Starting phenix.real_space_refine on Mon Jul 6 23:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ewq_31361/07_2026/7ewq_31361.map" } resolution = 3.5 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= 0.000 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: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 247 5.16 5 C 25246 2.51 5 N 6890 2.21 5 O 7683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 247 residue(s): 0.04s 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: 40144 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, Y, D, F, H, J, L, N, P, R, T, V, X, Z Time building chain proxies: 4.71, per 1000 atoms: 0.12 Number of scatterers: 40144 At special positions: 0 Unit cell: (202.99, 202.46, 83.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 247 16.00 P 78 15.00 O 7683 8.00 N 6890 7.00 C 25246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=39, symmetry=0 Number of additional bonds: simple=39, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9074 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 13 sheets defined 70.9% alpha, 3.5% beta 0 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 44 through 61 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY A 144 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 145' Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET A 210 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY A 307 " --> pdb=" O TYR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 311 removed outlier: 3.910A pdb=" N ARG A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 318 through 323 Processing helix chain 'A' and resid 325 through 328 Processing helix chain 'A' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 374 Processing helix chain 'C' and resid 2 through 18 Processing helix chain 'C' and resid 19 through 21 No H-bonds generated for 'chain 'C' and resid 19 through 21' Processing helix chain 'C' and resid 44 through 61 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 141 through 145 removed outlier: 4.038A pdb=" N GLY C 144 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 145 " --> pdb=" O ASN C 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 141 through 145' Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY C 154 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 225 Processing helix chain 'C' and resid 227 through 241 Processing helix chain 'C' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 289 through 307 removed outlier: 4.050A pdb=" N LEU C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 311 removed outlier: 3.910A pdb=" N ARG C 311 " --> pdb=" O GLU C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 308 through 311' Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 325 through 328 Processing helix chain 'C' and resid 329 through 344 removed outlier: 4.438A pdb=" N VAL C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 358 through 374 Processing helix chain 'E' and resid 2 through 18 Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 44 through 61 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 83 through 92 removed outlier: 4.075A pdb=" N LEU E 90 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 141 through 145 removed outlier: 4.038A pdb=" N GLY E 144 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR E 145 " --> pdb=" O ASN E 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 141 through 145' Processing helix chain 'E' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS E 180 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET E 210 " --> pdb=" O ALA E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 227 through 241 Processing helix chain 'E' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 Processing helix chain 'E' and resid 282 through 287 Processing helix chain 'E' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU E 293 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY E 307 " --> pdb=" O TYR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 311 removed outlier: 3.908A pdb=" N ARG E 311 " --> pdb=" O GLU E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 308 through 311' Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 318 through 323 Processing helix chain 'E' and resid 325 through 328 Processing helix chain 'E' and resid 329 through 344 removed outlier: 4.438A pdb=" N VAL E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 358 through 374 Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 44 through 61 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU G 90 " --> pdb=" O ASN G 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA G 91 " --> pdb=" O HIS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY G 144 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR G 145 " --> pdb=" O ASN G 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 145' Processing helix chain 'G' and resid 150 through 155 removed outlier: 4.388A pdb=" N GLY G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET G 210 " --> pdb=" O ALA G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 225 Processing helix chain 'G' and resid 227 through 241 Processing helix chain 'G' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 277 Processing helix chain 'G' and resid 282 through 287 Processing helix chain 'G' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU G 293 " --> pdb=" O PHE G 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG G 311 " --> pdb=" O GLU G 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 308 through 311' Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 318 through 323 Processing helix chain 'G' and resid 325 through 328 Processing helix chain 'G' and resid 329 through 344 removed outlier: 4.438A pdb=" N VAL G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 358 through 374 Processing helix chain 'I' and resid 2 through 18 Processing helix chain 'I' and resid 19 through 21 No H-bonds generated for 'chain 'I' and resid 19 through 21' Processing helix chain 'I' and resid 44 through 61 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 83 through 92 removed outlier: 4.075A pdb=" N LEU I 90 " --> pdb=" O ASN I 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 141 through 145 removed outlier: 4.038A pdb=" N GLY I 144 " --> pdb=" O ILE I 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 145 " --> pdb=" O ASN I 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 141 through 145' Processing helix chain 'I' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY I 154 " --> pdb=" O ALA I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS I 180 " --> pdb=" O VAL I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 202 Processing helix chain 'I' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET I 210 " --> pdb=" O ALA I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 225 Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 277 Processing helix chain 'I' and resid 282 through 287 Processing helix chain 'I' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU I 293 " --> pdb=" O PHE I 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY I 307 " --> pdb=" O TYR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 311 removed outlier: 3.910A pdb=" N ARG I 311 " --> pdb=" O GLU I 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 308 through 311' Processing helix chain 'I' and resid 312 through 317 Processing helix chain 'I' and resid 318 through 323 Processing helix chain 'I' and resid 325 through 328 Processing helix chain 'I' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL I 342 " --> pdb=" O GLY I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 350 Processing helix chain 'I' and resid 358 through 374 Processing helix chain 'K' and resid 2 through 18 Processing helix chain 'K' and resid 19 through 21 No H-bonds generated for 'chain 'K' and resid 19 through 21' Processing helix chain 'K' and resid 44 through 61 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 83 through 92 removed outlier: 4.075A pdb=" N LEU K 90 " --> pdb=" O ASN K 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA K 91 " --> pdb=" O HIS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY K 144 " --> pdb=" O ILE K 141 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR K 145 " --> pdb=" O ASN K 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 141 through 145' Processing helix chain 'K' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY K 154 " --> pdb=" O ALA K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS K 180 " --> pdb=" O VAL K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 202 Processing helix chain 'K' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET K 210 " --> pdb=" O ALA K 207 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 225 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 277 Processing helix chain 'K' and resid 282 through 287 Processing helix chain 'K' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU K 293 " --> pdb=" O PHE K 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG K 311 " --> pdb=" O GLU K 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 308 through 311' Processing helix chain 'K' and resid 312 through 317 Processing helix chain 'K' and resid 318 through 323 Processing helix chain 'K' and resid 325 through 328 Processing helix chain 'K' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL K 342 " --> pdb=" O GLY K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 350 Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'M' and resid 2 through 18 Processing helix chain 'M' and resid 19 through 21 No H-bonds generated for 'chain 'M' and resid 19 through 21' Processing helix chain 'M' and resid 44 through 61 Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 83 through 92 removed outlier: 4.075A pdb=" N LEU M 90 " --> pdb=" O ASN M 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 141 through 145 removed outlier: 4.038A pdb=" N GLY M 144 " --> pdb=" O ILE M 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR M 145 " --> pdb=" O ASN M 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 141 through 145' Processing helix chain 'M' and resid 150 through 155 removed outlier: 4.388A pdb=" N GLY M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS M 180 " --> pdb=" O VAL M 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 202 Processing helix chain 'M' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET M 210 " --> pdb=" O ALA M 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 225 Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 277 Processing helix chain 'M' and resid 282 through 287 Processing helix chain 'M' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU M 293 " --> pdb=" O PHE M 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 311 removed outlier: 3.910A pdb=" N ARG M 311 " --> pdb=" O GLU M 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 308 through 311' Processing helix chain 'M' and resid 312 through 317 Processing helix chain 'M' and resid 318 through 323 Processing helix chain 'M' and resid 325 through 328 Processing helix chain 'M' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL M 342 " --> pdb=" O GLY M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 