REVERT: I 306 LYS cc_start: 0.7796 (tttm) cc_final: 0.7577 (tttt) REVERT: I 333 GLU cc_start: 0.7627 (tt0) cc_final: 0.7352 (tt0) REVERT: I 356 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6841 (tt0) REVERT: I 456 LEU cc_start: 0.8108 (mt) cc_final: 0.7802 (mp) REVERT: I 483 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: I 550 ARG cc_start: 0.7412 (ttp-170) cc_final: 0.7004 (ttm-80) REVERT: D 601 GLN cc_start: 0.8625 (pt0) cc_final: 0.8286 (pt0) outliers start: 35 outliers final: 23 residues processed: 403 average time/residue: 1.2092 time to fit residues: 554.3647 Evaluate side-chains 381 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 169 LYS Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 461 ASN Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 169 LYS Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 154 ILE Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 483 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 165 GLN D 165 GLN D 198 GLN D 359 GLN G 165 GLN G 198 GLN I 165 GLN I 359 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119996 restraints weight = 50556.939| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.60 r_work: 0.3250 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17860 Z= 0.221 Angle : 0.643 8.805 24204 Z= 0.326 Chirality : 0.046 0.159 2676 Planarity : 0.005 0.037 3088 Dihedral : 6.891 38.953 2624 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.78 % Favored : 98.03 % Rotamer: Outliers : 2.18 % Allowed : 15.02 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2136 helix: 0.53 (0.16), residues: 928 sheet: -1.23 (0.25), residues: 396 loop : 0.16 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 481 TYR 0.014 0.002 TYR I 42 PHE 0.020 0.002 PHE I 163 TRP 0.009 0.002 TRP G 358 HIS 0.007 0.002 HIS D 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (17856) covalent geometry : angle 0.63561 / 0.32 (24196) SS BOND : bond 0.01584 / 0.77 ( 4) SS BOND : angle 5.36998 / 2.70 ( 8) hydrogen bonds : bond 0.04248 / 2.79 ( 758) hydrogen bonds : angle 4.90073 / 3.51 ( 2226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 360 time to evaluate : 0.842 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: C 202 ARG cc_start: 0.8428 (tmm-80) cc_final: 0.8049 (ttm-80) REVERT: C 243 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7189 (t) REVERT: C 310 PHE cc_start: 0.7337 (t80) cc_final: 0.7107 (t80) REVERT: C 331 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7887 (mtpp) REVERT: C 333 GLU cc_start: 0.7846 (tt0) cc_final: 0.7571 (tt0) REVERT: C 356 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6896 (tt0) REVERT: C 392 LYS cc_start: 0.7531 (mmmm) cc_final: 0.7104 (mptp) REVERT: C 550 ARG cc_start: 0.7489 (ttp-170) cc_final: 0.7108 (ttm-80) REVERT: D 173 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: D 243 CYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7168 (t) REVERT: D 333 GLU cc_start: 0.7855 (tt0) cc_final: 0.7595 (tt0) REVERT: D 356 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6966 (tt0) REVERT: D 392 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7108 (mptp) REVERT: D 550 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7101 (ttm-80) REVERT: G 202 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8087 (ttm-80) REVERT: G 243 CYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7158 (t) REVERT: G 259 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7427 (tm-30) REVERT: G 356 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6887 (mt-10) REVERT: G 456 LEU cc_start: 0.8249 (mt) cc_final: 0.7956 (mp) REVERT: G 550 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.7108 (ttm-80) REVERT: I 157 MET cc_start: 0.8573 (mtt) cc_final: 0.8238 (mtp) REVERT: I 173 GLU cc_start: 0.8118 (pt0) cc_final: 0.7882 (pm20) REVERT: I 202 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8095 (ttm-80) REVERT: I 243 CYS cc_start: 0.7508 (OUTLIER) cc_final: 0.7191 (t) REVERT: I 268 ARG cc_start: 0.7492 (ttm170) cc_final: 0.7189 (ttp-110) REVERT: I 306 LYS cc_start: 0.7915 (tttm) cc_final: 0.7687 (tttt) REVERT: I 331 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7933 (mtpp) REVERT: I 333 GLU cc_start: 0.7799 (tt0) cc_final: 0.7545 (tt0) REVERT: I 356 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6894 (tt0) REVERT: I 383 GLN cc_start: 0.7499 (mm110) cc_final: 0.7103 (mp10) REVERT: I 456 LEU cc_start: 0.8253 (mt) cc_final: 0.7966 (mp) REVERT: I 550 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.7105 (ttm-80) outliers start: 42 outliers final: 25 residues processed: 375 average time/residue: 1.1889 time to fit residues: 506.8767 Evaluate side-chains 377 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 345 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 461 ASN Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 202 ARG Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 483 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 25 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 198 GLN I 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120887 restraints weight = 50531.262| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.61 r_work: 0.3263 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17860 Z= 0.162 Angle : 0.580 7.250 24204 Z= 0.294 Chirality : 0.044 0.157 2676 Planarity : 0.004 0.036 3088 Dihedral : 6.380 40.083 2622 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.73 % Favored : 98.08 % Rotamer: Outliers : 1.98 % Allowed : 14.97 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2136 helix: 0.74 (0.17), residues: 936 sheet: -1.26 (0.25), residues: 396 loop : 0.28 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 481 TYR 0.013 0.002 TYR D 42 PHE 0.014 0.002 PHE I 163 TRP 0.008 0.001 TRP G 358 HIS 0.006 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (17856) covalent geometry : angle 0.57516 / 0.29 (24196) SS BOND : bond 0.01220 / 0.60 ( 4) SS BOND : angle 4.30352 / 2.16 ( 8) hydrogen bonds : bond 0.03811 / 2.52 ( 758) hydrogen bonds : angle 4.72792 / 3.39 ( 2226) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 371 time to evaluate : 0.993 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: C 202 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8035 (ttm-80) REVERT: C 205 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7944 (mtm-85) REVERT: C 243 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7280 (t) REVERT: C 306 LYS cc_start: 0.8052 (tttm) cc_final: 0.7851 (ptmt) REVERT: C 333 GLU cc_start: 0.7793 (tt0) cc_final: 0.7531 (tt0) REVERT: C 356 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6961 (tt0) REVERT: C 392 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7178 (mptp) REVERT: C 550 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.7134 (ttm-80) REVERT: D 173 GLU cc_start: 0.8143 (pm20) cc_final: 0.7877 (pm20) REVERT: D 205 ARG cc_start: 0.8312 (mtt90) cc_final: 0.7955 (mtm-85) REVERT: D 243 CYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7236 (t) REVERT: D 333 GLU cc_start: 0.7803 (tt0) cc_final: 0.7548 (tt0) REVERT: D 383 GLN cc_start: 0.7673 (mm110) cc_final: 0.7213 (mp10) REVERT: D 392 LYS cc_start: 0.7540 (mmmm) cc_final: 0.7142 (mptp) REVERT: D 550 ARG cc_start: 0.7523 (ttp-170) cc_final: 0.7151 (ttm-80) REVERT: G 205 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7940 (mtm-85) REVERT: G 243 CYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7279 (t) REVERT: G 306 LYS cc_start: 0.8076 (tttm) cc_final: 0.7876 (ptmt) REVERT: G 356 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6879 (mt-10) REVERT: G 383 GLN cc_start: 0.7690 (mm110) cc_final: 0.6993 (mt0) REVERT: G 456 LEU cc_start: 0.8273 (mt) cc_final: 0.7990 (mp) REVERT: G 514 LEU cc_start: 0.7997 (tp) cc_final: 0.7583 (tt) REVERT: G 550 ARG cc_start: 0.7534 (ttp-170) cc_final: 0.7171 (ttm-80) REVERT: I 157 MET cc_start: 0.8529 (mtt) cc_final: 0.8209 (mtp) REVERT: I 173 GLU cc_start: 0.8208 (pt0) cc_final: 0.7963 (pm20) REVERT: I 202 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8088 (ttm-80) REVERT: I 205 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7956 (mtm-85) REVERT: I 243 CYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7287 (t) REVERT: I 268 ARG cc_start: 0.7522 (ttm170) cc_final: 0.7300 (ttp-110) REVERT: I 331 LYS cc_start: 0.8319 (mtmt) cc_final: 0.8010 (mtpp) REVERT: I 333 GLU cc_start: 0.7754 (tt0) cc_final: 0.7519 (tt0) REVERT: I 356 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6966 (tt0) REVERT: I 383 GLN cc_start: 0.7649 (mm110) cc_final: 0.7184 (mp10) REVERT: I 456 LEU cc_start: 0.8242 (mt) cc_final: 0.7965 (mp) REVERT: I 550 ARG cc_start: 0.7528 (ttp-170) cc_final: 0.7126 (ttm-80) outliers start: 38 outliers final: 24 residues processed: 388 average time/residue: 1.3214 time to fit residues: 579.8326 Evaluate side-chains 393 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 364 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 202 ARG Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 483 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 34 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 49 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 159 optimal weight: 0.4980 chunk 177 optimal weight: 0.0980 chunk 37 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121589 restraints weight = 50683.163| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.62 r_work: 0.3272 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17860 Z= 0.138 Angle : 0.556 6.677 24204 Z= 0.280 Chirality : 0.043 0.152 2676 Planarity : 0.004 0.036 3088 Dihedral : 6.123 39.806 2620 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.54 % Favored : 98.27 % Rotamer: Outliers : 1.66 % Allowed : 15.44 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.18), residues: 2136 helix: 0.97 (0.17), residues: 932 sheet: -0.95 (0.26), residues: 352 loop : 0.39 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 481 TYR 0.012 0.001 TYR I 42 PHE 0.014 0.001 PHE G 163 TRP 0.008 0.001 TRP G 358 HIS 0.005 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17856) covalent geometry : angle 0.55095 / 0.28 (24196) SS BOND : bond 0.01008 / 0.49 ( 4) SS BOND : angle 4.06293 / 2.04 ( 8) hydrogen bonds : bond 0.03572 / 2.36 ( 758) hydrogen bonds : angle 4.59984 / 3.30 ( 2226) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 385 time to evaluate : 0.867 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: C 202 ARG cc_start: 0.8437 (tmm-80) cc_final: 0.8033 (ttm-80) REVERT: C 205 ARG cc_start: 0.8269 (mtt90) cc_final: 0.7917 (mtm-85) REVERT: C 243 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7270 (t) REVERT: C 333 GLU cc_start: 0.7779 (tt0) cc_final: 0.7509 (tt0) REVERT: C 392 LYS cc_start: 0.7571 (mmmm) cc_final: 0.7213 (mptp) REVERT: C 550 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7137 (ttm-80) REVERT: D 173 GLU cc_start: 0.8195 (pm20) cc_final: 0.7903 (pm20) REVERT: D 202 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8121 (ttp80) REVERT: D 205 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7923 (mtm-85) REVERT: D 243 CYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7184 (t) REVERT: D 333 GLU cc_start: 0.7820 (tt0) cc_final: 0.7565 (tt0) REVERT: D 383 GLN cc_start: 0.7649 (mm110) cc_final: 0.7138 (mp10) REVERT: D 392 LYS cc_start: 0.7542 (mmmm) cc_final: 0.7182 (mptp) REVERT: D 550 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.7169 (ttm-80) REVERT: G 205 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7921 (mtm-85) REVERT: G 232 MET cc_start: 0.7248 (mmm) cc_final: 0.6923 (mtm) REVERT: G 243 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7235 (t) REVERT: G 356 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6917 (mt-10) REVERT: G 383 GLN cc_start: 0.7659 (mm110) cc_final: 0.6922 (mt0) REVERT: G 456 LEU cc_start: 0.8275 (mt) cc_final: 0.7985 (mp) REVERT: G 514 LEU cc_start: 0.7985 (tp) cc_final: 0.7593 (tt) REVERT: G 550 ARG cc_start: 0.7486 (ttp-170) cc_final: 0.7188 (ttm-80) REVERT: I 157 MET cc_start: 0.8510 (mtt) cc_final: 0.8144 (mtp) REVERT: I 173 GLU cc_start: 0.8189 (pt0) cc_final: 0.7963 (pm20) REVERT: I 205 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7923 (mtm-85) REVERT: I 243 CYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7193 (t) REVERT: I 331 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8023 (mtpp) REVERT: I 333 GLU cc_start: 0.7767 (tt0) cc_final: 0.7537 (tt0) REVERT: I 383 GLN cc_start: 0.7602 (mm110) cc_final: 0.6890 (mt0) REVERT: I 456 LEU cc_start: 0.8235 (mt) cc_final: 0.7957 (mp) REVERT: I 550 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7121 (ttm-80) outliers start: 32 outliers final: 27 residues processed: 398 average time/residue: 1.3034 time to fit residues: 586.4972 Evaluate side-chains 396 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.151107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118625 restraints weight = 50198.371| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.55 r_work: 0.3209 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17860 Z= 0.174 Angle : 0.584 7.447 24204 Z= 0.294 Chirality : 0.044 0.155 2676 Planarity : 0.004 0.036 3088 Dihedral : 6.279 38.690 2620 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.78 % Favored : 98.13 % Rotamer: Outliers : 1.77 % Allowed : 15.85 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.18), residues: 2136 helix: 0.94 (0.17), residues: 936 sheet: -1.18 (0.24), residues: 396 loop : 0.28 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 481 TYR 0.012 0.002 TYR I 42 PHE 0.014 0.002 PHE D 163 TRP 0.008 0.001 TRP G 358 HIS 0.006 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (17856) covalent geometry : angle 0.57943 / 0.29 (24196) SS BOND : bond 0.01216 / 0.59 ( 4) SS BOND : angle 4.17339 / 2.09 ( 8) hydrogen bonds : bond 0.03776 / 2.49 ( 758) hydrogen bonds : angle 4.61602 / 3.30 ( 2226) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 202 ARG cc_start: 0.8443 (tmm-80) cc_final: 0.8026 (ttm-80) REVERT: C 205 ARG cc_start: 0.8343 (mtt90) cc_final: 0.7982 (mtm-85) REVERT: C 243 CYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7366 (t) REVERT: C 333 GLU cc_start: 0.7846 (tt0) cc_final: 0.7597 (tt0) REVERT: C 392 LYS cc_start: 0.7651 (mmmm) cc_final: 0.7207 (mptp) REVERT: C 550 ARG cc_start: 0.7457 (ttp-170) cc_final: 0.7135 (ttm-80) REVERT: D 173 GLU cc_start: 0.8162 (pm20) cc_final: 0.7949 (pm20) REVERT: D 202 ARG cc_start: 0.8459 (tmm-80) cc_final: 0.8126 (ttp80) REVERT: D 205 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7988 (mtm-85) REVERT: D 243 CYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7200 (t) REVERT: D 333 GLU cc_start: 0.7867 (tt0) cc_final: 0.7618 (tt0) REVERT: D 383 GLN cc_start: 0.7589 (mm110) cc_final: 0.6967 (mt0) REVERT: D 392 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7153 (mptp) REVERT: D 550 ARG cc_start: 0.7446 (ttp-170) cc_final: 0.7166 (ttm-80) REVERT: G 205 ARG cc_start: 0.8354 (mtt90) cc_final: 0.7972 (mtm-85) REVERT: G 243 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7353 (t) REVERT: G 356 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6861 (mt-10) REVERT: G 383 GLN cc_start: 0.7619 (mm110) cc_final: 0.6927 (mt0) REVERT: G 456 LEU cc_start: 0.8301 (mt) cc_final: 0.8019 (mp) REVERT: G 514 LEU cc_start: 0.7995 (tp) cc_final: 0.7619 (tt) REVERT: G 550 ARG cc_start: 0.7485 (ttp-170) cc_final: 0.7184 (ttm-80) REVERT: I 157 MET cc_start: 0.8597 (mtt) cc_final: 0.8204 (mtp) REVERT: I 173 GLU cc_start: 0.8202 (pt0) cc_final: 0.7960 (pm20) REVERT: I 205 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7978 (mtm-85) REVERT: I 243 CYS cc_start: 0.7570 (t) cc_final: 0.7251 (t) REVERT: I 268 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.7267 (ttp-110) REVERT: I 331 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8052 (mtpp) REVERT: I 333 GLU cc_start: 0.7829 (tt0) cc_final: 0.7608 (tt0) REVERT: I 383 GLN cc_start: 0.7601 (mm110) cc_final: 0.7114 (mp10) REVERT: I 456 LEU cc_start: 0.8285 (mt) cc_final: 0.8005 (mp) outliers start: 34 outliers final: 27 residues processed: 394 average time/residue: 1.3175 time to fit residues: 589.1996 Evaluate side-chains 389 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 chunk 186 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 183 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 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 = 0.3739 r_free = 0.3739 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120264 restraints weight = 50360.765| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.57 r_work: 0.3231 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17860 Z= 0.120 Angle : 0.541 6.825 24204 Z= 0.271 Chirality : 0.043 0.149 2676 Planarity : 0.004 0.039 3088 Dihedral : 5.881 39.867 2620 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.77 % Allowed : 16.11 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.18), residues: 2136 helix: 1.20 (0.17), residues: 932 sheet: -0.97 (0.26), residues: 352 loop : 0.39 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 481 TYR 0.011 0.001 TYR I 42 PHE 0.013 0.001 PHE D 163 TRP 0.008 0.001 TRP G 358 HIS 0.004 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (17856) covalent geometry : angle 0.53658 / 0.27 (24196) SS BOND : bond 0.01020 / 0.50 ( 4) SS BOND : angle 3.92645 / 1.96 ( 8) hydrogen bonds : bond 0.03361 / 2.23 ( 758) hydrogen bonds : angle 4.46916 / 3.20 ( 2226) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 387 time to evaluate : 1.118 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: C 202 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8114 (ttp80) REVERT: C 205 ARG cc_start: 0.8299 (mtt90) cc_final: 0.7965 (mtm-85) REVERT: C 243 CYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7191 (t) REVERT: C 331 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7917 (mtpp) REVERT: C 333 GLU cc_start: 0.7770 (tt0) cc_final: 0.7527 (tt0) REVERT: C 392 LYS cc_start: 0.7635 (mmmm) cc_final: 0.7213 (mptp) REVERT: C 550 ARG cc_start: 0.7476 (ttp-170) cc_final: 0.7116 (ttm-80) REVERT: D 173 GLU cc_start: 0.8186 (pm20) cc_final: 0.7891 (pm20) REVERT: D 202 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8120 (ttp80) REVERT: D 205 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7973 (mtm-85) REVERT: D 243 CYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7318 (t) REVERT: D 331 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7909 (mtpp) REVERT: D 333 GLU cc_start: 0.7796 (tt0) cc_final: 0.7547 (tt0) REVERT: D 383 GLN cc_start: 0.7465 (mm110) cc_final: 0.6839 (mt0) REVERT: D 392 LYS cc_start: 0.7626 (mmmm) cc_final: 0.7199 (mptp) REVERT: D 465 ARG cc_start: 0.8191 (ttt-90) cc_final: 0.7719 (ttt180) REVERT: D 550 ARG cc_start: 0.7482 (ttp-170) cc_final: 0.7153 (ttm-80) REVERT: G 205 ARG cc_start: 0.8294 (mtt90) cc_final: 0.7943 (mtm-85) REVERT: G 232 MET cc_start: 0.7240 (mmm) cc_final: 0.6896 (mtm) REVERT: G 243 CYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7198 (t) REVERT: G 331 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7944 (mtpp) REVERT: G 356 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6825 (mt-10) REVERT: G 383 GLN cc_start: 0.7488 (mm110) cc_final: 0.6919 (mt0) REVERT: G 456 LEU cc_start: 0.8308 (mt) cc_final: 0.8005 (mp) REVERT: G 514 LEU cc_start: 0.7969 (tp) cc_final: 0.7632 (tt) REVERT: G 550 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7150 (ttm-80) REVERT: I 157 MET cc_start: 0.8523 (mtt) cc_final: 0.8225 (mtp) REVERT: I 173 GLU cc_start: 0.8177 (pt0) cc_final: 0.7942 (pm20) REVERT: I 202 ARG cc_start: 0.8545 (tmm-80) cc_final: 0.8065 (ttm-80) REVERT: I 205 ARG cc_start: 0.8311 (mtt90) cc_final: 0.7971 (mtm-85) REVERT: I 243 CYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7132 (t) REVERT: I 268 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7298 (ttp-110) REVERT: I 331 LYS cc_start: 0.8402 (mtmt) cc_final: 0.8080 (mtpp) REVERT: I 333 GLU cc_start: 0.7799 (tt0) cc_final: 0.7582 (tt0) REVERT: I 383 GLN cc_start: 0.7468 (mm110) cc_final: 0.6861 (mt0) REVERT: I 456 LEU cc_start: 0.8281 (mt) cc_final: 0.7991 (mp) REVERT: I 465 ARG cc_start: 0.8165 (ttt-90) cc_final: 0.7682 (ttt180) outliers start: 34 outliers final: 27 residues processed: 404 average time/residue: 1.2479 time to fit residues: 570.7234 Evaluate side-chains 403 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 372 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 243 CYS Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 22 optimal weight: 0.0870 chunk 199 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117613 restraints weight = 50228.316| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.57 r_work: 0.3190 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17860 Z= 0.160 Angle : 0.570 7.735 24204 Z= 0.286 Chirality : 0.044 0.154 2676 Planarity : 0.004 0.068 3088 Dihedral : 6.145 39.102 2620 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.66 % Allowed : 16.74 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.18), residues: 2136 helix: 1.12 (0.17), residues: 936 sheet: -1.14 (0.25), residues: 396 loop : 0.39 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 481 TYR 0.012 0.001 TYR D 42 PHE 0.013 0.001 PHE G 163 TRP 0.008 0.001 TRP C 358 HIS 0.006 0.001 HIS G 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (17856) covalent geometry : angle 0.56521 / 0.28 (24196) SS BOND : bond 0.01256 / 0.61 ( 4) SS BOND : angle 4.15368 / 2.08 ( 8) hydrogen bonds : bond 0.03626 / 2.39 ( 758) hydrogen bonds : angle 4.52614 / 3.24 ( 2226) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 375 time to evaluate : 0.957 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: C 202 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.7995 (ttm-80) REVERT: C 205 ARG cc_start: 0.8314 (mtt90) cc_final: 0.7941 (mtm-85) REVERT: C 243 CYS cc_start: 0.7636 (t) cc_final: 0.7329 (t) REVERT: C 331 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7936 (mtpp) REVERT: C 333 GLU cc_start: 0.7843 (tt0) cc_final: 0.7592 (tt0) REVERT: C 383 GLN cc_start: 0.7475 (mm110) cc_final: 0.6896 (mt0) REVERT: C 392 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7155 (mptp) REVERT: C 534 ILE cc_start: 0.8531 (tp) cc_final: 0.8279 (pp) REVERT: C 550 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7105 (ttm-80) REVERT: D 202 ARG cc_start: 0.8457 (tmm-80) cc_final: 0.8097 (ttp80) REVERT: D 205 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7950 (mtm-85) REVERT: D 243 CYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7135 (t) REVERT: D 331 LYS cc_start: 0.8323 (ttpt) cc_final: 0.7998 (mtpp) REVERT: D 333 GLU cc_start: 0.7865 (tt0) cc_final: 0.7636 (tt0) REVERT: D 383 GLN cc_start: 0.7435 (mm110) cc_final: 0.6787 (mt0) REVERT: D 392 LYS cc_start: 0.7586 (mmmm) cc_final: 0.7157 (mptp) REVERT: D 550 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.7120 (ttm-80) REVERT: G 205 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7945 (mtm-85) REVERT: G 232 MET cc_start: 0.7214 (mmm) cc_final: 0.6891 (mtm) REVERT: G 243 CYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7278 (t) REVERT: G 331 LYS cc_start: 0.8298 (ttpt) cc_final: 0.7922 (mtpp) REVERT: G 356 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6854 (mt-10) REVERT: G 383 GLN cc_start: 0.7441 (mm110) cc_final: 0.6868 (mt0) REVERT: G 456 LEU cc_start: 0.8306 (mt) cc_final: 0.8007 (mp) REVERT: G 514 LEU cc_start: 0.7978 (tp) cc_final: 0.7659 (tt) REVERT: G 550 ARG cc_start: 0.7413 (ttp-170) cc_final: 0.7129 (ttm-80) REVERT: I 157 MET cc_start: 0.8562 (mtt) cc_final: 0.8252 (mtp) REVERT: I 173 GLU cc_start: 0.8194 (pt0) cc_final: 0.7961 (pm20) REVERT: I 205 ARG cc_start: 0.8339 (mtt90) cc_final: 0.7957 (mtm-85) REVERT: I 232 MET cc_start: 0.7192 (mmm) cc_final: 0.6763 (mpm) REVERT: I 243 CYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7216 (t) REVERT: I 331 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8060 (mtpp) REVERT: I 333 GLU cc_start: 0.7866 (tt0) cc_final: 0.7647 (tt0) REVERT: I 383 GLN cc_start: 0.7414 (mm110) cc_final: 0.6789 (mt0) REVERT: I 456 LEU cc_start: 0.8313 (mt) cc_final: 0.8026 (mp) outliers start: 32 outliers final: 24 residues processed: 391 average time/residue: 1.2399 time to fit residues: 548.4798 Evaluate side-chains 391 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 364 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 203 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118199 restraints weight = 50446.848| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.59 r_work: 0.3199 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17860 Z= 0.138 Angle : 0.551 8.236 24204 Z= 0.276 Chirality : 0.043 0.149 2676 Planarity : 0.004 0.035 3088 Dihedral : 5.941 39.915 2620 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.61 % Allowed : 16.89 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2136 helix: 1.18 (0.17), residues: 940 sheet: -1.14 (0.25), residues: 396 loop : 0.44 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 481 TYR 0.011 0.001 TYR I 42 PHE 0.014 0.001 PHE D 163 TRP 0.008 0.001 TRP C 358 HIS 0.005 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (17856) covalent geometry : angle 0.54634 / 0.27 (24196) SS BOND : bond 0.01091 / 0.53 ( 4) SS BOND : angle 4.11006 / 2.08 ( 8) hydrogen bonds : bond 0.03450 / 2.28 ( 758) hydrogen bonds : angle 4.47532 / 3.20 ( 2226) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Residue LYS 229 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 377 time to evaluate : 0.959 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: C 202 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.8075 (ttp80) REVERT: C 243 CYS cc_start: 0.7625 (t) cc_final: 0.7276 (t) REVERT: C 331 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7915 (mtpp) REVERT: C 333 GLU cc_start: 0.7867 (tt0) cc_final: 0.7612 (tt0) REVERT: C 383 GLN cc_start: 0.7371 (mm110) cc_final: 0.6783 (mt0) REVERT: C 392 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7157 (mptp) REVERT: C 534 ILE cc_start: 0.8521 (tp) cc_final: 0.8275 (pp) REVERT: C 550 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7104 (ttm-80) REVERT: D 202 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.8124 (ttp80) REVERT: D 205 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7949 (mtm-85) REVERT: D 243 CYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7319 (t) REVERT: D 331 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8002 (mtpp) REVERT: D 333 GLU cc_start: 0.7856 (tt0) cc_final: 0.7622 (tt0) REVERT: D 383 GLN cc_start: 0.7414 (mm110) cc_final: 0.6767 (mt0) REVERT: D 392 LYS cc_start: 0.7554 (mmmm) cc_final: 0.7130 (mptp) REVERT: D 550 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7128 (ttm-80) REVERT: G 205 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7928 (mtm-85) REVERT: G 232 MET cc_start: 0.7220 (mmm) cc_final: 0.6933 (mtm) REVERT: G 243 CYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7225 (t) REVERT: G 331 LYS cc_start: 0.8346 (ttpt) cc_final: 0.7969 (mtpp) REVERT: G 356 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6842 (mt-10) REVERT: G 383 GLN cc_start: 0.7404 (mm110) cc_final: 0.6812 (mt0) REVERT: G 456 LEU cc_start: 0.8318 (mt) cc_final: 0.8009 (mp) REVERT: G 514 LEU cc_start: 0.7985 (tp) cc_final: 0.7663 (tt) REVERT: G 534 ILE cc_start: 0.8540 (tp) cc_final: 0.8302 (pp) REVERT: G 550 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.7128 (ttm-80) REVERT: I 157 MET cc_start: 0.8560 (mtt) cc_final: 0.8252 (mtp) REVERT: I 173 GLU cc_start: 0.8184 (pt0) cc_final: 0.7963 (pm20) REVERT: I 205 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7949 (mtm-85) REVERT: I 232 MET cc_start: 0.7242 (mmm) cc_final: 0.6828 (mpm) REVERT: I 243 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7198 (t) REVERT: I 331 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8045 (mtpp) REVERT: I 333 GLU cc_start: 0.7828 (tt0) cc_final: 0.7602 (tt0) REVERT: I 383 GLN cc_start: 0.7428 (mm110) cc_final: 0.6802 (mt0) REVERT: I 456 LEU cc_start: 0.8322 (mt) cc_final: 0.8036 (mp) REVERT: I 465 ARG cc_start: 0.8197 (ttt-90) cc_final: 0.7964 (ttt90) outliers start: 31 outliers final: 28 residues processed: 392 average time/residue: 1.2988 time to fit residues: 573.0338 Evaluate side-chains 401 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 370 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 218 CYS Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 232 MET Chi-restraints excluded: chain D residue 243 CYS Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 537 SER Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 243 CYS Chi-restraints excluded: chain G residue 287 GLU Chi-restraints excluded: chain G residue 474 LEU Chi-restraints excluded: chain G residue 483 GLU Chi-restraints excluded: chain G residue 537 SER Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 SER Chi-restraints excluded: chain I residue 243 CYS Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 474 LEU Chi-restraints excluded: chain I residue 537 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 200 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.152072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119286 restraints weight = 50091.526| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.58 r_work: 0.3214 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17860 Z= 0.118 Angle : 0.535 9.615 24204 Z= 0.268 Chirality : 0.043 0.148 2676 Planarity : 0.004 0.035 3088 Dihedral : 5.774 40.077 2620 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.56 % Allowed : 17.20 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2136 helix: 1.32 (0.17), residues: 940 sheet: -1.14 (0.25), residues: 396 loop : 0.47 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 481 TYR 0.011 0.001 TYR G 42 PHE 0.011 0.001 PHE G 163 TRP 0.007 0.001 TRP C 358 HIS 0.004 0.001 HIS I 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (17856) covalent geometry : angle 0.53076 / 0.27 (24196) SS BOND : bond 0.00957 / 0.47 ( 4) SS BOND : angle 3.80739 / 1.92 ( 8) hydrogen bonds : bond 0.03244 / 2.16 ( 758) hydrogen bonds : angle 4.37673 / 3.14 ( 2226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14500.53 seconds wall clock time: 245 minutes 31.65 seconds (14731.65 seconds total)