Starting phenix.real_space_refine on Sat Mar 7 08:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ewq_31361/03_2026/7ewq_31361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ewq_31361/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ewq_31361/03_2026/7ewq_31361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ewq_31361/03_2026/7ewq_31361.map" model { file = "/net/cci-nas-00/data/ceres_data/7ewq_31361/03_2026/7ewq_31361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ewq_31361/03_2026/7ewq_31361.cif" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.40, per 1000 atoms: 0.11 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: 4.00 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: 4.78 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: 8.42 Time building geometry restraints manager: 4.95 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: 21601 16.72 - 33.44: 2773 33.44 - 50.16: 378 50.16 - 66.88: 247 66.88 - 83.61: 104 Dihedral angle restraints: 25103 sinusoidal: 10907 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 25100 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: 0.11 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: 24.280 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: 0.030 Extract box with map and model: 1.110 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.150 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.150 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 15.958 83.606 16029 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 covalent geometry : bond 0.00618 (41093) covalent geometry : angle 0.78076 (55952) hydrogen bonds : bond 0.13572 ( 2197) hydrogen bonds : angle 6.38915 ( 6279) Misc. bond : bond 0.76005 ( 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 : 1.527 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: 0.3047 time to fit residues: 491.9402 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 : 1.285 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 18 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 18 GLN W 212 GLN W 231 GLN W 346 GLN W 373 GLN Y 18 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: 74 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.080840 restraints weight = 105774.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084081 restraints weight = 55085.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086320 restraints weight = 35622.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087904 restraints weight = 25941.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089071 restraints weight = 20322.844| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 41132 Z= 0.148 Angle : 0.677 6.908 55952 Z= 0.355 Chirality : 0.047 0.285 6240 Planarity : 0.009 0.184 7059 Dihedral : 9.994 60.208 6708 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.53 % Allowed : 13.81 % Favored : 84.66 % 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: -1.11 (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 K 251 PHE 0.018 0.002 PHE Q 270 TRP 0.004 0.001 TRP O 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00327 (41093) covalent geometry : angle 0.67720 (55952) hydrogen bonds : bond 0.04624 ( 2197) hydrogen bonds : angle 4.84120 ( 6279) Misc. bond : bond 0.00367 ( 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 1014 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 952 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.7922 (tpt) cc_final: 0.7586 (tpt) REVERT: A 256 ASP cc_start: 0.8788 (t0) cc_final: 0.8536 (t0) REVERT: A 301 MET cc_start: 0.8759 (mtm) cc_final: 0.8426 (mtt) REVERT: A 309 GLN cc_start: 0.8217 (mp10) cc_final: 0.7916 (mp10) REVERT: C 10 ARG cc_start: 0.8182 (ttp-110) cc_final: 0.7942 (ttp-110) REVERT: C 161 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8163 (tm-30) REVERT: C 199 TYR cc_start: 0.8408 (m-10) cc_final: 0.8018 (m-80) REVERT: C 256 ASP cc_start: 0.8794 (t0) cc_final: 0.8075 (t0) REVERT: C 297 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8574 (mtp-110) REVERT: C 301 MET cc_start: 0.8718 (mtm) cc_final: 0.8456 (mpp) REVERT: E 200 GLN cc_start: 0.8832 (mt0) cc_final: 0.8587 (mm110) REVERT: E 256 ASP cc_start: 0.8804 (t0) cc_final: 0.8496 (t0) REVERT: E 297 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8549 (ttp80) REVERT: E 301 MET cc_start: 0.8747 (mtm) cc_final: 0.8449 (mpp) REVERT: E 309 GLN cc_start: 0.8252 (mp10) cc_final: 0.7940 (mp10) REVERT: G 256 ASP cc_start: 0.8746 (t0) cc_final: 0.8013 (t0) REVERT: G 295 LYS cc_start: 0.8787 (tptm) cc_final: 0.8585 (tptm) REVERT: G 297 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8651 (ttp80) REVERT: G 301 MET cc_start: 0.8739 (mtm) cc_final: 0.8467 (mpp) REVERT: G 309 GLN cc_start: 0.8269 (mp10) cc_final: 0.7855 (mp10) REVERT: I 6 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8640 (tptp) REVERT: I 256 ASP cc_start: 0.8812 (t0) cc_final: 0.8503 (t0) REVERT: I 297 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8658 (ttp80) REVERT: I 301 MET cc_start: 0.8729 (mtm) cc_final: 0.8454 (mpp) REVERT: K 200 GLN cc_start: 0.8837 (mt0) cc_final: 0.8579 (mm110) REVERT: K 256 ASP cc_start: 0.8802 (t0) cc_final: 0.8504 (t0) REVERT: K 262 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6385 (mt-10) REVERT: K 297 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8701 (ttp80) REVERT: K 301 MET cc_start: 0.8772 (mtm) cc_final: 0.8435 (mpp) REVERT: M 297 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8712 (ttp80) REVERT: M 301 MET cc_start: 0.8727 (mtm) cc_final: 0.8405 (mpp) REVERT: O 256 ASP cc_start: 0.8778 (t0) cc_final: 0.8502 (t0) REVERT: O 274 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8623 (tttt) REVERT: O 297 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8571 (mtp-110) REVERT: O 301 MET cc_start: 0.8734 (mtm) cc_final: 0.8449 (mpp) REVERT: Q 256 ASP cc_start: 0.8808 (t0) cc_final: 0.8088 (t0) REVERT: Q 274 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8590 (tttt) REVERT: Q 297 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8609 (mtp-110) REVERT: Q 301 MET cc_start: 0.8743 (mtm) cc_final: 0.8430 (mpp) REVERT: S 200 GLN cc_start: 0.8796 (mt0) cc_final: 0.8557 (mm110) REVERT: S 253 MET cc_start: 0.7951 (tpt) cc_final: 0.5717 (tpt) REVERT: S 256 ASP cc_start: 0.8807 (t0) cc_final: 0.8109 (t0) REVERT: S 274 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8618 (tttt) REVERT: S 297 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8488 (mtp-110) REVERT: S 301 MET cc_start: 0.8747 (mtm) cc_final: 0.8427 (mpp) REVERT: U 200 GLN cc_start: 0.8800 (mt0) cc_final: 0.8546 (mm110) REVERT: U 253 MET cc_start: 0.7832 (tpt) cc_final: 0.7625 (tpt) REVERT: U 256 ASP cc_start: 0.8795 (t0) cc_final: 0.8527 (t0) REVERT: U 274 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8594 (tttt) REVERT: U 297 ARG cc_start: 0.9014 (ttp80) cc_final: 0.8564 (mtp-110) REVERT: U 301 MET cc_start: 0.8743 (mtm) cc_final: 0.8471 (mpp) REVERT: W 161 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8160 (tm-30) REVERT: W 199 TYR cc_start: 0.8437 (m-10) cc_final: 0.8106 (m-80) REVERT: W 256 ASP cc_start: 0.8807 (t0) cc_final: 0.8022 (t0) REVERT: W 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8607 (mtp-110) REVERT: W 301 MET cc_start: 0.8762 (mtm) cc_final: 0.8460 (mpp) REVERT: W 309 GLN cc_start: 0.8185 (mp10) cc_final: 0.7896 (mp10) REVERT: Y 256 ASP cc_start: 0.8773 (t0) cc_final: 0.8460 (t0) REVERT: Y 297 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8679 (ttp80) REVERT: Y 301 MET cc_start: 0.8775 (mtm) cc_final: 0.8387 (mpp) outliers start: 62 outliers final: 29 residues processed: 983 average time/residue: 0.2664 time to fit residues: 415.2490 Evaluate side-chains 841 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 812 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain G residue 157 CYS 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 157 CYS Chi-restraints excluded: chain U residue 185 TYR 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 Y residue 157 CYS 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: 1.9990 chunk 250 optimal weight: 0.7980 chunk 416 optimal weight: 7.9990 chunk 408 optimal weight: 0.9980 chunk 272 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 203 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 126 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Y 87 HIS Y 212 GLN Y 263 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.098941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.083520 restraints weight = 102739.