350 Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'O' and resid 2 through 18 Processing helix chain 'O' and resid 19 through 21 No H-bonds generated for 'chain 'O' and resid 19 through 21' Processing helix chain 'O' and resid 44 through 61 Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU O 90 " --> pdb=" O ASN O 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA O 91 " --> pdb=" O HIS O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY O 144 " --> pdb=" O ILE O 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR O 145 " --> pdb=" O ASN O 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 141 through 145' Processing helix chain 'O' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY O 154 " --> pdb=" O ALA O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS O 180 " --> pdb=" O VAL O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 202 Processing helix chain 'O' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET O 210 " --> pdb=" O ALA O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 225 Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 248 through 262 removed outlier: 4.164A pdb=" N TYR O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 277 Processing helix chain 'O' and resid 282 through 287 Processing helix chain 'O' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU O 293 " --> pdb=" O PHE O 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY O 307 " --> pdb=" O TYR O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG O 311 " --> pdb=" O GLU O 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 308 through 311' Processing helix chain 'O' and resid 312 through 317 Processing helix chain 'O' and resid 318 through 323 Processing helix chain 'O' and resid 325 through 328 Processing helix chain 'O' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL O 342 " --> pdb=" O GLY O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 350 Processing helix chain 'O' and resid 358 through 374 Processing helix chain 'Q' and resid 2 through 18 Processing helix chain 'Q' and resid 19 through 21 No H-bonds generated for 'chain 'Q' and resid 19 through 21' Processing helix chain 'Q' and resid 44 through 61 Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 83 through 92 removed outlier: 4.075A pdb=" N LEU Q 90 " --> pdb=" O ASN Q 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA Q 91 " --> pdb=" O HIS Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY Q 144 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Q 145 " --> pdb=" O ASN Q 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 141 through 145' Processing helix chain 'Q' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS Q 180 " --> pdb=" O VAL Q 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 202 Processing helix chain 'Q' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET Q 210 " --> pdb=" O ALA Q 207 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 225 Processing helix chain 'Q' and resid 227 through 241 Processing helix chain 'Q' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR Q 260 " --> pdb=" O ASP Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 266 through 277 Processing helix chain 'Q' and resid 282 through 287 Processing helix chain 'Q' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU Q 293 " --> pdb=" O PHE Q 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY Q 307 " --> pdb=" O TYR Q 303 " (cutoff:3.500A) Processing helix chain 'Q' and resid 308 through 311 removed outlier: 3.910A pdb=" N ARG Q 311 " --> pdb=" O GLU Q 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 308 through 311' Processing helix chain 'Q' and resid 312 through 317 Processing helix chain 'Q' and resid 318 through 323 Processing helix chain 'Q' and resid 325 through 328 Processing helix chain 'Q' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL Q 342 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 350 Processing helix chain 'Q' and resid 358 through 374 Processing helix chain 'S' and resid 2 through 18 Processing helix chain 'S' and resid 19 through 21 No H-bonds generated for 'chain 'S' and resid 19 through 21' Processing helix chain 'S' and resid 44 through 61 Processing helix chain 'S' and resid 65 through 77 Processing helix chain 'S' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU S 90 " --> pdb=" O ASN S 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA S 91 " --> pdb=" O HIS S 87 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY S 144 " --> pdb=" O ILE S 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR S 145 " --> pdb=" O ASN S 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 141 through 145' Processing helix chain 'S' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY S 154 " --> pdb=" O ALA S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS S 180 " --> pdb=" O VAL S 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 202 Processing helix chain 'S' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET S 210 " --> pdb=" O ALA S 207 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 225 Processing helix chain 'S' and resid 227 through 241 Processing helix chain 'S' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR S 260 " --> pdb=" O ASP S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 266 through 277 Processing helix chain 'S' and resid 282 through 287 Processing helix chain 'S' and resid 289 through 307 removed outlier: 4.051A pdb=" N LEU S 293 " --> pdb=" O PHE S 289 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY S 307 " --> pdb=" O TYR S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG S 311 " --> pdb=" O GLU S 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 308 through 311' Processing helix chain 'S' and resid 312 through 317 Processing helix chain 'S' and resid 318 through 323 Processing helix chain 'S' and resid 325 through 328 Processing helix chain 'S' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 350 Processing helix chain 'S' and resid 358 through 374 Processing helix chain 'U' and resid 2 through 18 Processing helix chain 'U' and resid 19 through 21 No H-bonds generated for 'chain 'U' and resid 19 through 21' Processing helix chain 'U' and resid 44 through 61 Processing helix chain 'U' and resid 65 through 77 Processing helix chain 'U' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU U 90 " --> pdb=" O ASN U 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY U 144 " --> pdb=" O ILE U 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR U 145 " --> pdb=" O ASN U 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 141 through 145' Processing helix chain 'U' and resid 150 through 155 removed outlier: 4.388A pdb=" N GLY U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 180 removed outlier: 4.283A pdb=" N LYS U 180 " --> pdb=" O VAL U 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 202 Processing helix chain 'U' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET U 210 " --> pdb=" O ALA U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 225 Processing helix chain 'U' and resid 227 through 241 Processing helix chain 'U' and resid 248 through 262 removed outlier: 4.165A pdb=" N TYR U 260 " --> pdb=" O ASP U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 277 Processing helix chain 'U' and resid 282 through 287 Processing helix chain 'U' and resid 289 through 307 removed outlier: 4.050A pdb=" N LEU U 293 " --> pdb=" O PHE U 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY U 307 " --> pdb=" O TYR U 303 " (cutoff:3.500A) Processing helix chain 'U' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG U 311 " --> pdb=" O GLU U 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 308 through 311' Processing helix chain 'U' and resid 312 through 317 Processing helix chain 'U' and resid 318 through 323 Processing helix chain 'U' and resid 325 through 328 Processing helix chain 'U' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 345 through 350 Processing helix chain 'U' and resid 358 through 374 Processing helix chain 'W' and resid 2 through 18 Processing helix chain 'W' and resid 19 through 21 No H-bonds generated for 'chain 'W' and resid 19 through 21' Processing helix chain 'W' and resid 44 through 61 Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU W 90 " --> pdb=" O ASN W 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA W 91 " --> pdb=" O HIS W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 141 through 145 removed outlier: 4.037A pdb=" N GLY W 144 " --> pdb=" O ILE W 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR W 145 " --> pdb=" O ASN W 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 141 through 145' Processing helix chain 'W' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS W 180 " --> pdb=" O VAL W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 189 through 202 Processing helix chain 'W' and resid 206 through 210 removed outlier: 3.585A pdb=" N MET W 210 " --> pdb=" O ALA W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 225 Processing helix chain 'W' and resid 227 through 241 Processing helix chain 'W' and resid 248 through 262 removed outlier: 4.164A pdb=" N TYR W 260 " --> pdb=" O ASP W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 277 Processing helix chain 'W' and resid 282 through 287 Processing helix chain 'W' and resid 289 through 307 removed outlier: 4.050A pdb=" N LEU W 293 " --> pdb=" O PHE W 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY W 307 " --> pdb=" O TYR W 303 " (cutoff:3.500A) Processing helix chain 'W' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG W 311 " --> pdb=" O GLU W 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 308 through 311' Processing helix chain 'W' and resid 312 through 317 Processing helix chain 'W' and resid 318 through 323 Processing helix chain 'W' and resid 325 through 328 Processing helix chain 'W' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 350 Processing helix chain 'W' and resid 358 through 374 Processing helix chain 'Y' and resid 2 through 18 Processing helix chain 'Y' and resid 19 through 21 No H-bonds generated for 'chain 'Y' and resid 19 through 21' Processing helix chain 'Y' and resid 44 through 61 Processing helix chain 'Y' and resid 65 through 77 Processing helix chain 'Y' and resid 83 through 92 removed outlier: 4.076A pdb=" N LEU Y 90 " --> pdb=" O ASN Y 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA Y 91 " --> pdb=" O HIS Y 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 123 through 134 Processing helix chain 'Y' and resid 141 through 145 removed outlier: 4.038A pdb=" N GLY Y 144 " --> pdb=" O ILE Y 141 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR Y 145 " --> pdb=" O ASN Y 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 141 through 145' Processing helix chain 'Y' and resid 150 through 155 removed outlier: 4.389A pdb=" N GLY Y 154 " --> pdb=" O ALA Y 150 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 180 removed outlier: 4.284A pdb=" N LYS Y 180 " --> pdb=" O VAL Y 176 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 202 Processing helix chain 'Y' and resid 206 through 210 removed outlier: 3.586A pdb=" N MET Y 210 " --> pdb=" O ALA Y 207 