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086763 restraints weight = 51947.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.088986 restraints weight = 32904.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.090559 restraints weight = 23574.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091757 restraints weight = 18203.847| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3212 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 : 0.607 7.853 55952 Z= 0.312 Chirality : 0.044 0.260 6240 Planarity : 0.007 0.129 7059 Dihedral : 9.703 59.979 6708 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.25 % Allowed : 16.03 % Favored : 80.72 % 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: -0.72 (0.46), residues: 156 loop : -1.02 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 230 TYR 0.018 0.001 TYR G 251 PHE 0.014 0.001 PHE Y 270 TRP 0.010 0.001 TRP G 281 HIS 0.001 0.000 HIS O 87 Details of bonding type rmsd covalent geometry : bond 0.00285 (41093) covalent geometry : angle 0.60710 (55952) hydrogen bonds : bond 0.04038 ( 2197) hydrogen bonds : angle 4.54225 ( 6279) Misc. bond : bond 0.00359 ( 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 1015 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 883 time to evaluate : 1.533 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: A 199 TYR cc_start: 0.8319 (m-80) cc_final: 0.7957 (m-10) REVERT: A 256 ASP cc_start: 0.8794 (t0) cc_final: 0.8100 (t0) REVERT: A 301 MET cc_start: 0.8652 (mtm) cc_final: 0.8357 (mpp) REVERT: A 309 GLN cc_start: 0.8342 (mp10) cc_final: 0.8042 (mp10) REVERT: C 6 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8661 (tptp) REVERT: C 161 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8074 (tm-30) REVERT: C 165 ASP cc_start: 0.8559 (m-30) cc_final: 0.7629 (m-30) REVERT: C 199 TYR cc_start: 0.8381 (m-80) cc_final: 0.8112 (m-80) REVERT: C 200 GLN cc_start: 0.8813 (mt0) cc_final: 0.8601 (mm110) REVERT: C 256 ASP cc_start: 0.8758 (t0) cc_final: 0.8174 (t0) REVERT: C 289 PHE cc_start: 0.8267 (m-80) cc_final: 0.8062 (m-10) REVERT: C 297 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8535 (mtp-110) REVERT: C 311 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6661 (mtm110) REVERT: C 322 MET cc_start: 0.8271 (mmm) cc_final: 0.8061 (tpt) REVERT: E 253 MET cc_start: 0.7879 (tpt) cc_final: 0.6476 (tpt) REVERT: E 256 ASP cc_start: 0.8759 (t0) cc_final: 0.8034 (t0) REVERT: E 289 PHE cc_start: 0.8325 (m-80) cc_final: 0.7766 (m-10) REVERT: E 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8551 (mtp-110) REVERT: E 301 MET cc_start: 0.8627 (mtm) cc_final: 0.8413 (mpp) REVERT: E 309 GLN cc_start: 0.8349 (mp10) cc_final: 0.8031 (mp10) REVERT: G 200 GLN cc_start: 0.8783 (mt0) cc_final: 0.8458 (mm110) REVERT: G 297 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8561 (mtp-110) REVERT: G 301 MET cc_start: 0.8639 (mtm) cc_final: 0.8413 (mpp) REVERT: G 309 GLN cc_start: 0.8378 (mp10) cc_final: 0.8054 (mp10) REVERT: G 347 MET cc_start: 0.8463 (ttp) cc_final: 0.8250 (ttp) REVERT: I 253 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.6799 (tpt) REVERT: I 274 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8658 (tttt) REVERT: I 297 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8597 (mtp-110) REVERT: I 301 MET cc_start: 0.8609 (mtm) cc_final: 0.8399 (mpp) REVERT: K 200 GLN cc_start: 0.8784 (mt0) cc_final: 0.8558 (mm110) REVERT: K 256 ASP cc_start: 0.8788 (t0) cc_final: 0.8442 (t0) REVERT: K 274 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8630 (tttt) REVERT: K 297 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8621 (mtp-110) REVERT: K 301 MET cc_start: 0.8655 (mtm) cc_final: 0.8399 (mpp) REVERT: M 289 PHE cc_start: 0.8308 (m-80) cc_final: 0.8045 (m-10) REVERT: M 297 ARG cc_start: 0.9003 (ttp80) cc_final: 0.8479 (mtp-110) REVERT: M 301 MET cc_start: 0.8653 (mtm) cc_final: 0.8360 (mpp) REVERT: O 161 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7612 (tm-30) REVERT: O 256 ASP cc_start: 0.8753 (t0) cc_final: 0.8498 (t0) REVERT: O 274 LYS cc_start: 0.8868 (ttpp) cc_final: 0.8663 (tttt) REVERT: O 297 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8559 (mtp-110) REVERT: O 301 MET cc_start: 0.8628 (mtm) cc_final: 0.8402 (mpp) REVERT: Q 14 GLU cc_start: 0.9153 (tp30) cc_final: 0.8744 (mp0) REVERT: Q 274 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8654 (tttt) REVERT: Q 297 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8630 (mtp-110) REVERT: Q 301 MET cc_start: 0.8628 (mtm) cc_final: 0.8400 (mpp) REVERT: Q 309 GLN cc_start: 0.8254 (mp10) cc_final: 0.7983 (mp10) REVERT: S 161 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7619 (tm-30) REVERT: S 165 ASP cc_start: 0.7999 (m-30) cc_final: 0.7596 (m-30) REVERT: S 200 GLN cc_start: 0.8752 (mt0) cc_final: 0.8482 (mm110) REVERT: S 274 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8644 (tttt) REVERT: S 297 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8522 (mtp-110) REVERT: S 301 MET cc_start: 0.8635 (mtm) cc_final: 0.8393 (mpp) REVERT: U 199 TYR cc_start: 0.8351 (m-10) cc_final: 0.8013 (m-10) REVERT: U 256 ASP cc_start: 0.8773 (t0) cc_final: 0.8062 (t0) REVERT: U 274 LYS cc_start: 0.8850 (ttpp) cc_final: 0.8644 (tttt) REVERT: U 297 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8561 (mtp-110) REVERT: U 322 MET cc_start: 0.8372 (mmm) cc_final: 0.8166 (tpt) REVERT: W 161 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8079 (tm-30) REVERT: W 165 ASP cc_start: 0.8526 (m-30) cc_final: 0.7512 (m-30) REVERT: W 274 LYS cc_start: 0.8863 (ttpp) cc_final: 0.8652 (tttt) REVERT: W 297 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8535 (mtp-110) REVERT: W 301 MET cc_start: 0.8632 (mtm) cc_final: 0.8398 (mpp) REVERT: W 309 GLN cc_start: 0.8264 (mp10) cc_final: 0.7958 (mp10) REVERT: W 322 MET cc_start: 0.8226 (mmm) cc_final: 0.8018 (tpt) REVERT: Y 253 MET cc_start: 0.7836 (tpt) cc_final: 0.6141 (tpt) REVERT: Y 256 ASP cc_start: 0.8758 (t0) cc_final: 0.7966 (t0) REVERT: Y 274 LYS cc_start: 0.8853 (ttpp) cc_final: 0.8645 (tttt) REVERT: Y 289 PHE cc_start: 0.8345 (m-80) cc_final: 0.8135 (m-10) REVERT: Y 297 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8537 (mtp-110) REVERT: Y 301 MET cc_start: 0.8623 (mtm) cc_final: 0.8353 (mpp) REVERT: Y 309 GLN cc_start: 0.8337 (mp10) cc_final: 0.8040 (mp10) outliers start: 132 outliers final: 71 residues processed: 950 average time/residue: 0.2664 time to fit residues: 401.6925 Evaluate side-chains 889 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 817 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 253 MET 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 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 185 TYR 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 253 MET Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 304 ARG 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 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: 7.9990 chunk 118 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 470 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 296 optimal weight: 1.9990 chunk 440 optimal weight: 3.9990 chunk 461 optimal weight: 0.7980 chunk 448 optimal weight: 0.3980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 63 ASN A 263 ASN C 63 ASN E 18 GLN E 63 ASN E 238 GLN E 263 ASN G 18 GLN G 63 ASN G 263 ASN 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 63 ASN Q 263 ASN S 18 GLN S 63 ASN S 263 ASN U 18 GLN U 63 ASN U 238 GLN U 263 ASN W 63 ASN W 263 ASN Y 63 ASN Y 238 GLN Y 263 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.100197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.084644 restraints weight = 106124.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087690 restraints weight = 57120.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.089796 restraints weight = 37664.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.091313 restraints weight = 27755.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092390 restraints weight = 21891.153| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41132 Z= 0.160 Angle : 0.738 15.259 55952 Z= 0.371 Chirality : 0.046 0.569 6240 Planarity : 0.007 0.132 7059 Dihedral : 9.744 59.792 6708 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.35 % Allowed : 17.97 % Favored : 78.67 % Cbeta Deviations : 0.02 % 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: -0.23 (0.12), residues: 4836 helix: 0.36 (0.10), residues: 2964 sheet: -0.61 (0.46), residues: 156 loop : -0.86 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 10 TYR 0.017 0.001 TYR A 275 PHE 0.031 0.002 PHE M 289 TRP 0.046 0.003 TRP K 281 HIS 0.002 0.000 HIS W 87 Details of bonding type rmsd covalent geometry : bond 0.00366 (41093) covalent geometry : angle 0.73847 (55952) hydrogen bonds : bond 0.04184 ( 2197) hydrogen bonds : angle 4.53582 ( 6279) Misc. bond : bond 0.00338 ( 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 955 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 819 time to evaluate : 1.491 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: A 161 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7620 (tm-30) REVERT: C 6 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8656 (tptp) REVERT: C 200 GLN cc_start: 0.8803 (mt0) cc_final: 0.8590 (mm110) REVERT: C 256 ASP cc_start: 0.8742 (t0) cc_final: 0.8149 (t0) REVERT: C 297 ARG cc_start: 0.9172 (ttp80) cc_final: 0.8722 (mtp-110) REVERT: C 301 MET cc_start: 0.8775 (mpp) cc_final: 0.8194 (mpp) REVERT: C 322 MET cc_start: 0.8249 (mmm) cc_final: 0.8008 (tpt) REVERT: E 256 ASP cc_start: 0.8537 (t0) cc_final: 0.8261 (t0) REVERT: E 297 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8623 (mtp-110) REVERT: G 161 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7487 (tm-30) REVERT: G 200 GLN cc_start: 0.8776 (mt0) cc_final: 0.8463 (mm110) REVERT: G 297 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8617 (mtp-110) REVERT: I 161 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7675 (tm-30) REVERT: I 256 ASP cc_start: 0.8578 (t0) cc_final: 0.8300 (t0) REVERT: I 297 ARG cc_start: 0.9067 (ttp80) cc_final: 0.8650 (mtp-110) REVERT: K 161 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7590 (tm-30) REVERT: K 165 ASP cc_start: 0.7975 (m-30) cc_final: 0.7640 (m-30) REVERT: K 200 GLN cc_start: 0.8755 (mt0) cc_final: 0.8552 (mm110) REVERT: K 256 ASP cc_start: 0.8766 (t0) cc_final: 0.8438 (t0) REVERT: K 297 ARG cc_start: 0.9081 (ttp80) cc_final: 0.8618 (mtp-110) REVERT: M 295 LYS cc_start: 0.8802 (tptm) cc_final: 0.8389 (tptm) REVERT: M 297 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8612 (mtp-110) REVERT: O 161 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7567 (tm-30) REVERT: O 256 ASP cc_start: 0.8743 (t0) cc_final: 0.8067 (t0) REVERT: O 274 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8576 (tttt) REVERT: O 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8550 (mtm110) REVERT: Q 14 GLU cc_start: 0.9100 (tp30) cc_final: 0.8777 (mp0) REVERT: Q 161 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7566 (tm-30) REVERT: Q 297 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8641 (mtp-110) REVERT: S 161 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7518 (tm-30) REVERT: S 165 ASP cc_start: 0.7966 (m-30) cc_final: 0.7438 (m-30) REVERT: S 200 GLN cc_start: 0.8743 (mt0) cc_final: 0.8502 (mm110) REVERT: S 297 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8616 (mtp-110) REVERT: U 256 ASP cc_start: 0.8743 (t0) cc_final: 0.8057 (t0) REVERT: U 297 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8912 (mtp-110) REVERT: W 161 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8023 (tm-30) REVERT: W 165 ASP cc_start: 0.8529 (m-30) cc_final: 0.7098 (m-30) REVERT: W 256 ASP cc_start: 0.8552 (t0) cc_final: 0.8292 (t0) REVERT: W 274 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8563 (tttt) REVERT: W 297 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8606 (mtp-110) REVERT: W 322 MET cc_start: 0.8210 (mmm) cc_final: 0.7977 (tpt) REVERT: Y 161 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7665 (tm-30) REVERT: Y 297 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8610 (mtp-110) outliers start: 136 outliers final: 87 residues processed: 886 average time/residue: 0.2670 time to fit residues: 377.4988 Evaluate side-chains 849 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 762 time to evaluate : 1.598 ------------------------------------------------------------------------------- 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 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 253 MET 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 157 CYS Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU 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 170 VAL 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 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 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: 6.9990 chunk 91 optimal weight: 0.0980 chunk 415 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 443 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 306 optimal weight: 0.2980 chunk 357 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 263 ASN E 63 ASN E 238 GLN E 263 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.100225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084654 restraints weight = 104557.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087739 restraints weight = 55961.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089910 restraints weight = 36733.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091490 restraints weight = 26942.