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 225 Processing helix chain 'Y' and resid 227 through 241 Processing helix chain 'Y' and resid 248 through 262 removed outlier: 4.164A pdb=" N TYR Y 260 " --> pdb=" O ASP Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 277 Processing helix chain 'Y' and resid 282 through 287 Processing helix chain 'Y' and resid 289 through 307 removed outlier: 4.050A pdb=" N LEU Y 293 " --> pdb=" O PHE Y 289 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY Y 307 " --> pdb=" O TYR Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 308 through 311 removed outlier: 3.909A pdb=" N ARG Y 311 " --> pdb=" O GLU Y 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 308 through 311' Processing helix chain 'Y' and resid 312 through 317 Processing helix chain 'Y' and resid 318 through 323 Processing helix chain 'Y' and resid 325 through 328 Processing helix chain 'Y' and resid 329 through 344 removed outlier: 4.439A pdb=" N VAL Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 350 Processing helix chain 'Y' and resid 358 through 374 Processing sheet with id=1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE A 115 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'C' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE C 115 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'E' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE E 115 " --> pdb=" O ASP E 105 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'G' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE G 115 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'I' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE I 115 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'K' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE K 115 " --> pdb=" O ASP K 105 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'M' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE M 115 " --> pdb=" O ASP M 105 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'O' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE O 115 " --> pdb=" O ASP O 105 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'Q' and resid 36 through 40 removed outlier: 6.662A pdb=" N ILE Q 115 " --> pdb=" O ASP Q 105 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'S' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE S 115 " --> pdb=" O ASP S 105 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'U' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE U 115 " --> pdb=" O ASP U 105 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'W' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE W 115 " --> pdb=" O ASP W 105 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'Y' and resid 36 through 40 removed outlier: 6.661A pdb=" N ILE Y 115 " --> pdb=" O ASP Y 105 " (cutoff:3.500A) 2197 hydrogen bonds defined for protein. 6279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 8.08 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11665 1.33 - 1.45: 6789 1.45 - 1.57: 22093 1.57 - 1.69: 143 1.69 - 1.81: 403 Bond restraints: 41093 Sorted by residual: bond pdb=" C GLN C 155 " pdb=" N PRO C 156 " ideal model delta sigma weight residual 1.331 1.309 0.021 1.31e-02 5.83e+03 2.59e+00 bond pdb=" C GLN W 155 " pdb=" N PRO W 156 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.31e-02 5.83e+03 2.56e+00 bond pdb=" C GLN Q 155 " pdb=" N PRO Q 156 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.31e-02 5.83e+03 2.46e+00 bond pdb=" C GLN Y 155 " pdb=" N PRO Y 156 " ideal model delta sigma weight residual 1.331 1.310 0.021 1.31e-02 5.83e+03 2.45e+00 bond pdb=" C GLN A 155 " pdb=" N PRO A 156 " ideal model delta sigma weight residual 1.331 1.310 0.020 1.31e-02 5.83e+03 2.40e+00 ... (remaining 41088 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 49456 1.11 - 2.22: 5307 2.22 - 3.34: 841 3.34 - 4.45: 270 4.45 - 5.56: 78 Bond angle restraints: 55952 Sorted by residual: angle pdb=" C2' U X 21 " pdb=" C1' U X 21 " pdb=" N1 U X 21 " ideal model delta sigma weight residual 112.00 115.88 -3.88 1.50e+00 4.44e-01 6.68e+00 angle pdb=" C2' U R 21 " pdb=" C1' U R 21 " pdb=" N1 U R 21 " ideal model delta sigma weight residual 112.00 115.87 -3.87 1.50e+00 4.44e-01 6.64e+00 angle pdb=" C2' U V 21 " pdb=" C1' U V 21 " pdb=" N1 U V 21 " ideal model delta sigma weight residual 112.00 115.86 -3.86 1.50e+00 4.44e-01 6.64e+00 angle pdb=" C2' U P 21 " pdb=" C1' U P 21 " pdb=" N1 U P 21 " ideal model delta sigma weight residual 112.00 115.86 -3.86 1.50e+00 4.44e-01 6.62e+00 angle pdb=" C2' U F 21 " pdb=" C1' U F 21 " pdb=" N1 U F 21 " ideal model delta sigma weight residual 112.00 115.85 -3.85 1.50e+00 4.44e-01 6.57e+00 ... (remaining 55947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 21523 16.72 - 33.44: 2643 33.44 - 50.16: 378 50.16 - 66.88: 143 66.88 - 83.61: 104 Dihedral angle restraints: 24791 sinusoidal: 10595 harmonic: 14196 Sorted by residual: dihedral pdb=" CA ALA W 288 " pdb=" C ALA W 288 " pdb=" N PHE W 289 " pdb=" CA PHE W 289 " ideal model delta harmonic sigma weight residual -180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ALA M 288 " pdb=" C ALA M 288 " pdb=" N PHE M 289 " pdb=" CA PHE M 289 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ALA I 288 " pdb=" C ALA I 288 " pdb=" N PHE I 289 " pdb=" CA PHE I 289 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 24788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 4091 0.040 - 0.080: 1727 0.080 - 0.120: 374 0.120 - 0.160: 35 0.160 - 0.200: 13 Chirality restraints: 6240 Sorted by residual: chirality pdb=" C1' U H 21 " pdb=" O4' U H 21 " pdb=" C2' U H 21 " pdb=" N1 U H 21 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" C1' U R 21 " pdb=" O4' U R 21 " pdb=" C2' U R 21 " pdb=" N1 U R 21 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.90e-01 chirality pdb=" C1' U X 21 " pdb=" O4' U X 21 " pdb=" C2' U X 21 " pdb=" N1 U X 21 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.83e-01 ... (remaining 6237 not shown) Planarity restraints: 7059 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U Z 21 " 0.031 2.00e-02 2.50e+03 1.56e-02 5.45e+00 pdb=" N1 U Z 21 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U Z 21 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U Z 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U Z 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U Z 21 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U Z 21 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U Z 21 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U Z 21 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U J 21 " 0.030 2.00e-02 2.50e+03 1.55e-02 5.38e+00 pdb=" N1 U J 21 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U J 21 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U J 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U J 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U J 21 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U J 21 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U J 21 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U J 21 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U D 21 " 0.030 2.00e-02 2.50e+03 1.54e-02 5.36e+00 pdb=" N1 U D 21 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U D 21 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U D 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 U D 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U D 21 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U D 21 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U D 21 " -0.006 2.00e-02 2.50e+03 pdb=" C6 U D 21 " -0.003 2.00e-02 2.50e+03 ... (remaining 7056 not shown) Histogram of nonbonded interaction distances: 0.50 - 1.38: 195 1.38 - 2.26: 729 2.26 - 3.14: 37877 3.14 - 4.02: 108361 4.02 - 4.90: 197666 Warning: very small nonbonded interaction distances. Nonbonded interactions: 344828 Sorted by model distance: nonbonded pdb=" OE2 GLU Q 161 " pdb=" CB SER S 33 " model vdw 0.503 3.440 nonbonded pdb=" OE2 GLU M 161 " pdb=" CB SER O 33 " model vdw 0.503 3.440 nonbonded pdb=" OE2 GLU W 161 " pdb=" CB SER Y 33 " model vdw 0.504 3.440 nonbonded pdb=" OE2 GLU O 161 " pdb=" CB SER Q 33 " model vdw 0.504 3.440 nonbonded pdb=" OE2 GLU U 161 " pdb=" CB SER W 33 " model vdw 0.504 3.440 ... (remaining 344823 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.200 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 35.380 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.110 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 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 : 0.024 0.957 41132 Z= 2.358 Angle : 0.781 5.560 55952 Z= 0.461 Chirality : 0.044 0.200 6240 Planarity : 0.004 0.036 7059 Dihedral : 15.237 83.606 15717 Min Nonbonded Distance : 0.503 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.41 (0.10), residues: 4836 helix: -2.20 (0.08), residues: 2834 sheet: -1.78 (0.39), residues: 156 loop : -2.15 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 10 TYR 0.016 0.002 TYR O 361 PHE 0.017 0.002 PHE G 8 TRP 0.010 0.002 TRP M 175 HIS 0.002 0.001 HIS W 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.29 (41093) covalent geometry : angle 0.78076 / 0.46 (55952) hydrogen bonds : bond 0.13572 / 8.93 ( 2197) hydrogen bonds : angle 6.38915 / 4.56 ( 6279) Misc. bond : bond 0.76005 / 51.15 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1064 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8312 (tptp) REVERT: A 253 MET cc_start: 0.7878 (tpt) cc_final: 0.7556 (tpt) REVERT: A 256 ASP cc_start: 0.8592 (t0) cc_final: 0.8224 (t0) REVERT: A 297 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8691 (ttp80) REVERT: A 301 MET cc_start: 0.9005 (mtm) cc_final: 0.8450 (mpp) REVERT: C 6 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8351 (tptp) REVERT: C 162 GLN cc_start: 0.8797 (mt0) cc_final: 0.8540 (tp-100) REVERT: C 297 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8556 (ttp80) REVERT: C 301 MET cc_start: 0.8980 (mtm) cc_final: 0.8486 (mpp) REVERT: E 6 LYS cc_start: 0.8639 (tmtt) cc_final: 0.8419 (tptp) REVERT: E 256 ASP cc_start: 0.8589 (t0) cc_final: 0.8221 (t0) REVERT: E 297 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8546 (ttp80) REVERT: E 301 MET cc_start: 0.8983 (mtm) cc_final: 0.8488 (mpp) REVERT: G 6 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8327 (tptp) REVERT: G 297 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8631 (ttp80) REVERT: G 301 MET cc_start: 0.8988 (mtm) cc_final: 0.8479 (mpp) REVERT: I 6 LYS cc_start: 0.8653 (tmtt) cc_final: 0.8344 (tptp) REVERT: I 297 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8651 (ttp80) REVERT: I 301 MET cc_start: 0.8981 (mtm) cc_final: 0.8480 (mpp) REVERT: K 297 ARG cc_start: 0.9029 (ttp80) cc_final: 0.8722 (ttp80) REVERT: K 301 MET cc_start: 0.8986 (mtm) cc_final: 0.8467 (mpp) REVERT: M 6 LYS cc_start: 0.8632 (tmtt) cc_final: 0.8350 (tptp) REVERT: M 253 MET cc_start: 0.7823 (tpt) cc_final: 0.7567 (tpt) REVERT: M 297 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8645 (ttp80) REVERT: M 301 MET cc_start: 0.8986 (mtm) cc_final: 0.8460 (mpp) REVERT: O 6 LYS cc_start: 0.8661 (tmtt) cc_final: 0.8415 (tptp) REVERT: O 297 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8586 (ttp80) REVERT: O 301 MET cc_start: 0.8977 (mtm) cc_final: 0.8490 (mpp) REVERT: Q 6 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8353 (tptp) REVERT: Q 297 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8678 (ttp80) REVERT: Q 301 MET cc_start: 0.8989 (mtm) cc_final: 0.8461 (mpp) REVERT: Q 309 GLN cc_start: 0.8536 (mt0) cc_final: 0.8332 (mp10) REVERT: S 6 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8411 (tptp) REVERT: S 200 GLN cc_start: 0.9009 (mt0) cc_final: 0.8665 (mm110) REVERT: S 297 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8575 (ttp80) REVERT: S 301 MET cc_start: 0.8980 (mtm) cc_final: 0.8503 (mpp) REVERT: U 6 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8346 (tptp) REVERT: U 200 GLN cc_start: 0.9003 (mt0) cc_final: 0.8662 (mm110) REVERT: U 297 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8565 (ttp80) REVERT: U 301 MET cc_start: 0.8978 (mtm) cc_final: 0.8479 (mpp) REVERT: W 6 LYS cc_start: 0.8666 (tmtt) cc_final: 0.8360 (tptp) REVERT: W 200 GLN cc_start: 0.9001 (mt0) cc_final: 0.8517 (mm110) REVERT: W 297 ARG cc_start: 0.9027 (ttp80) cc_final: 0.8636 (ttp80) REVERT: W 301 MET cc_start: 0.8990 (mtm) cc_final: 0.8498 (mpp) REVERT: Y 200 GLN cc_start: 0.9039 (mt0) cc_final: 0.8570 (mm110) REVERT: Y 297 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8670 (ttp80) REVERT: Y 301 MET cc_start: 0.8987 (mtm) cc_final: 0.8443 (mpp) outliers start: 0 outliers final: 0 residues processed: 1064 average time/residue: 0.2922 time to fit residues: 476.5854 Evaluate side-chains 774 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 774 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 125 ASN A 212 GLN A 231 GLN A 346 GLN A 373 GLN C 68 HIS C 125 ASN C 212 GLN C 231 GLN C 346 GLN C 373 GLN E 68 HIS E 125 ASN E 212 GLN E 231 GLN E 346 GLN E 373 GLN G 68 HIS G 125 ASN G 162 GLN G 212 GLN G 231 GLN G 346 GLN G 373 GLN I 68 HIS I 125 ASN I 212 GLN I 231 GLN I 346 GLN I 373 GLN K 68 HIS K 125 ASN K 212 GLN K 346 GLN K 373 GLN M 68 HIS M 125 ASN M 212 GLN M 238 GLN M 346 GLN M 373 GLN O 125 ASN O 212 GLN O 231 GLN O 346 GLN O 373 GLN Q 68 HIS Q 212 GLN Q 346 GLN Q 373 GLN S 68 HIS S 125 ASN S 212 GLN S 346 GLN S 373 GLN U 68 HIS U 125 ASN U 212 GLN U 346 GLN U 373 GLN W 212 GLN W 231 GLN W 346 GLN W 373 GLN Y 68 HIS Y 125 ASN Y 212 GLN Y 231 GLN Y 346 GLN Y 373 GLN Total number of N/Q/H flips: 71 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.080760 restraints weight = 106061.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083962 restraints weight = 55278.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.086208 restraints weight = 35892.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087788 restraints weight = 26185.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088957 restraints weight = 20552.768| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41132 Z= 0.158 Angle : 0.674 6.942 55952 Z= 0.356 Chirality : 0.046 0.274 6240 Planarity : 0.009 0.187 7059 Dihedral : 5.689 36.867 6396 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 14.00 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.11), residues: 4836 helix: -0.34 (0.09), residues: 2899 sheet: -1.10 (0.45), residues: 156 loop : -1.41 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 242 TYR 0.028 0.002 TYR Q 251 PHE 0.018 0.002 PHE Q 270 TRP 0.004 0.001 TRP K 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (41093) covalent geometry : angle 0.67419 / 0.36 (55952) hydrogen bonds : bond 0.04581 / 3.04 ( 2197) hydrogen bonds : angle 4.83346 / 3.43 ( 6279) Misc. bond : bond 0.00397 / 0.28 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 956 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7907 (tpt) cc_final: 0.7583 (tpt) REVERT: A 256 ASP cc_start: 0.8785 (t0) cc_final: 0.8538 (t0) REVERT: A 301 MET cc_start: 0.8753 (mtm) cc_final: 0.8420 (mtt) REVERT: A 309 GLN cc_start: 0.8220 (mp10) cc_final: 0.7918 (mp10) REVERT: C 10 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7930 (ttp-110) REVERT: C 199 TYR cc_start: 0.8411 (m-10) cc_final: 0.8008 (m-80) REVERT: C 256 ASP cc_start: 0.8789 (t0) cc_final: 0.8086 (t0) REVERT: C 297 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8578 (mtp-110) REVERT: C 301 MET cc_start: 0.8710 (mtm) cc_final: 0.8468 (mpp) REVERT: E 200 GLN cc_start: 0.8831 (mt0) cc_final: 0.8589 (mm110) REVERT: E 256 ASP cc_start: 0.8803 (t0) cc_final: 0.8497 (t0) REVERT: E 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8550 (ttp80) REVERT: E 301 MET cc_start: 0.8738 (mtm) cc_final: 0.8449 (mpp) REVERT: E 309 GLN cc_start: 0.8257 (mp10) cc_final: 0.7943 (mp10) REVERT: G 200 GLN cc_start: 0.8845 (mt0) cc_final: 0.8543 (mm110) REVERT: G 256 ASP cc_start: 0.8743 (t0) cc_final: 0.8013 (t0) REVERT: G 297 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8652 (ttp80) REVERT: G 301 MET cc_start: 0.8732 (mtm) cc_final: 0.8464 (mpp) REVERT: G 309 GLN cc_start: 0.8270 (mp10) cc_final: 0.7849 (mp10) REVERT: I 6 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8643 (tptp) REVERT: I 256 ASP cc_start: 0.8807 (t0) cc_final: 0.8500 (t0) REVERT: I 297 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8659 (ttp80) REVERT: I 301 MET cc_start: 0.8718 (mtm) cc_final: 0.8449 (mpp) REVERT: K 200 GLN cc_start: 0.8835 (mt0) cc_final: 0.8571 (mm110) REVERT: K 256 ASP cc_start: 0.8799 (t0) cc_final: 0.8507 (t0) REVERT: K 297 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8692 (ttp80) REVERT: K 301 MET cc_start: 0.8764 (mtm) cc_final: 0.8443 (mpp) REVERT: M 161 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8201 (tm-30) REVERT: M 297 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8704 (ttp80) REVERT: M 301 MET cc_start: 0.8719 (mtm) cc_final: 0.8409 (mpp) REVERT: O 256 ASP cc_start: 0.8777 (t0) cc_final: 0.8496 (t0) REVERT: O 274 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8628 (tttt) REVERT: O 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8572 (mtp-110) REVERT: O 301 MET cc_start: 0.8727 (mtm) cc_final: 0.8444 (mpp) REVERT: Q 256 ASP cc_start: 0.8804 (t0) cc_final: 0.8087 (t0) REVERT: Q 274 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8590 (tttt) REVERT: Q 297 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8612 (mtp-110) REVERT: Q 301 MET cc_start: 0.8734 (mtm) cc_final: 0.8432 (mpp) REVERT: S 253 MET cc_start: 0.7936 (tpt) cc_final: 0.5697 (tpt) REVERT: S 256 ASP cc_start: 0.8799 (t0) cc_final: 0.8105 (t0) REVERT: S 274 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8618 (tttt) REVERT: S 297 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8476 (mtm110) REVERT: S 301 MET cc_start: 0.8740 (mtm) cc_final: 0.8434 (mpp) REVERT: U 199 TYR cc_start: 0.8415 (m-10) cc_final: 0.7949 (m-10) REVERT: U 200 GLN cc_start: 0.8793 (mt0) cc_final: 0.8547 (mm110) REVERT: U 256 ASP cc_start: 0.8793 (t0) cc_final: 0.8005 (t0) REVERT: U 274 LYS cc_start: 0.8847 (ttpp) cc_final: 0.8596 (tttt) REVERT: U 297 ARG cc_start: 0.9017 (ttp80) cc_final: 0.8570 (mtp-110) REVERT: U 301 MET cc_start: 0.8738 (mtm) cc_final: 0.8476 (mpp) REVERT: W 161 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8142 (tm-30) REVERT: W 199 TYR cc_start: 0.8441 (m-10) cc_final: 0.8122 (m-80) REVERT: W 256 ASP cc_start: 0.8807 (t0) cc_final: 0.8029 (t0) REVERT: W 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8606 (mtp-110) REVERT: W 301 MET cc_start: 0.8758 (mtm) cc_final: 0.8464 (mpp) REVERT: W 309 GLN cc_start: 0.8184 (mp10) cc_final: 0.7771 (mp10) REVERT: Y 256 ASP cc_start: 0.8765 (t0) cc_final: 0.8456 (t0) REVERT: Y 297 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8667 (ttp80) REVERT: Y 301 MET cc_start: 0.8763 (mtm) cc_final: 0.8390 (mpp) REVERT: Y 309 GLN cc_start: 0.8230 (mp10) cc_final: 0.7917 (mp10) outliers start: 59 outliers final: 26 residues processed: 983 average time/residue: 0.2635 time to fit residues: 412.4950 Evaluate side-chains 830 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 804 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 157 CYS Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 238 GLN Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 157 CYS Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain Y residue 185 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 134 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 416 optimal weight: 7.9990 chunk 408 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 203 optimal weight: 0.1980 chunk 113 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 117 optimal weight: 0.0270 chunk 434 optimal weight: 2.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS A 212 GLN C 212 GLN E 87 HIS E 212 GLN E 238 GLN G 87 HIS G 212 GLN I 87 HIS I 212 GLN K 87 HIS K 212 GLN M 87 HIS M 212 GLN O 87 HIS O 212 GLN Q 87 HIS Q 212 GLN S 87 HIS S 212 GLN U 87 HIS U 212 GLN W 87 HIS W 212 GLN W 263 ASN Y 87 HIS Y 212 GLN Y 263 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.101503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086583 restraints weight = 104635.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089549 restraints weight = 55825.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091647 restraints weight = 36544.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093146 restraints weight = 26748.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.094300 restraints weight = 20851.262| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41132 Z= 0.126 Angle : 0.605 7.863 55952 Z= 0.311 Chirality : 0.043 0.252 6240 Planarity : 0.007 0.130 7059 Dihedral : 5.232 31.948 6396 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.38 % Allowed : 15.88 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.12), residues: 4836 helix: 0.29 (0.10), residues: 2951 sheet: -0.69 (0.46), residues: 156 loop : -1.03 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 10 TYR 0.018 0.001 TYR G 251 PHE 0.014 0.001 PHE K 270 TRP 0.015 0.002 TRP M 281 HIS 0.002 0.000 HIS O 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (41093) covalent geometry : angle 0.60460 / 0.31 (55952) hydrogen bonds : bond 0.04046 / 2.68 ( 2197) hydrogen bonds : angle 4.53520 / 3.22 ( 6279) Misc. bond : bond 0.00363 / 0.26 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 883 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TYR cc_start: 0.8280 (m-10) cc_final: 0.7963 (m-10) REVERT: A 256 ASP cc_start: 0.8751 (t0) cc_final: 0.8084 (t0) REVERT: A 309 GLN cc_start: 0.8358 (mp10) cc_final: 0.8062 (mp10) REVERT: C 161 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 199 TYR cc_start: 0.8337 (m-80) cc_final: 0.8133 (m-80) REVERT: C 256 ASP cc_start: 0.8723 (t0) cc_final: 0.8173 (t0) REVERT: C 289 PHE cc_start: 0.8257 (m-80) cc_final: 0.7999 (m-10) REVERT: C 297 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8593 (mtp-110) REVERT: C 311 ARG cc_start: 0.6929 (mtm-85) cc_final: 0.6649 (mtm110) REVERT: C 322 MET cc_start: 0.8195 (mmm) cc_final: 0.7993 (tpt) REVERT: E 161 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8020 (tm-30) REVERT: E 165 ASP cc_start: 0.8485 (m-30) cc_final: 0.7566 (m-30) REVERT: E 253 MET cc_start: 0.7772 (tpt) cc_final: 0.6398 (tpt) REVERT: E 256 ASP cc_start: 0.8722 (t0) cc_final: 0.8026 (t0) REVERT: E 289 PHE cc_start: 0.8322 (m-80) cc_final: 0.7725 (m-10) REVERT: E 297 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8577 (mtp-110) REVERT: E 309 GLN cc_start: 0.8362 (mp10) cc_final: 0.8044 (mp10) REVERT: E 322 MET cc_start: 0.8212 (mmm) cc_final: 0.8004 (tpt) REVERT: G 200 GLN cc_start: 0.8730 (mt0) cc_final: 0.8466 (mm110) REVERT: G 297 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8584 (mtp-110) REVERT: G 309 GLN cc_start: 0.8401 (mp10) cc_final: 0.8082 (mp10) REVERT: G 347 MET cc_start: 0.8378 (ttp) cc_final: 0.8169 (ttp) REVERT: I 165 ASP cc_start: 0.8016 (m-30) cc_final: 0.7581 (m-30) REVERT: I 253 MET cc_start: 0.7775 (tpt) cc_final: 0.6745 (tpt) REVERT: I 289 PHE cc_start: 0.8270 (m-80) cc_final: 0.8020 (m-10) REVERT: I 297 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8614 (mtp-110) REVERT: K 256 ASP cc_start: 0.8751 (t0) cc_final: 0.8440 (t0) REVERT: K 297 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8641 (mtp-110) REVERT: M 297 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8516 (mtp-110) REVERT: O 161 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7597 (tm-30) REVERT: O 253 MET cc_start: 0.7672 (tpt) cc_final: 0.7356 (tpt) REVERT: O 256 ASP cc_start: 0.8730 (t0) cc_final: 0.8515 (t0) REVERT: O 297 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8590 (mtp-110) REVERT: Q 161 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7598 (tm-30) REVERT: Q 297 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8645 (mtp-110) REVERT: Q 309 GLN cc_start: 0.8268 (mp10) cc_final: 0.7999 (mp10) REVERT: S 161 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7616 (tm-30) REVERT: S 165 ASP cc_start: 0.7908 (m-30) cc_final: 0.7548 (m-30) REVERT: S 274 LYS cc_start: 0.8873 (ttpp) cc_final: 0.8670 (tttt) REVERT: S 297 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8549 (mtp-110) REVERT: S 322 MET cc_start: 0.8278 (mmm) cc_final: 0.8056 (tpt) REVERT: U 161 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7624 (tm-30) REVERT: U 165 ASP cc_start: 0.7940 (m-30) cc_final: 0.7607 (m-30) REVERT: U 256 ASP cc_start: 0.8740 (t0) cc_final: 0.8048 (t0) REVERT: U 297 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8587 (mtp-110) REVERT: U 322 MET cc_start: 0.8285 (mmm) cc_final: 0.8078 (tpt) REVERT: W 165 ASP cc_start: 0.8469 (m-30) cc_final: 0.7441 (m-30) REVERT: W 297 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8557 (mtp-110) REVERT: W 309 GLN cc_start: 0.8303 (mp10) cc_final: 0.7905 (mp10) REVERT: W 322 MET cc_start: 0.8148 (mmm) cc_final: 0.7935 (tpt) REVERT: Y 253 MET cc_start: 0.7756 (tpt) cc_final: 0.6092 (tpt) REVERT: Y 256 ASP cc_start: 0.8735 (t0) cc_final: 0.7984 (t0) REVERT: Y 289 PHE cc_start: 0.8331 (m-80) cc_final: 0.8074 (m-10) REVERT: Y 297 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8566 (mtp-110) REVERT: Y 309 GLN cc_start: 0.8350 (mp10) cc_final: 0.8051 (mp10) REVERT: Y 322 MET cc_start: 0.8168 (mmm) cc_final: 0.7964 (tpt) outliers start: 137 outliers final: 77 residues processed: 953 average time/residue: 0.2708 time to fit residues: 410.2147 Evaluate side-chains 883 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 806 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 238 GLN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 339 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 339 VAL Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 157 CYS Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 339 VAL Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 157 CYS Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 157 CYS Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 157 CYS Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 253 MET Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 339 VAL Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 157 CYS Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain Y residue 92 ASP Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 339 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 417 optimal weight: 5.9990 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 470 optimal weight: 4.9990 chunk 100 optimal weight: 0.0370 chunk 336 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 296 optimal weight: 4.9990 chunk 440 optimal weight: 3.9990 chunk 461 optimal weight: 2.9990 chunk 448 optimal weight: 0.6980 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 63 ASN A 263 ASN C 63 ASN E 18 GLN E 63 ASN E 238 GLN G 18 GLN G 63 ASN G 263 ASN I 18 GLN I 63 ASN I 263 ASN K 18 GLN K 63 ASN K 263 ASN M 18 GLN M 63 ASN O 18 GLN O 63 ASN Q 18 GLN Q 63 ASN Q 263 ASN S 18 GLN S 63 ASN S 263 ASN U 18 GLN U 63 ASN U 263 ASN W 18 GLN W 63 ASN W 263 ASN Y 18 GLN Y 63 ASN Y 238 GLN Y 263 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.099812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084332 restraints weight = 106353.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087312 restraints weight = 57088.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089429 restraints weight = 37729.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.090957 restraints weight = 27787.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092079 restraints weight = 21841.774| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 41132 Z= 0.166 Angle : 0.748 15.568 55952 Z= 0.374 Chirality : 0.046 0.508 6240 Planarity : 0.007 0.136 7059 Dihedral : 5.444 40.943 6396 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.25 % Allowed : 18.10 % Favored : 78.65 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4836 helix: 0.31 (0.10), residues: 2964 sheet: -0.61 (0.46), residues: 156 loop : -0.88 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 10 TYR 0.017 0.001 TYR Y 275 PHE 0.028 0.002 PHE M 289 TRP 0.045 0.003 TRP K 281 HIS 0.002 0.000 HIS W 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (41093) covalent geometry : angle 0.74760 / 0.37 (55952) hydrogen bonds : bond 0.04257 / 2.83 ( 2197) hydrogen bonds : angle 4.56177 / 3.23 ( 6279) Misc. bond : bond 0.00429 / 0.29 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 814 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 161 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7505 (tm-30) REVERT: C 165 ASP cc_start: 0.8127 (m-30) cc_final: 0.7505 (m-30) REVERT: C 256 ASP cc_start: 0.8725 (t0) cc_final: 0.8108 (t0) REVERT: C 297 ARG cc_start: 0.9165 (ttp80) cc_final: 0.8712 (mtp-110) REVERT: C 301 MET cc_start: 0.8779 (mpp) cc_final: 0.8176 (mpp) REVERT: C 322 MET cc_start: 0.8269 (mmm) cc_final: 0.8013 (tpt) REVERT: E 84 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6758 (ttp) REVERT: E 161 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8188 (tm-30) REVERT: E 256 ASP cc_start: 0.8535 (t0) cc_final: 0.8256 (t0) REVERT: E 274 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8575 (tttt) REVERT: E 297 ARG cc_start: 0.9147 (ttp80) cc_final: 0.8753 (mtp-110) REVERT: E 301 MET cc_start: 0.8757 (mpp) cc_final: 0.8165 (mpp) REVERT: G 200 GLN cc_start: 0.8773 (mt0) cc_final: 0.8465 (mm110) REVERT: G 297 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8703 (mtp-110) REVERT: G 301 MET cc_start: 0.8785 (mpp) cc_final: 0.8177 (mpp) REVERT: I 256 ASP cc_start: 0.8579 (t0) cc_final: 0.8295 (t0) REVERT: I 297 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8741 (mtp-110) REVERT: I 301 MET cc_start: 0.8725 (mpp) cc_final: 0.8173 (mpp) REVERT: K 161 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7587 (tm-30) REVERT: K 165 ASP cc_start: 0.7991 (m-30) cc_final: 0.7675 (m-30) REVERT: K 256 ASP cc_start: 0.8738 (t0) cc_final: 0.8419 (t0) REVERT: K 297 ARG cc_start: 0.9144 (ttp80) cc_final: 0.8912 (mtp-110) REVERT: M 161 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7578 (tm-30) REVERT: M 256 ASP cc_start: 0.8619 (t0) cc_final: 0.8416 (t0) REVERT: M 297 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8853 (mtp-110) REVERT: O 4 VAL cc_start: 0.8791 (p) cc_final: 0.8581 (p) REVERT: O 161 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7575 (tm-30) REVERT: O 253 MET cc_start: 0.7652 (tpt) cc_final: 0.7393 (tpt) REVERT: O 256 ASP cc_start: 0.8740 (t0) cc_final: 0.8526 (t0) REVERT: Q 161 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7625 (tm-30) REVERT: Q 297 ARG cc_start: 0.9154 (ttp80) cc_final: 0.8918 (mtp-110) REVERT: Q 309 GLN cc_start: 0.8349 (mp10) cc_final: 0.8002 (mp10) REVERT: S 161 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7557 (tm-30) REVERT: S 165 ASP cc_start: 0.7960 (m-30) cc_final: 0.7479 (m-30) REVERT: U 161 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7534 (tm-30) REVERT: U 165 ASP cc_start: 0.8060 (m-30) cc_final: 0.7585 (m-30) REVERT: U 297 ARG cc_start: 0.9141 (ttp80) cc_final: 0.8918 (mtp-110) REVERT: W 161 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7667 (tm-30) REVERT: W 256 ASP cc_start: 0.8545 (t0) cc_final: 0.8272 (t0) REVERT: W 295 LYS cc_start: 0.8803 (tptm) cc_final: 0.8526 (tptm) REVERT: W 297 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8889 (mtp-110) REVERT: W 322 MET cc_start: 0.8256 (mmm) cc_final: 0.8031 (tpt) REVERT: Y 161 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7599 (tm-30) REVERT: Y 256 ASP cc_start: 0.8488 (t0) cc_final: 0.8269 (t0) REVERT: Y 297 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8655 (mtp-110) REVERT: Y 301 MET cc_start: 0.8762 (mpp) cc_final: 0.8218 (mpp) REVERT: Y 322 MET cc_start: 0.8275 (mmm) cc_final: 0.8059 (tpt) outliers start: 132 outliers final: 85 residues processed: 882 average time/residue: 0.2658 time to fit residues: 374.3946 Evaluate side-chains 845 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 759 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 238 GLN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 253 MET Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 157 CYS Chi-restraints excluded: chain M residue 170 VAL Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 289 PHE Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 157 CYS Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 157 CYS Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 253 MET Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 279 THR Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 157 CYS Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 289 PHE Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 238 GLN Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 261 ILE Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 422 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 415 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 chunk 443 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 319 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 306 optimal weight: 3.9990 chunk 357 optimal weight: 9.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 263 ASN E 63 ASN G 263 ASN I 263 ASN K 263 ASN M 263 ASN Q 63 ASN Q 263 ASN S 63 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.099858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084193 restraints weight = 105327.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087326 restraints weight = 56427.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089485 restraints weight = 37015.