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092625 restraints weight = 21058.474| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 41132 Z= 0.141 Angle : 0.739 24.320 55952 Z= 0.371 Chirality : 0.044 0.443 6240 Planarity : 0.007 0.133 7059 Dihedral : 9.727 59.823 6708 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.03 % Allowed : 19.55 % Favored : 77.42 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4836 helix: 0.50 (0.10), residues: 2964 sheet: -0.21 (0.41), 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 0.016 0.001 TYR Q 250 PHE 0.029 0.002 PHE Y 289 TRP 0.035 0.002 TRP K 281 HIS 0.001 0.000 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00317 (41093) covalent geometry : angle 0.73916 (55952) hydrogen bonds : bond 0.04020 ( 2197) hydrogen bonds : angle 4.50199 ( 6279) Misc. bond : bond 0.00533 ( 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 927 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 804 time to evaluate : 1.632 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: A 161 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 301 MET cc_start: 0.8759 (mpp) cc_final: 0.8200 (mpp) REVERT: C 1 MET cc_start: 0.5848 (mmm) cc_final: 0.5552 (mmp) REVERT: C 161 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8007 (tm-30) REVERT: C 256 ASP cc_start: 0.8658 (t0) cc_final: 0.8347 (t0) REVERT: C 297 ARG cc_start: 0.9164 (ttp80) cc_final: 0.8897 (mtp-110) REVERT: E 1 MET cc_start: 0.5830 (mmm) cc_final: 0.5568 (mmp) REVERT: E 161 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7662 (tm-30) REVERT: E 256 ASP cc_start: 0.8508 (t0) cc_final: 0.8239 (t0) REVERT: G 1 MET cc_start: 0.5819 (mmm) cc_final: 0.5465 (mmp) REVERT: G 161 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7495 (tm-30) REVERT: G 200 GLN cc_start: 0.8755 (mt0) cc_final: 0.8437 (mm110) REVERT: G 297 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8871 (mtp-110) REVERT: I 161 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7690 (tm-30) REVERT: I 256 ASP cc_start: 0.8590 (t0) cc_final: 0.8322 (t0) REVERT: K 161 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7529 (tm-30) REVERT: K 165 ASP cc_start: 0.8015 (m-30) cc_final: 0.7565 (m-30) REVERT: K 256 ASP cc_start: 0.8740 (t0) cc_final: 0.8428 (t0) REVERT: K 274 LYS cc_start: 0.8855 (ttpp) cc_final: 0.8643 (tttt) REVERT: K 297 ARG cc_start: 0.9126 (ttp80) cc_final: 0.8669 (mtp-110) REVERT: K 301 MET cc_start: 0.8770 (mpp) cc_final: 0.8215 (mpp) REVERT: M 297 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8671 (mtp-110) REVERT: M 301 MET cc_start: 0.8761 (mpp) cc_final: 0.8210 (mpp) REVERT: O 161 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7517 (tm-30) REVERT: O 297 ARG cc_start: 0.9091 (ttp80) cc_final: 0.8850 (mtp-110) REVERT: Q 10 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7779 (mtm-85) REVERT: Q 14 GLU cc_start: 0.9137 (tp30) cc_final: 0.8745 (mp0) REVERT: Q 161 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7745 (tm-30) REVERT: Q 297 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8867 (mtp-110) REVERT: Q 309 GLN cc_start: 0.8285 (mp10) cc_final: 0.7998 (mp10) REVERT: S 200 GLN cc_start: 0.8720 (mt0) cc_final: 0.8458 (mm110) REVERT: U 161 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7651 (tm-30) REVERT: U 165 ASP cc_start: 0.8025 (m-30) cc_final: 0.7705 (m-30) REVERT: W 161 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8065 (tm-30) REVERT: W 165 ASP cc_start: 0.8519 (m-30) cc_final: 0.7337 (m-30) REVERT: W 256 ASP cc_start: 0.8560 (t0) cc_final: 0.8304 (t0) REVERT: W 274 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8561 (tttt) REVERT: W 297 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8874 (mtp-110) REVERT: Y 161 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7595 (tm-30) REVERT: Y 238 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7509 (pp30) REVERT: Y 297 ARG cc_start: 0.9055 (ttp80) cc_final: 0.8817 (mtp-110) outliers start: 123 outliers final: 91 residues processed: 863 average time/residue: 0.2719 time to fit residues: 373.1749 Evaluate side-chains 849 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 757 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 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 238 GLN Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 MET 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 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 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 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 253 MET 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 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 253 MET 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 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 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 99 ILE 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: 0.9990 chunk 307 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 265 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 452 optimal weight: 0.3980 chunk 436 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN C 18 GLN C 63 ASN E 63 ASN E 263 ASN G 63 ASN I 18 GLN M 63 ASN Q 63 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 = 0.3631 r_free = 0.3631 target = 0.098330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082810 restraints weight = 105961.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.085895 restraints weight = 56754.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088025 restraints weight = 37157.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.089568 restraints weight = 27193.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090694 restraints weight = 21300.264| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 41132 Z= 0.159 Angle : 0.707 24.677 55952 Z= 0.355 Chirality : 0.043 0.367 6240 Planarity : 0.007 0.129 7059 Dihedral : 9.670 59.871 6708 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.23 % Allowed : 20.19 % Favored : 76.58 % Cbeta Deviations : 0.07 % 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: -0.04 (0.12), residues: 4836 helix: 0.49 (0.10), residues: 2964 sheet: 0.06 (0.43), residues: 182 loop : -0.81 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 230 TYR 0.018 0.001 TYR Q 250 PHE 0.023 0.002 PHE Q 289 TRP 0.032 0.002 TRP I 281 HIS 0.002 0.000 HIS G 87 Details of bonding type rmsd covalent geometry : bond 0.00362 (41093) covalent geometry : angle 0.70719 (55952) hydrogen bonds : bond 0.04014 ( 2197) hydrogen bonds : angle 4.48558 ( 6279) Misc. bond : bond 0.00540 ( 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 904 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 773 time to evaluate : 1.686 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: A 1 MET cc_start: 0.5702 (mmm) cc_final: 0.5112 (mmp) REVERT: A 161 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7730 (tm-30) REVERT: C 161 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8002 (tm-30) REVERT: C 256 ASP cc_start: 0.8674 (t0) cc_final: 0.8357 (t0) REVERT: C 297 ARG cc_start: 0.9174 (ttp80) cc_final: 0.8615 (mtp-110) REVERT: C 301 MET cc_start: 0.8797 (mpp) cc_final: 0.8272 (mpp) REVERT: E 1 MET cc_start: 0.5982 (mmm) cc_final: 0.5664 (mmp) REVERT: E 161 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7739 (tm-30) REVERT: E 256 ASP cc_start: 0.8544 (t0) cc_final: 0.8268 (t0) REVERT: G 161 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7459 (tm-30) REVERT: G 200 GLN cc_start: 0.8799 (mt0) cc_final: 0.8449 (mm110) REVERT: G 297 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8920 (mtp-110) REVERT: I 256 ASP cc_start: 0.8621 (t0) cc_final: 0.8352 (t0) REVERT: K 52 LEU cc_start: 0.8538 (tt) cc_final: 0.8332 (tp) REVERT: K 161 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7486 (tm-30) REVERT: K 165 ASP cc_start: 0.8024 (m-30) cc_final: 0.7450 (m-30) REVERT: K 256 ASP cc_start: 0.8704 (t0) cc_final: 0.8421 (t0) REVERT: K 297 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8913 (mtp-110) REVERT: M 297 ARG cc_start: 0.9125 (ttp80) cc_final: 0.8836 (mtp-110) REVERT: O 4 VAL cc_start: 0.8808 (p) cc_final: 0.8595 (p) REVERT: O 161 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7502 (tm-30) REVERT: O 297 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8827 (mtm110) REVERT: Q 10 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7892 (mtm-85) REVERT: Q 14 GLU cc_start: 0.9146 (tp30) cc_final: 0.8753 (mp0) REVERT: Q 161 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7698 (tm-30) REVERT: S 161 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7600 (tm-30) REVERT: S 165 ASP cc_start: 0.8122 (m-30) cc_final: 0.7616 (m-30) REVERT: S 200 GLN cc_start: 0.8768 (mt0) cc_final: 0.8459 (mm110) REVERT: U 161 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7590 (tm-30) REVERT: U 165 ASP cc_start: 0.8038 (m-30) cc_final: 0.7592 (m-30) REVERT: U 238 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7506 (pp30) REVERT: U 301 MET cc_start: 0.8720 (mtm) cc_final: 0.8435 (mpp) REVERT: W 6 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8620 (tptp) REVERT: W 161 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8056 (tm-30) REVERT: W 165 ASP cc_start: 0.8549 (m-30) cc_final: 0.7374 (m-30) REVERT: W 256 ASP cc_start: 0.8609 (t0) cc_final: 0.8348 (t0) REVERT: W 297 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8884 (mtp-110) REVERT: Y 161 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 131 outliers final: 99 residues processed: 839 average time/residue: 0.2566 time to fit residues: 345.6177 Evaluate side-chains 847 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 747 time to evaluate : 1.367 ------------------------------------------------------------------------------- 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 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 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 253 MET 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 157 CYS 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 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 261 ILE Chi-restraints excluded: chain I residue 267 THR 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 170 VAL 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 253 MET 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 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 253 MET 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 90 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 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 261 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 460 optimal weight: 4.9990 chunk 246 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 443 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 0.9990 chunk 473 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 GLN E 63 ASN I 263 ASN M 63 ASN U 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082785 restraints weight = 106289.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085820 restraints weight = 57287.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.087952 restraints weight = 37881.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089482 restraints weight = 28013.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090628 restraints weight = 22114.669| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 41132 Z= 0.160 Angle : 0.753 25.099 55952 Z= 0.375 Chirality : 0.043 0.314 6240 Planarity : 0.007 0.129 7059 Dihedral : 9.669 59.532 6708 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 3.28 % Allowed : 21.10 % Favored : 75.62 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4836 helix: 0.52 (0.10), residues: 2964 sheet: 0.26 (0.44), residues: 182 loop : -0.76 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 304 TYR 0.017 0.001 TYR G 250 PHE 0.021 0.002 PHE G 289 TRP 0.042 0.002 TRP Y 281 HIS 0.002 0.000 HIS M 87 Details of bonding type rmsd covalent geometry : bond 0.00365 (41093) covalent geometry : angle 0.75316 (55952) hydrogen bonds : bond 0.04028 ( 2197) hydrogen bonds : angle 4.50166 ( 6279) Misc. bond : bond 0.00512 ( 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 896 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 763 time to evaluate : 1.477 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: A 161 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 274 LYS cc_start: 0.8628 (tttt) cc_final: 0.8304 (ttpt) REVERT: C 161 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8028 (tm-30) REVERT: C 256 ASP cc_start: 0.8651 (t0) cc_final: 0.8367 (t0) REVERT: C 297 ARG cc_start: 0.9190 (ttp80) cc_final: 0.8941 (mtp-110) REVERT: E 1 MET cc_start: 0.6014 (mmm) cc_final: 0.5739 (mmp) REVERT: E 10 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.8032 (mtm110) REVERT: E 14 GLU cc_start: 0.9162 (tp30) cc_final: 0.8762 (mp0) REVERT: E 161 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7732 (tm-30) REVERT: E 256 ASP cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: G 6 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8630 (tptp) REVERT: G 161 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7463 (tm-30) REVERT: G 200 GLN cc_start: 0.8829 (mt0) cc_final: 0.8452 (mm110) REVERT: G 297 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8524 (mtp-110) REVERT: G 301 MET cc_start: 0.8668 (mtm) cc_final: 0.8410 (mpp) REVERT: I 256 ASP cc_start: 0.8669 (t0) cc_final: 0.8401 (t0) REVERT: K 161 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7614 (tm-30) REVERT: K 165 ASP cc_start: 0.8056 (m-30) cc_final: 0.7723 (m-30) REVERT: K 256 ASP cc_start: 0.8694 (t0) cc_final: 0.8430 (t0) REVERT: K 297 ARG cc_start: 0.9095 (ttp80) cc_final: 0.8586 (mtp-110) REVERT: K 301 MET cc_start: 0.8573 (mtm) cc_final: 0.8332 (mpp) REVERT: M 253 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7431 (tpt) REVERT: M 297 ARG cc_start: 0.9111 (ttp80) cc_final: 0.8864 (mtm110) REVERT: O 161 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7644 (tm-30) REVERT: O 297 ARG cc_start: 0.9100 (ttp80) cc_final: 0.8584 (mtm110) REVERT: O 301 MET cc_start: 0.8747 (mpp) cc_final: 0.8235 (mpp) REVERT: Q 6 LYS cc_start: 0.8843 (tttt) cc_final: 0.8509 (tmtt) REVERT: Q 14 GLU cc_start: 0.9153 (tp30) cc_final: 0.8752 (mp0) REVERT: Q 161 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7668 (tm-30) REVERT: S 161 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7727 (tm-30) REVERT: S 200 GLN cc_start: 0.8779 (mt0) cc_final: 0.8464 (mm110) REVERT: S 274 LYS cc_start: 0.8515 (tttt) cc_final: 0.8196 (ttpt) REVERT: U 161 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7569 (tm-30) REVERT: U 165 ASP cc_start: 0.8055 (m-30) cc_final: 0.7527 (m-30) REVERT: U 238 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7486 (pp30) REVERT: U 301 MET cc_start: 0.8699 (mtm) cc_final: 0.8389 (mpp) REVERT: W 6 LYS cc_start: 0.9073 (tmtt) cc_final: 0.8636 (tptp) REVERT: W 256 ASP cc_start: 0.8616 (t0) cc_final: 0.8345 (t0) REVERT: W 297 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8602 (mtp-110) REVERT: W 301 MET cc_start: 0.8693 (mtm) cc_final: 0.8403 (mpp) REVERT: Y 161 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7562 (tm-30) REVERT: Y 165 ASP cc_start: 0.8078 (m-30) cc_final: 0.7558 (m-30) outliers start: 133 outliers final: 107 residues processed: 832 average time/residue: 0.2458 time to fit residues: 328.9862 Evaluate side-chains 853 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 744 time to evaluate : 1.465 ------------------------------------------------------------------------------- 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 261 ILE 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 