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.091065 restraints weight = 27165.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092217 restraints weight = 21304.606| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 41132 Z= 0.142 Angle : 0.741 23.954 55952 Z= 0.372 Chirality : 0.044 0.433 6240 Planarity : 0.007 0.131 7059 Dihedral : 5.534 55.627 6396 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 19.03 % Favored : 77.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.06 (0.12), residues: 4836 helix: 0.51 (0.10), residues: 2964 sheet: -0.19 (0.42), residues: 182 loop : -0.87 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 230 TYR 0.014 0.001 TYR S 275 PHE 0.030 0.002 PHE Y 289 TRP 0.033 0.002 TRP K 281 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (41093) covalent geometry : angle 0.74083 / 0.37 (55952) hydrogen bonds : bond 0.03948 / 2.62 ( 2197) hydrogen bonds : angle 4.48126 / 3.18 ( 6279) Misc. bond : bond 0.00585 / 0.43 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 803 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7725 (tm-30) REVERT: C 1 MET cc_start: 0.5886 (mmm) cc_final: 0.5591 (mmp) REVERT: C 161 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7492 (tm-30) REVERT: C 256 ASP cc_start: 0.8597 (t0) cc_final: 0.8313 (t0) REVERT: C 297 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8888 (mtp-110) REVERT: E 1 MET cc_start: 0.5842 (mmm) cc_final: 0.5575 (mmp) REVERT: E 161 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8000 (tm-30) REVERT: E 165 ASP cc_start: 0.8540 (m-30) cc_final: 0.7675 (m-30) REVERT: E 256 ASP cc_start: 0.8516 (t0) cc_final: 0.8236 (t0) REVERT: E 274 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8538 (tttt) REVERT: E 297 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8937 (mtp-110) REVERT: G 1 MET cc_start: 0.5778 (mmm) cc_final: 0.5217 (mmp) REVERT: G 200 GLN cc_start: 0.8761 (mt0) cc_final: 0.8431 (mm110) REVERT: G 297 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8909 (mtp-110) REVERT: I 161 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7565 (tm-30) REVERT: I 165 ASP cc_start: 0.8020 (m-30) cc_final: 0.7677 (m-30) REVERT: I 256 ASP cc_start: 0.8589 (t0) cc_final: 0.8322 (t0) REVERT: I 297 ARG cc_start: 0.9173 (ttp80) cc_final: 0.8964 (mtp-110) REVERT: K 161 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7521 (tm-30) REVERT: K 165 ASP cc_start: 0.8030 (m-30) cc_final: 0.7564 (m-30) REVERT: K 256 ASP cc_start: 0.8725 (t0) cc_final: 0.8434 (t0) REVERT: K 297 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8869 (mtp-110) REVERT: K 301 MET cc_start: 0.8765 (mpp) cc_final: 0.8207 (mtm) REVERT: M 161 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7454 (tm-30) REVERT: M 256 ASP cc_start: 0.8627 (t0) cc_final: 0.8419 (t0) REVERT: M 297 ARG cc_start: 0.9106 (ttp80) cc_final: 0.8840 (mtp-110) REVERT: O 4 VAL cc_start: 0.8734 (p) cc_final: 0.8515 (p) REVERT: O 161 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7526 (tm-30) REVERT: O 253 MET cc_start: 0.7646 (tpt) cc_final: 0.7430 (tpt) REVERT: O 256 ASP cc_start: 0.8734 (t0) cc_final: 0.8521 (t0) REVERT: Q 161 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7581 (tm-30) REVERT: Q 297 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8600 (mtp-110) REVERT: Q 301 MET cc_start: 0.8629 (mtm) cc_final: 0.8360 (mpp) REVERT: U 161 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7460 (tm-30) REVERT: U 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7502 (m-30) REVERT: W 161 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7482 (tm-30) REVERT: W 165 ASP cc_start: 0.8190 (m-30) cc_final: 0.7434 (m-30) REVERT: W 256 ASP cc_start: 0.8586 (t0) cc_final: 0.8301 (t0) REVERT: W 297 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8735 (mtp-110) REVERT: W 301 MET cc_start: 0.8608 (mtm) cc_final: 0.8359 (mpp) REVERT: W 322 MET cc_start: 0.8252 (mmm) cc_final: 0.8029 (tpt) REVERT: Y 161 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7469 (tm-30) REVERT: Y 238 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7539 (pp30) REVERT: Y 256 ASP cc_start: 0.8510 (t0) cc_final: 0.8289 (t0) REVERT: Y 297 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8884 (mtp-110) outliers start: 130 outliers final: 94 residues processed: 864 average time/residue: 0.2672 time to fit residues: 368.9973 Evaluate side-chains 849 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 754 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 157 CYS Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 263 ASN Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 301 MET Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 157 CYS Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 157 CYS Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 238 GLN Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 379 optimal weight: 0.2980 chunk 307 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 265 optimal weight: 0.0670 chunk 326 optimal weight: 0.6980 chunk 452 optimal weight: 5.9990 chunk 436 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 87 HIS C 212 GLN C 263 ASN E 63 ASN G 63 ASN I 63 ASN M 63 ASN S 63 ASN U 238 GLN Y 238 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085814 restraints weight = 104830.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088998 restraints weight = 55717.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091243 restraints weight = 36489.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.092828 restraints weight = 26603.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093994 restraints weight = 20848.866| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 41132 Z= 0.132 Angle : 0.707 25.598 55952 Z= 0.350 Chirality : 0.042 0.362 6240 Planarity : 0.007 0.129 7059 Dihedral : 5.541 49.747 6396 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.08 % Allowed : 19.58 % Favored : 77.34 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 0.06 (0.12), residues: 4836 helix: 0.59 (0.10), residues: 2977 sheet: -0.11 (0.41), residues: 182 loop : -0.80 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 230 TYR 0.014 0.001 TYR Q 250 PHE 0.024 0.001 PHE Y 289 TRP 0.033 0.002 TRP I 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (41093) covalent geometry : angle 0.70743 / 0.35 (55952) hydrogen bonds : bond 0.03756 / 2.49 ( 2197) hydrogen bonds : angle 4.35415 / 3.09 ( 6279) Misc. bond : bond 0.00549 / 0.40 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 787 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5582 (mmm) cc_final: 0.5365 (mmp) REVERT: A 161 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7761 (tm-30) REVERT: C 161 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 165 ASP cc_start: 0.8190 (m-30) cc_final: 0.7423 (m-30) REVERT: C 256 ASP cc_start: 0.8593 (t0) cc_final: 0.8331 (t0) REVERT: C 297 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8598 (mtp-110) REVERT: C 301 MET cc_start: 0.8788 (mpp) cc_final: 0.8228 (mpp) REVERT: C 309 GLN cc_start: 0.8446 (mp10) cc_final: 0.8106 (mp10) REVERT: E 1 MET cc_start: 0.5945 (mmm) cc_final: 0.5572 (mmp) REVERT: E 161 GLU cc_start: 0.8471 (mm-30) cc_final: 0.7927 (tm-30) REVERT: E 165 ASP cc_start: 0.8536 (m-30) cc_final: 0.7338 (m-30) REVERT: E 256 ASP cc_start: 0.8543 (t0) cc_final: 0.8268 (t0) REVERT: E 297 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8541 (mtp-110) REVERT: E 301 MET cc_start: 0.8789 (mpp) cc_final: 0.8240 (mpp) REVERT: G 161 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7555 (tm-30) REVERT: G 165 ASP cc_start: 0.7761 (m-30) cc_final: 0.7334 (m-30) REVERT: G 200 GLN cc_start: 0.8788 (mt0) cc_final: 0.8428 (mm110) REVERT: G 297 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8871 (mtp-110) REVERT: I 256 ASP cc_start: 0.8605 (t0) cc_final: 0.8336 (t0) REVERT: I 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8819 (mtm110) REVERT: K 16 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7731 (mm-30) REVERT: K 161 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7478 (tm-30) REVERT: K 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7486 (m-30) REVERT: K 256 ASP cc_start: 0.8706 (t0) cc_final: 0.8437 (t0) REVERT: K 297 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8817 (mtm110) REVERT: M 16 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7791 (mm-30) REVERT: M 161 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7488 (tm-30) REVERT: M 256 ASP cc_start: 0.8649 (t0) cc_final: 0.8341 (t0) REVERT: O 161 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7502 (tm-30) REVERT: O 256 ASP cc_start: 0.8724 (t0) cc_final: 0.8488 (t0) REVERT: O 301 MET cc_start: 0.8630 (mtm) cc_final: 0.8319 (mpp) REVERT: Q 161 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7579 (tm-30) REVERT: Q 297 ARG cc_start: 0.9082 (ttp80) cc_final: 0.8629 (mtp-110) REVERT: Q 309 GLN cc_start: 0.8401 (mp10) cc_final: 0.8155 (mp10) REVERT: S 161 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7627 (tm-30) REVERT: S 165 ASP cc_start: 0.8124 (m-30) cc_final: 0.7499 (m-30) REVERT: S 301 MET cc_start: 0.8670 (mtm) cc_final: 0.8320 (mpp) REVERT: U 161 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7595 (tm-30) REVERT: U 165 ASP cc_start: 0.8074 (m-30) cc_final: 0.7673 (m-30) REVERT: U 274 LYS cc_start: 0.8536 (tttt) cc_final: 0.8204 (ttpt) REVERT: U 301 MET cc_start: 0.8658 (mtm) cc_final: 0.8354 (mpp) REVERT: W 1 MET cc_start: 0.5742 (mmm) cc_final: 0.5452 (mmp) REVERT: W 6 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8611 (tptp) REVERT: W 161 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7577 (tm-30) REVERT: W 165 ASP cc_start: 0.8242 (m-30) cc_final: 0.7708 (m-30) REVERT: W 256 ASP cc_start: 0.8611 (t0) cc_final: 0.8359 (t0) REVERT: W 297 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8607 (mtp-110) REVERT: W 322 MET cc_start: 0.8272 (mmm) cc_final: 0.8071 (tpt) REVERT: Y 161 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7741 (tm-30) REVERT: Y 256 ASP cc_start: 0.8552 (t0) cc_final: 0.8347 (t0) REVERT: Y 297 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8480 (mtp-110) outliers start: 125 outliers final: 97 residues processed: 848 average time/residue: 0.2686 time to fit residues: 363.9734 Evaluate side-chains 847 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 750 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 MET Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 238 GLN Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 170 VAL Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 238 GLN Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 460 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 443 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 473 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 388 optimal weight: 9.9990 chunk 230 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN E 63 ASN G 63 ASN G 212 GLN I 63 ASN I 263 ASN M 63 ASN Q 63 ASN S 63 ASN U 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.086151 restraints weight = 104939.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089330 restraints weight = 56673.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091524 restraints weight = 37248.