C residue 334 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 MET 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 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 261 ILE Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 267 THR 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 170 VAL 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 246 LEU Chi-restraints excluded: chain M residue 253 MET 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 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 253 MET 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 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 261 ILE 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 322 MET 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 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 261 ILE Chi-restraints excluded: chain U residue 267 THR 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 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 170 VAL 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: 2.9990 chunk 332 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 465 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 166 optimal weight: 0.0010 chunk 322 optimal weight: 0.7980 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 263 ASN E 263 ASN I 263 ASN O 63 ASN Q 63 ASN Q 162 GLN Y 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.098202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082481 restraints weight = 106278.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085495 restraints weight = 57986.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087602 restraints weight = 38543.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089119 restraints weight = 28532.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.090234 restraints weight = 22609.612| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 41132 Z= 0.175 Angle : 0.826 26.548 55952 Z= 0.409 Chirality : 0.044 0.311 6240 Planarity : 0.007 0.129 7059 Dihedral : 9.732 59.442 6708 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 3.21 % Allowed : 21.65 % Favored : 75.15 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 4836 helix: 0.50 (0.10), residues: 2964 sheet: 0.32 (0.45), residues: 182 loop : -0.72 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 304 TYR 0.015 0.002 TYR C 275 PHE 0.024 0.002 PHE C 289 TRP 0.036 0.002 TRP Y 281 HIS 0.002 0.000 HIS Y 87 Details of bonding type rmsd covalent geometry : bond 0.00405 (41093) covalent geometry : angle 0.82599 (55952) hydrogen bonds : bond 0.04127 ( 2197) hydrogen bonds : angle 4.55611 ( 6279) Misc. bond : bond 0.00594 ( 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 889 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 759 time to evaluate : 1.743 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: A 6 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8598 (tptp) REVERT: A 161 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 161 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8190 (tm-30) REVERT: C 165 ASP cc_start: 0.8467 (m-30) cc_final: 0.8090 (p0) REVERT: C 256 ASP cc_start: 0.8644 (t0) cc_final: 0.8415 (t0) REVERT: C 297 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8647 (mtp-110) REVERT: E 1 MET cc_start: 0.5924 (mmm) cc_final: 0.5663 (mmp) REVERT: E 161 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7656 (tm-30) REVERT: E 256 ASP cc_start: 0.8568 (t0) cc_final: 0.8297 (t0) REVERT: G 161 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 200 GLN cc_start: 0.8810 (mt0) cc_final: 0.8449 (mm110) REVERT: G 253 MET cc_start: 0.7583 (tpt) cc_final: 0.6495 (tpt) REVERT: G 256 ASP cc_start: 0.8638 (t0) cc_final: 0.8026 (t0) REVERT: G 274 LYS cc_start: 0.8548 (tttt) cc_final: 0.8201 (ttpp) REVERT: G 297 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8496 (mtp-110) REVERT: G 301 MET cc_start: 0.8609 (mtm) cc_final: 0.8394 (mpp) REVERT: I 256 ASP cc_start: 0.8641 (t0) cc_final: 0.8412 (t0) REVERT: I 274 LYS cc_start: 0.8621 (tttt) cc_final: 0.8307 (ttpt) REVERT: K 161 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7622 (tm-30) REVERT: K 165 ASP cc_start: 0.8058 (m-30) cc_final: 0.7718 (m-30) REVERT: K 253 MET cc_start: 0.7647 (tpt) cc_final: 0.7350 (tpt) REVERT: K 256 ASP cc_start: 0.8678 (t0) cc_final: 0.8469 (t0) REVERT: K 297 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8563 (mtp-110) REVERT: K 301 MET cc_start: 0.8555 (mtm) cc_final: 0.8333 (mpp) REVERT: M 253 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7408 (tpt) REVERT: M 274 LYS cc_start: 0.8599 (tttt) cc_final: 0.8238 (ttpp) REVERT: M 297 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8600 (mtp-110) REVERT: M 301 MET cc_start: 0.8642 (mtm) cc_final: 0.8346 (mpp) REVERT: O 161 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7644 (tm-30) REVERT: O 253 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7546 (tpt) REVERT: O 297 ARG cc_start: 0.9121 (ttp80) cc_final: 0.8593 (mtm110) REVERT: O 301 MET cc_start: 0.8740 (mpp) cc_final: 0.8227 (mpp) REVERT: Q 6 LYS cc_start: 0.8867 (tttt) cc_final: 0.8529 (tmtt) REVERT: Q 14 GLU cc_start: 0.9139 (tp30) cc_final: 0.8754 (mp0) REVERT: Q 161 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7497 (tm-30) REVERT: S 161 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7512 (tm-30) REVERT: S 165 ASP cc_start: 0.8128 (m-30) cc_final: 0.7531 (m-30) REVERT: S 200 GLN cc_start: 0.8778 (mt0) cc_final: 0.8471 (mm110) REVERT: U 1 MET cc_start: 0.5765 (mmm) cc_final: 0.5429 (mmp) REVERT: U 161 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7496 (tm-30) REVERT: U 165 ASP cc_start: 0.8105 (m-30) cc_final: 0.7528 (m-30) REVERT: U 238 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7494 (pp30) REVERT: W 161 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8067 (tm-30) REVERT: W 256 ASP cc_start: 0.8622 (t0) cc_final: 0.8361 (t0) REVERT: W 297 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8562 (mtp-110) REVERT: W 301 MET cc_start: 0.8635 (mtm) cc_final: 0.8379 (mpp) REVERT: Y 161 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7617 (tm-30) REVERT: Y 274 LYS cc_start: 0.8545 (tttt) cc_final: 0.8226 (ttpp) outliers start: 130 outliers final: 109 residues processed: 824 average time/residue: 0.2649 time to fit residues: 349.5691 Evaluate side-chains 854 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 742 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 261 ILE 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 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 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 263 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 322 MET 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 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 261 ILE Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 267 THR 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 170 VAL 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 246 LEU Chi-restraints excluded: chain M residue 253 MET 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 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 253 MET 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 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 261 ILE 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 322 MET 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 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 261 ILE Chi-restraints excluded: chain U residue 267 THR 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 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 4 VAL 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 261 ILE 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: 5.9990 chunk 401 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 0.2980 chunk 354 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 360 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 304 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 212 GLN C 63 ASN E 263 ASN G 212 GLN I 63 ASN I 212 GLN I 263 ASN K 63 ASN U 63 ASN U 263 ASN W 63 ASN ** Y 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.084788 restraints weight = 104552.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087877 restraints weight = 56835.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090056 restraints weight = 37648.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091609 restraints weight = 27810.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092742 restraints weight = 21918.895| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 41132 Z= 0.148 Angle : 0.852 27.137 55952 Z= 0.415 Chirality : 0.042 0.305 6240 Planarity : 0.007 0.126 7059 Dihedral : 9.676 59.538 6708 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.91 % Allowed : 22.34 % Favored : 74.75 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.46 % 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: 0.21 (0.12), residues: 4836 helix: 0.62 (0.10), residues: 2964 sheet: 0.33 (0.44), residues: 182 loop : -0.58 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG G 230 TYR 0.017 0.001 TYR Q 250 PHE 0.023 0.002 PHE C 289 TRP 0.032 0.002 TRP Y 281 HIS 0.001 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00337 (41093) covalent geometry : angle 0.85227 (55952) hydrogen bonds : bond 0.03970 ( 2197) hydrogen bonds : angle 4.52220 ( 6279) Misc. bond : bond 0.00624 ( 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 883 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 765 time to evaluate : 1.527 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: 0.7945 (tm-30) cc_final: 0.7554 (tm-30) REVERT: A 274 LYS cc_start: 0.8558 (tttt) cc_final: 0.8256 (ttpt) REVERT: C 161 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8039 (tm-30) REVERT: C 162 GLN cc_start: 0.8546 (mt0) cc_final: 0.8221 (mm-40) REVERT: C 256 ASP cc_start: 0.8644 (t0) cc_final: 0.8425 (t0) REVERT: C 274 LYS cc_start: 0.8585 (tttt) cc_final: 0.8313 (ttpt) REVERT: C 297 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8893 (mtp-110) REVERT: E 1 MET cc_start: 0.5799 (mmm) cc_final: 0.5556 (mmp) REVERT: E 16 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 161 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7568 (tm-30) REVERT: E 256 ASP cc_start: 0.8565 (t0) cc_final: 0.8298 (t0) REVERT: E 301 MET cc_start: 0.8732 (mtm) cc_final: 0.8377 (mpp) REVERT: G 161 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7486 (tm-30) REVERT: G 200 GLN cc_start: 0.8791 (mt0) cc_final: 0.8427 (mm110) REVERT: G 297 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8471 (mtp-110) REVERT: I 301 MET cc_start: 0.8684 (mtm) cc_final: 0.8339 (mpp) REVERT: K 6 LYS cc_start: 0.8994 (tptp) cc_final: 0.8654 (tptp) REVERT: K 161 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7593 (tm-30) REVERT: K 165 ASP cc_start: 0.8042 (m-30) cc_final: 0.7699 (m-30) REVERT: K 253 MET cc_start: 0.7617 (tpt) cc_final: 0.7346 (tpt) REVERT: K 297 ARG cc_start: 0.9089 (ttp80) cc_final: 0.8795 (mtp-110) REVERT: M 161 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7596 (tm-30) REVERT: M 256 ASP cc_start: 0.8647 (t0) cc_final: 0.8199 (t0) REVERT: M 297 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8398 (mtm110) REVERT: M 301 MET cc_start: 0.8571 (mtm) cc_final: 0.8298 (mpp) REVERT: M 308 GLU cc_start: 0.8582 (pm20) cc_final: 0.8377 (pm20) REVERT: O 161 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7597 (tm-30) REVERT: O 297 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8564 (mtm110) REVERT: O 301 MET cc_start: 0.8735 (mpp) cc_final: 0.8169 (mpp) REVERT: Q 6 LYS cc_start: 0.8865 (tttt) cc_final: 0.8533 (tmtt) REVERT: Q 14 GLU cc_start: 0.9131 (tp30) cc_final: 0.8748 (mp0) REVERT: Q 161 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7529 (tm-30) REVERT: Q 301 MET cc_start: 0.8743 (mtm) cc_final: 0.8388 (mpp) REVERT: S 161 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7613 (tm-30) REVERT: S 165 ASP cc_start: 0.8127 (m-30) cc_final: 0.7600 (m-30) REVERT: S 200 GLN cc_start: 0.8739 (mt0) cc_final: 0.8450 (mm110) REVERT: S 274 LYS cc_start: 0.8637 (tttt) cc_final: 0.8264 (ttpp) REVERT: S 301 MET cc_start: 0.8717 (mtm) cc_final: 0.8365 (mpp) REVERT: U 1 MET cc_start: 0.5812 (mmm) cc_final: 0.5506 (mmp) REVERT: U 161 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7480 (tm-30) REVERT: U 165 ASP cc_start: 0.8072 (m-30) cc_final: 0.7477 (m-30) REVERT: U 238 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7465 (pp30) REVERT: W 6 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8776 (tptp) REVERT: W 16 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7665 (mm-30) REVERT: W 161 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7999 (tm-30) REVERT: W 256 ASP cc_start: 0.8635 (t0) cc_final: 0.8398 (t0) REVERT: W 295 LYS cc_start: 0.8611 (tttt) cc_final: 0.8244 (ttpt) REVERT: W 297 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8539 (mtm110) REVERT: W 301 MET cc_start: 0.8529 (mtm) cc_final: 0.8296 (mpp) REVERT: Y 1 MET cc_start: 0.5160 (mmm) cc_final: 0.4685 (mmp) REVERT: Y 6 LYS cc_start: 0.8858 (tptp) cc_final: 0.8511 (tptp) REVERT: Y 161 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7505 (tm-30) REVERT: Y 165 ASP cc_start: 0.8022 (m-30) cc_final: 0.7399 (m-30) REVERT: Y 301 MET cc_start: 0.8722 (mtm) cc_final: 0.8341 (mpp) outliers start: 118 outliers final: 105 residues processed: 826 average time/residue: 0.2614 time to fit residues: 346.8415 Evaluate side-chains 839 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 733 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 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 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 263 ASN Chi-restraints excluded: chain E residue 267 THR Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 322 MET 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 261 ILE 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 261 ILE Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 267 THR 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 246 LEU Chi-restraints excluded: chain M residue 253 MET 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 246 LEU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 322 MET 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 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 322 MET 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 280 LYS 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 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 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 4 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 170 VAL 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: 0.9990 chunk 332 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 358 optimal weight: 0.7980 chunk 475 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 247 optimal weight: 0.5980 chunk 412 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN C 87 HIS C 263 ASN I 125 ASN I 263 ASN Q 263 ASN S 63 ASN W 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.101291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.085377 restraints weight = 104397.