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.093103 restraints weight = 27289.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.094276 restraints weight = 21415.023| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 41132 Z= 0.132 Angle : 0.709 19.257 55952 Z= 0.351 Chirality : 0.042 0.324 6240 Planarity : 0.007 0.130 7059 Dihedral : 5.595 48.103 6396 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.21 % Allowed : 20.56 % Favored : 76.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.15 (0.12), residues: 4836 helix: 0.62 (0.10), residues: 2977 sheet: 0.10 (0.41), residues: 182 loop : -0.70 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 230 TYR 0.016 0.001 TYR Q 250 PHE 0.021 0.001 PHE Y 289 TRP 0.037 0.002 TRP Y 281 HIS 0.002 0.000 HIS G 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (41093) covalent geometry : angle 0.70923 / 0.35 (55952) hydrogen bonds : bond 0.03763 / 2.48 ( 2197) hydrogen bonds : angle 4.36389 / 3.11 ( 6279) Misc. bond : bond 0.00501 / 0.36 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 783 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 162 GLN cc_start: 0.8461 (mt0) cc_final: 0.8213 (mm-40) REVERT: A 309 GLN cc_start: 0.8418 (mp10) cc_final: 0.8063 (mp10) REVERT: C 161 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7631 (tm-30) REVERT: C 297 ARG cc_start: 0.9177 (ttp80) cc_final: 0.8919 (mtp-110) REVERT: C 309 GLN cc_start: 0.8441 (mp10) cc_final: 0.8093 (mp10) REVERT: E 161 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7974 (tm-30) REVERT: E 165 ASP cc_start: 0.8529 (m-30) cc_final: 0.7503 (m-30) REVERT: E 297 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8721 (mtm110) REVERT: G 161 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7528 (tm-30) REVERT: G 165 ASP cc_start: 0.7782 (m-30) cc_final: 0.7259 (m-30) REVERT: G 200 GLN cc_start: 0.8782 (mt0) cc_final: 0.8419 (mm110) REVERT: G 297 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8900 (mtp-110) REVERT: I 256 ASP cc_start: 0.8589 (t0) cc_final: 0.8375 (t0) REVERT: I 274 LYS cc_start: 0.8597 (tttt) cc_final: 0.8294 (ttpt) REVERT: I 297 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8827 (mtm110) REVERT: K 132 LEU cc_start: 0.9405 (mp) cc_final: 0.8988 (tp) REVERT: K 161 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7580 (tm-30) REVERT: K 165 ASP cc_start: 0.8060 (m-30) cc_final: 0.7732 (m-30) REVERT: K 253 MET cc_start: 0.7629 (tpt) cc_final: 0.7325 (tpt) REVERT: K 256 ASP cc_start: 0.8682 (t0) cc_final: 0.8478 (t0) REVERT: K 274 LYS cc_start: 0.8765 (tttt) cc_final: 0.8420 (ttpp) REVERT: K 297 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8780 (mtm110) REVERT: M 16 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7689 (mm-30) REVERT: M 132 LEU cc_start: 0.9405 (mp) cc_final: 0.8955 (tp) REVERT: M 161 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7583 (tm-30) REVERT: M 301 MET cc_start: 0.8668 (mtm) cc_final: 0.8306 (mpp) REVERT: O 161 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7451 (tm-30) REVERT: O 256 ASP cc_start: 0.8697 (t0) cc_final: 0.8491 (t0) REVERT: O 274 LYS cc_start: 0.8658 (tttt) cc_final: 0.8380 (ttpt) REVERT: O 301 MET cc_start: 0.8550 (mtm) cc_final: 0.8303 (mpp) REVERT: Q 161 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7592 (tm-30) REVERT: Q 256 ASP cc_start: 0.8619 (t0) cc_final: 0.8343 (t0) REVERT: U 161 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7531 (tm-30) REVERT: U 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7611 (m-30) REVERT: U 238 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: U 253 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7630 (tpt) REVERT: U 293 LEU cc_start: 0.8717 (mt) cc_final: 0.8503 (mp) REVERT: W 1 MET cc_start: 0.5810 (mmm) cc_final: 0.5583 (mmp) REVERT: W 6 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8636 (tptp) REVERT: W 161 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7535 (tm-30) REVERT: W 165 ASP cc_start: 0.8241 (m-30) cc_final: 0.7650 (m-30) REVERT: W 256 ASP cc_start: 0.8611 (t0) cc_final: 0.8345 (t0) REVERT: W 322 MET cc_start: 0.8281 (mmm) cc_final: 0.8060 (tpt) REVERT: Y 161 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7657 (tm-30) REVERT: Y 274 LYS cc_start: 0.8612 (tttt) cc_final: 0.8259 (ttpp) outliers start: 130 outliers final: 104 residues processed: 847 average time/residue: 0.2683 time to fit residues: 363.7312 Evaluate side-chains 848 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 742 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 301 MET Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 253 MET Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 280 LYS Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 238 GLN Chi-restraints excluded: chain U residue 253 MET Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 84 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 463 optimal weight: 0.5980 chunk 332 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 465 optimal weight: 0.8980 chunk 329 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 338 optimal weight: 4.9990 chunk 166 optimal weight: 8.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 263 ASN E 263 ASN G 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.101649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085811 restraints weight = 105023.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088897 restraints weight = 57259.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.091085 restraints weight = 38000.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092631 restraints weight = 27985.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093737 restraints weight = 22095.197| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 41132 Z= 0.143 Angle : 0.742 25.526 55952 Z= 0.368 Chirality : 0.042 0.255 6240 Planarity : 0.007 0.127 7059 Dihedral : 5.758 58.189 6396 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 2.93 % Allowed : 21.47 % Favored : 75.59 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 4836 helix: 0.68 (0.10), residues: 2964 sheet: 0.34 (0.43), residues: 182 loop : -0.58 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 230 TYR 0.017 0.001 TYR C 199 PHE 0.018 0.002 PHE Y 289 TRP 0.034 0.002 TRP A 281 HIS 0.002 0.000 HIS Y 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (41093) covalent geometry : angle 0.74171 / 0.37 (55952) hydrogen bonds : bond 0.03829 / 2.54 ( 2197) hydrogen bonds : angle 4.39607 / 3.13 ( 6279) Misc. bond : bond 0.00512 / 0.37 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 764 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 309 GLN cc_start: 0.8427 (mp10) cc_final: 0.8060 (mp10) REVERT: C 14 GLU cc_start: 0.9081 (tp30) cc_final: 0.8737 (mp0) REVERT: C 161 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 165 ASP cc_start: 0.8171 (m-30) cc_final: 0.7427 (m-30) REVERT: C 274 LYS cc_start: 0.8705 (tttt) cc_final: 0.8371 (ttpt) REVERT: C 297 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8823 (mtm110) REVERT: C 309 GLN cc_start: 0.8447 (mp10) cc_final: 0.8095 (mp10) REVERT: E 14 GLU cc_start: 0.9121 (tp30) cc_final: 0.8761 (mp0) REVERT: E 161 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7976 (tm-30) REVERT: E 165 ASP cc_start: 0.8530 (m-30) cc_final: 0.7470 (m-30) REVERT: E 297 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8746 (mtm110) REVERT: G 161 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7475 (tm-30) REVERT: G 165 ASP cc_start: 0.7787 (m-30) cc_final: 0.7178 (m-30) REVERT: G 200 GLN cc_start: 0.8798 (mt0) cc_final: 0.8426 (mm110) REVERT: G 256 ASP cc_start: 0.8622 (t0) cc_final: 0.8035 (t0) REVERT: G 274 LYS cc_start: 0.8584 (tttt) cc_final: 0.8240 (ttpp) REVERT: G 297 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8913 (mtp-110) REVERT: G 308 GLU cc_start: 0.8569 (pm20) cc_final: 0.8214 (pm20) REVERT: I 297 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8838 (mtm110) REVERT: K 132 LEU cc_start: 0.9404 (mp) cc_final: 0.8998 (tp) REVERT: K 161 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7604 (tm-30) REVERT: K 165 ASP cc_start: 0.8046 (m-30) cc_final: 0.7696 (m-30) REVERT: K 253 MET cc_start: 0.7598 (tpt) cc_final: 0.7294 (tpt) REVERT: K 295 LYS cc_start: 0.8522 (tttt) cc_final: 0.8129 (ttpp) REVERT: K 297 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8876 (mtm110) REVERT: M 132 LEU cc_start: 0.9399 (mp) cc_final: 0.8971 (tp) REVERT: M 161 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7585 (tm-30) REVERT: M 274 LYS cc_start: 0.8611 (tttt) cc_final: 0.8254 (ttpp) REVERT: M 301 MET cc_start: 0.8674 (mtm) cc_final: 0.8310 (mpp) REVERT: O 6 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8702 (tptp) REVERT: O 161 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7618 (tm-30) REVERT: Q 161 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7519 (tm-30) REVERT: Q 256 ASP cc_start: 0.8625 (t0) cc_final: 0.8359 (t70) REVERT: Q 274 LYS cc_start: 0.8597 (tttt) cc_final: 0.8221 (ttpt) REVERT: Q 309 GLN cc_start: 0.8439 (mp10) cc_final: 0.8162 (mp10) REVERT: S 10 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7892 (mtm-85) REVERT: S 14 GLU cc_start: 0.9149 (tp30) cc_final: 0.8764 (mp0) REVERT: S 161 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7580 (tm-30) REVERT: S 165 ASP cc_start: 0.8067 (m-30) cc_final: 0.7524 (m-30) REVERT: U 161 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7588 (tm-30) REVERT: U 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7579 (m-30) REVERT: U 293 LEU cc_start: 0.8720 (mt) cc_final: 0.8507 (mp) REVERT: W 1 MET cc_start: 0.5908 (mmm) cc_final: 0.5697 (mmp) REVERT: W 6 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8609 (tptp) REVERT: W 161 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7712 (tm-30) REVERT: W 256 ASP cc_start: 0.8599 (t0) cc_final: 0.8327 (t0) REVERT: W 322 MET cc_start: 0.8298 (mmm) cc_final: 0.8079 (tpt) REVERT: Y 161 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7698 (tm-30) outliers start: 119 outliers final: 102 residues processed: 833 average time/residue: 0.2617 time to fit residues: 351.2675 Evaluate side-chains 842 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 740 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 253 MET Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 280 LYS Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 84 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 288 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 401 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 199 optimal weight: 0.3980 chunk 354 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 360 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 368 optimal weight: 0.0870 chunk 304 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN C 63 ASN E 63 ASN E 263 ASN I 263 ASN K 63 ASN K 263 ASN M 63 ASN Q 63 ASN S 63 ASN U 63 ASN U 238 GLN U 263 ASN W 63 ASN Y 63 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.103890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087875 restraints weight = 103556.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091038 restraints weight = 56106.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.093292 restraints weight = 37079.