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088505 restraints weight = 56852.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.090663 restraints weight = 37626.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092217 restraints weight = 27857.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.093396 restraints weight = 21984.735| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 41132 Z= 0.157 Angle : 0.891 27.502 55952 Z= 0.435 Chirality : 0.043 0.411 6240 Planarity : 0.007 0.125 7059 Dihedral : 9.696 59.374 6708 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.86 % Allowed : 22.86 % Favored : 74.29 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: 0.21 (0.12), residues: 4836 helix: 0.61 (0.10), residues: 2964 sheet: 0.37 (0.44), residues: 182 loop : -0.57 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 230 TYR 0.045 0.001 TYR Q 199 PHE 0.022 0.002 PHE G 289 TRP 0.030 0.002 TRP Y 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00365 (41093) covalent geometry : angle 0.89112 (55952) hydrogen bonds : bond 0.04034 ( 2197) hydrogen bonds : angle 4.58603 ( 6279) Misc. bond : bond 0.00606 ( 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 873 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 757 time to evaluate : 1.719 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: A 161 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 165 ASP cc_start: 0.8083 (m-30) cc_final: 0.7184 (m-30) REVERT: C 161 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8063 (tm-30) REVERT: C 162 GLN cc_start: 0.8527 (mt0) cc_final: 0.8173 (mm-40) REVERT: C 297 ARG cc_start: 0.9090 (ttp80) cc_final: 0.8731 (mtm110) REVERT: E 1 MET cc_start: 0.5817 (mmm) cc_final: 0.5560 (mmp) REVERT: E 161 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 165 ASP cc_start: 0.8122 (m-30) cc_final: 0.7453 (m-30) REVERT: E 256 ASP cc_start: 0.8544 (t0) cc_final: 0.8311 (t0) REVERT: G 161 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7433 (tm-30) REVERT: G 200 GLN cc_start: 0.8781 (mt0) cc_final: 0.8429 (mm110) REVERT: G 297 ARG cc_start: 0.8990 (ttp80) cc_final: 0.8700 (mtm110) REVERT: K 6 LYS cc_start: 0.8997 (tptp) cc_final: 0.8645 (tptp) REVERT: K 161 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7552 (tm-30) REVERT: K 165 ASP cc_start: 0.8012 (m-30) cc_final: 0.7538 (m-30) REVERT: K 297 ARG cc_start: 0.9071 (ttp80) cc_final: 0.8801 (mtp-110) REVERT: M 161 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7585 (tm-30) REVERT: M 297 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8448 (mtm110) REVERT: M 301 MET cc_start: 0.8543 (mtm) cc_final: 0.8292 (mpp) REVERT: M 308 GLU cc_start: 0.8590 (pm20) cc_final: 0.8384 (pm20) REVERT: O 161 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7607 (tm-30) REVERT: O 297 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8573 (mtm110) REVERT: O 301 MET cc_start: 0.8732 (mpp) cc_final: 0.8164 (mpp) REVERT: Q 6 LYS cc_start: 0.8872 (tttt) cc_final: 0.8543 (tmtt) REVERT: Q 14 GLU cc_start: 0.9118 (tp30) cc_final: 0.8755 (mp0) REVERT: Q 161 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7539 (tm-30) REVERT: Q 200 GLN cc_start: 0.8798 (mt0) cc_final: 0.8432 (mm110) REVERT: S 161 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7617 (tm-30) REVERT: S 165 ASP cc_start: 0.8098 (m-30) cc_final: 0.7577 (m-30) REVERT: S 200 GLN cc_start: 0.8736 (mt0) cc_final: 0.8456 (mm110) REVERT: U 1 MET cc_start: 0.5781 (mmm) cc_final: 0.5495 (mmp) REVERT: U 161 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7498 (tm-30) REVERT: U 165 ASP cc_start: 0.8026 (m-30) cc_final: 0.7414 (m-30) REVERT: U 238 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7482 (pp30) REVERT: U 301 MET cc_start: 0.8616 (mtm) cc_final: 0.8374 (mpp) REVERT: W 6 LYS cc_start: 0.9030 (tmtt) cc_final: 0.8751 (tptp) REVERT: W 161 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8009 (tm-30) REVERT: W 256 ASP cc_start: 0.8637 (t0) cc_final: 0.8407 (t0) REVERT: W 295 LYS cc_start: 0.8634 (tttt) cc_final: 0.8264 (ttpp) REVERT: W 297 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8510 (mtm110) REVERT: W 301 MET cc_start: 0.8490 (mtm) cc_final: 0.8281 (mpp) REVERT: Y 1 MET cc_start: 0.5119 (mmm) cc_final: 0.4650 (mmp) REVERT: Y 6 LYS cc_start: 0.8848 (tptp) cc_final: 0.8479 (tptp) REVERT: Y 161 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7634 (tm-30) REVERT: Y 256 ASP cc_start: 0.8594 (t0) cc_final: 0.8092 (t0) outliers start: 116 outliers final: 105 residues processed: 823 average time/residue: 0.2571 time to fit residues: 341.1506 Evaluate side-chains 843 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 737 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 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 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 304 ARG Chi-restraints excluded: chain E residue 322 MET 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 261 ILE 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 261 ILE Chi-restraints excluded: chain I residue 263 ASN Chi-restraints excluded: chain I residue 267 THR 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 246 LEU Chi-restraints excluded: chain M residue 253 MET 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 170 VAL Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 246 LEU Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 322 MET 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 263 ASN 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 322 MET 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 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 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 263 ASN 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 4 VAL 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: 0.9990 chunk 373 optimal weight: 9.9990 chunk 440 optimal weight: 0.6980 chunk 212 optimal weight: 1.9990 chunk 310 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 465 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN I 263 ASN Q 263 ASN U 263 ASN W 263 ASN Y 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.101359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.085376 restraints weight = 104732.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088550 restraints weight = 57004.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.090744 restraints weight = 37592.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092320 restraints weight = 27656.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093489 restraints weight = 21815.112| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.242 41132 Z= 0.239 Angle : 0.977 59.200 55952 Z= 0.504 Chirality : 0.053 2.200 6240 Planarity : 0.007 0.157 7059 Dihedral : 9.698 59.366 6708 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 2.86 % Allowed : 23.25 % Favored : 73.89 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: 0.21 (0.12), residues: 4836 helix: 0.61 (0.10), residues: 2964 sheet: 0.37 (0.44), residues: 182 loop : -0.57 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 230 TYR 0.062 0.002 TYR Y 199 PHE 0.051 0.002 PHE Q 235 TRP 0.051 0.003 TRP W 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd covalent geometry : bond 0.00522 (41093) covalent geometry : angle 0.97739 (55952) hydrogen bonds : bond 0.04054 ( 2197) hydrogen bonds : angle 4.62321 ( 6279) Misc. bond : bond 0.00599 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10911.65 seconds wall clock time: 188 minutes 16.03 seconds (11296.03 seconds total)