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.094897 restraints weight = 27190.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.096109 restraints weight = 21337.696| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 41132 Z= 0.137 Angle : 0.791 26.048 55952 Z= 0.387 Chirality : 0.041 0.342 6240 Planarity : 0.006 0.123 7059 Dihedral : 5.907 60.538 6396 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 2.84 % Allowed : 21.57 % Favored : 75.59 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.35 (0.12), residues: 4836 helix: 0.72 (0.10), residues: 2964 sheet: 0.37 (0.42), residues: 182 loop : -0.51 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 230 TYR 0.018 0.001 TYR A 199 PHE 0.034 0.001 PHE C 289 TRP 0.030 0.002 TRP Y 281 HIS 0.002 0.000 HIS Y 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (41093) covalent geometry : angle 0.79119 / 0.39 (55952) hydrogen bonds : bond 0.03790 / 2.50 ( 2197) hydrogen bonds : angle 4.39480 / 3.12 ( 6279) Misc. bond : bond 0.00574 / 0.37 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 791 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 301 MET cc_start: 0.8612 (mtm) cc_final: 0.8337 (mpp) REVERT: A 309 GLN cc_start: 0.8399 (mp10) cc_final: 0.8031 (mp10) REVERT: C 14 GLU cc_start: 0.9076 (tp30) cc_final: 0.8762 (mp0) REVERT: C 161 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 274 LYS cc_start: 0.8597 (tttt) cc_final: 0.8282 (ttpp) REVERT: C 297 ARG cc_start: 0.9216 (ttp80) cc_final: 0.8847 (mtm110) REVERT: C 309 GLN cc_start: 0.8443 (mp10) cc_final: 0.8085 (mp10) REVERT: E 14 GLU cc_start: 0.9131 (tp30) cc_final: 0.8776 (mp0) REVERT: E 161 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7982 (tm-30) REVERT: E 165 ASP cc_start: 0.8528 (m-30) cc_final: 0.7471 (m-30) REVERT: E 274 LYS cc_start: 0.8642 (tttt) cc_final: 0.8339 (ttpp) REVERT: E 297 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8770 (mtm110) REVERT: G 161 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7480 (tm-30) REVERT: G 165 ASP cc_start: 0.7762 (m-30) cc_final: 0.7129 (m-30) REVERT: G 200 GLN cc_start: 0.8782 (mt0) cc_final: 0.8409 (mm110) REVERT: G 297 ARG cc_start: 0.9077 (ttp80) cc_final: 0.8742 (mtm110) REVERT: I 297 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8825 (mtm110) REVERT: K 6 LYS cc_start: 0.8938 (tptp) cc_final: 0.8628 (tptp) REVERT: K 161 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7601 (tm-30) REVERT: K 165 ASP cc_start: 0.8023 (m-30) cc_final: 0.7672 (m-30) REVERT: K 295 LYS cc_start: 0.8494 (tttt) cc_final: 0.8113 (ttpp) REVERT: K 297 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8535 (mtp-110) REVERT: M 161 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7623 (tm-30) REVERT: O 161 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7657 (tm-30) REVERT: Q 161 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7581 (tm-30) REVERT: Q 309 GLN cc_start: 0.8424 (mp10) cc_final: 0.8144 (mp10) REVERT: S 161 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7737 (tm-30) REVERT: U 161 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7614 (tm-30) REVERT: U 165 ASP cc_start: 0.8056 (m-30) cc_final: 0.7572 (m-30) REVERT: U 301 MET cc_start: 0.8571 (mtm) cc_final: 0.8334 (mpp) REVERT: W 6 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8621 (tptp) REVERT: W 161 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7527 (tm-30) REVERT: W 165 ASP cc_start: 0.8205 (m-30) cc_final: 0.7588 (m-30) REVERT: W 256 ASP cc_start: 0.8585 (t0) cc_final: 0.8334 (t0) REVERT: Y 6 LYS cc_start: 0.8921 (tptp) cc_final: 0.8595 (tptp) REVERT: Y 161 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7748 (tm-30) REVERT: Y 309 GLN cc_start: 0.8404 (mp10) cc_final: 0.8029 (mp10) outliers start: 115 outliers final: 99 residues processed: 849 average time/residue: 0.2679 time to fit residues: 364.1995 Evaluate side-chains 855 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 756 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 63 ASN Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 280 LYS Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 238 GLN Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 324 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 475 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 412 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087244 restraints weight = 104831.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090413 restraints weight = 56998.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092621 restraints weight = 37682.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094184 restraints weight = 27746.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.095385 restraints weight = 21872.628| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.757 41132 Z= 0.371 Angle : 1.139 59.200 55952 Z= 0.615 Chirality : 0.046 0.563 6240 Planarity : 0.007 0.125 7059 Dihedral : 5.984 62.126 6396 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.42 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 22.41 % Favored : 75.00 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.12), residues: 4836 helix: 0.68 (0.10), residues: 2964 sheet: 0.39 (0.42), residues: 182 loop : -0.53 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Y 230 TYR 0.042 0.002 TYR O 199 PHE 0.063 0.002 PHE M 289 TRP 0.128 0.007 TRP I 281 HIS 0.001 0.000 HIS Y 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.36 (41093) covalent geometry : angle 1.13906 / 0.62 (55952) hydrogen bonds : bond 0.04203 / 2.80 ( 2197) hydrogen bonds : angle 4.44901 / 3.15 ( 6279) Misc. bond : bond 0.03148 / 2.43 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 751 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7516 (tm-30) REVERT: A 165 ASP cc_start: 0.8107 (m-30) cc_final: 0.7211 (m-30) REVERT: A 274 LYS cc_start: 0.8512 (tttt) cc_final: 0.8231 (ttpt) REVERT: A 301 MET cc_start: 0.8600 (mtm) cc_final: 0.8333 (mpp) REVERT: A 309 GLN cc_start: 0.8409 (mp10) cc_final: 0.8042 (mp10) REVERT: C 14 GLU cc_start: 0.9071 (tp30) cc_final: 0.8766 (mp0) REVERT: C 161 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7539 (tm-30) REVERT: C 165 ASP cc_start: 0.8193 (m-30) cc_final: 0.7465 (m-30) REVERT: C 274 LYS cc_start: 0.8616 (tttt) cc_final: 0.8291 (ttpp) REVERT: C 297 ARG cc_start: 0.9225 (ttp80) cc_final: 0.8860 (mtm110) REVERT: C 309 GLN cc_start: 0.8446 (mp10) cc_final: 0.8084 (mp10) REVERT: E 14 GLU cc_start: 0.9130 (tp30) cc_final: 0.8786 (mp0) REVERT: E 161 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7993 (tm-30) REVERT: E 165 ASP cc_start: 0.8529 (m-30) cc_final: 0.7460 (m-30) REVERT: E 274 LYS cc_start: 0.8662 (tttt) cc_final: 0.8373 (ttpp) REVERT: E 297 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8782 (mtm110) REVERT: G 161 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7486 (tm-30) REVERT: G 165 ASP cc_start: 0.7786 (m-30) cc_final: 0.7148 (m-30) REVERT: G 200 GLN cc_start: 0.8786 (mt0) cc_final: 0.8418 (mm110) REVERT: G 297 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8762 (mtm110) REVERT: I 297 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8840 (mtm110) REVERT: K 6 LYS cc_start: 0.8961 (tptp) cc_final: 0.8620 (tptp) REVERT: K 161 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7601 (tm-30) REVERT: K 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7588 (m-30) REVERT: K 295 LYS cc_start: 0.8485 (tttt) cc_final: 0.8124 (ttpp) REVERT: K 297 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8680 (mtm110) REVERT: M 161 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7635 (tm-30) REVERT: O 161 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7645 (tm-30) REVERT: Q 309 GLN cc_start: 0.8425 (mp10) cc_final: 0.8147 (mp10) REVERT: S 161 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7548 (tm-30) REVERT: S 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7453 (m-30) REVERT: S 301 MET cc_start: 0.8562 (mtm) cc_final: 0.8307 (mpp) REVERT: U 161 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7605 (tm-30) REVERT: U 165 ASP cc_start: 0.8050 (m-30) cc_final: 0.7565 (m-30) REVERT: U 274 LYS cc_start: 0.8583 (tttt) cc_final: 0.8196 (ttpt) REVERT: U 301 MET cc_start: 0.8555 (mtm) cc_final: 0.8334 (mpp) REVERT: W 6 LYS cc_start: 0.9059 (tmtt) cc_final: 0.8629 (tptp) REVERT: W 161 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7530 (tm-30) REVERT: W 165 ASP cc_start: 0.8208 (m-30) cc_final: 0.7581 (m-30) REVERT: W 256 ASP cc_start: 0.8592 (t0) cc_final: 0.8334 (t0) REVERT: Y 6 LYS cc_start: 0.8927 (tptp) cc_final: 0.8605 (tptp) REVERT: Y 161 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7761 (tm-30) REVERT: Y 274 LYS cc_start: 0.8583 (tttt) cc_final: 0.8281 (ttpt) REVERT: Y 309 GLN cc_start: 0.8409 (mp10) cc_final: 0.8037 (mp10) outliers start: 105 outliers final: 101 residues processed: 808 average time/residue: 0.2530 time to fit residues: 329.5369 Evaluate side-chains 849 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 748 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 301 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 261 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 301 MET Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 267 THR Chi-restraints excluded: chain Q residue 280 LYS Chi-restraints excluded: chain Q residue 304 ARG Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 76 LEU Chi-restraints excluded: chain S residue 99 ILE Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 280 LYS Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 263 ASN Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 84 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 217 optimal weight: 2.9990 chunk 373 optimal weight: 9.9990 chunk 440 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 465 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.103295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.087193 restraints weight = 105094.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090386 restraints weight = 57096.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.092602 restraints weight = 37680.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094184 restraints weight = 27737.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.095335 restraints weight = 21857.962| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.292 41132 Z= 0.282 Angle : 1.151 59.200 55952 Z= 0.615 Chirality : 0.051 1.576 6240 Planarity : 0.008 0.153 7059 Dihedral : 5.993 60.021 6396 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 22.56 % Favored : 74.95 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: 0.28 (0.12), residues: 4836 helix: 0.66 (0.10), residues: 2964 sheet: 0.40 (0.42), residues: 182 loop : -0.52 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG K 204 TYR 0.078 0.002 TYR K 199 PHE 0.052 0.002 PHE Q 235 TRP 0.066 0.005 TRP W 281 HIS 0.001 0.000 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00636 / 0.28 (41093) covalent geometry : angle 1.15149 / 0.62 (55952) hydrogen bonds : bond 0.04502 / 3.06 ( 2197) hydrogen bonds : angle 4.48903 / 3.18 ( 6279) Misc. bond : bond 0.01699 / 1.31 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10893.75 seconds wall clock time: 187 minutes 55.27 seconds (11275.27 seconds total)