Starting phenix.real_space_refine on Tue Sep 15 13:52:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ewq_31361/09_2026/7ewq_31361.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 247 5.16 5 C 25246 2.51 5 N 6890 2.21 5 O 7683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 247 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40144 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2968 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 19, 'TRANS': 354} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNAv2': 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: 6.04, per 1000 atoms: 0.15 Number of scatterers: 40144 At special positions: 0 Unit cell: (202.99, 202.46, 83.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 247 16.00 P 78 15.00 O 7683 8.00 N 6890 7.00 C 25246 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=39, symmetry=0 Number of additional bonds: simple=39, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.93 Conformation dependent library (CDL) restraints added in 1.9 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: 4.87 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: 8.89 Time building geometry restraints manager: 5.30 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: 49043 1.11 - 2.22: 5462 2.22 - 3.34: 957 3.34 - 4.45: 383 4.45 - 5.56: 107 Bond angle restraints: 55952 Sorted by residual: angle pdb=" C ILE M 261 " pdb=" CA ILE M 261 " pdb=" CB ILE M 261 " ideal model delta sigma weight residual 111.97 108.81 3.16 1.28e+00 6.10e-01 6.09e+00 angle pdb=" C ILE W 261 " pdb=" CA ILE W 261 " pdb=" CB ILE W 261 " ideal model delta sigma weight residual 111.97 108.83 3.14 1.28e+00 6.10e-01 6.03e+00 angle pdb=" C ILE K 261 " pdb=" CA ILE K 261 " pdb=" CB ILE K 261 " ideal model delta sigma weight residual 111.97 108.86 3.11 1.28e+00 6.10e-01 5.91e+00 angle pdb=" C ILE E 261 " pdb=" CA ILE E 261 " pdb=" CB ILE E 261 " ideal model delta sigma weight residual 111.97 108.86 3.11 1.28e+00 6.10e-01 5.89e+00 angle pdb=" C ILE C 261 " pdb=" CA ILE C 261 " pdb=" CB ILE C 261 " ideal model delta sigma weight residual 111.97 108.87 3.10 1.28e+00 6.10e-01 5.86e+00 ... (remaining 55947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 21367 16.72 - 33.44: 2643 33.44 - 50.16: 417 50.16 - 66.88: 234 66.88 - 83.61: 130 Dihedral angle restraints: 24791 sinusoidal: 10595 harmonic: 14196 Sorted by residual: dihedral pdb=" C4' U X 25 " pdb=" C3' U X 25 " pdb=" C2' U X 25 " pdb=" C1' U X 25 " ideal model delta sinusoidal sigma weight residual 36.34 -34.91 71.26 1 3.10e+00 1.04e-01 6.78e+02 dihedral pdb=" C4' U T 25 " pdb=" C3' U T 25 " pdb=" C2' U T 25 " pdb=" C1' U T 25 " ideal model delta sinusoidal sigma weight residual 36.34 -34.90 71.24 1 3.10e+00 1.04e-01 6.78e+02 dihedral pdb=" C4' U N 25 " pdb=" C3' U N 25 " pdb=" C2' U N 25 " pdb=" C1' U N 25 " ideal model delta sinusoidal sigma weight residual 36.34 -34.89 71.23 1 3.10e+00 1.04e-01 6.78e+02 ... (remaining 24788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4850 0.056 - 0.112: 1187 0.112 - 0.169: 73 0.169 - 0.225: 26 0.225 - 0.281: 104 Chirality restraints: 6240 Sorted by residual: chirality pdb=" C2' U H 22 " pdb=" C3' U H 22 " pdb=" O2' U H 22 " pdb=" C1' U H 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' U V 22 " pdb=" C3' U V 22 " pdb=" O2' U V 22 " pdb=" C1' U V 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C2' U X 22 " pdb=" C3' U X 22 " pdb=" O2' U X 22 " pdb=" C1' U X 22 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (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: 0.16 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: 29.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.470 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 39.970 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.024 0.957 41132 Z= 2.358 Angle : 0.819 5.560 55952 Z= 0.463 Chirality : 0.056 0.281 6240 Planarity : 0.004 0.036 7059 Dihedral : 16.277 83.606 15717 Min Nonbonded Distance : 0.503 Molprobity Statistics. All-atom Clashscore : 30.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.10), residues: 4836 helix: -2.20 (0.08), residues: 2834 sheet: -1.78 (0.39), residues: 156 loop : -2.15 (0.13), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 10 TYR 0.016 0.002 TYR O 361 PHE 0.017 0.002 PHE G 8 TRP 0.010 0.002 TRP M 175 HIS 0.002 0.001 HIS W 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.29 (41093) covalent geometry : angle 0.81913 / 0.46 (55952) hydrogen bonds : bond 0.13572 / 8.93 ( 2197) hydrogen bonds : angle 6.38915 / 4.55 ( 6279) Misc. bond : bond 0.76005 / 51.15 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1064 time to evaluate : 1.712 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: 0.3116 time to fit residues: 507.8888 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 : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.0020 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 125 ASN A 212 GLN A 231 GLN A 346 GLN A 373 GLN C 68 HIS C 125 ASN C 212 GLN C 231 GLN C 346 GLN C 373 GLN E 18 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 18 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: 76 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.096568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080507 restraints weight = 105579.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083722 restraints weight = 54998.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085960 restraints weight = 35551.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087540 restraints weight = 25825.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088730 restraints weight = 20167.500| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41132 Z= 0.155 Angle : 0.748 10.052 55952 Z= 0.369 Chirality : 0.055 0.463 6240 Planarity : 0.009 0.185 7059 Dihedral : 8.809 131.294 6396 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.45 % Allowed : 14.13 % Favored : 84.42 % 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: -1.26 (0.11), residues: 4836 helix: -0.37 (0.09), residues: 2899 sheet: -1.14 (0.45), residues: 156 loop : -1.42 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG U 304 TYR 0.030 0.002 TYR K 251 PHE 0.019 0.002 PHE Q 270 TRP 0.005 0.001 TRP O 281 HIS 0.002 0.000 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (41093) covalent geometry : angle 0.74845 / 0.37 (55952) hydrogen bonds : bond 0.04641 / 3.08 ( 2197) hydrogen bonds : angle 4.86890 / 3.44 ( 6279) Misc. bond : bond 0.00439 / 0.28 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9672 Ramachandran restraints generated. 4836 Oldfield, 0 Emsley, 4836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 936 time to evaluate : 1.599 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 253 MET cc_start: 0.7911 (tpt) cc_final: 0.7586 (tpt) REVERT: A 256 ASP cc_start: 0.8791 (t0) cc_final: 0.8534 (t0) REVERT: A 297 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8739 (ttp80) REVERT: A 301 MET cc_start: 0.8770 (mtm) cc_final: 0.8390 (mpp) REVERT: A 309 GLN cc_start: 0.8215 (mp10) cc_final: 0.7914 (mp10) REVERT: C 10 ARG cc_start: 0.8185 (ttp-110) cc_final: 0.7935 (ttp-110) REVERT: C 256 ASP cc_start: 0.8792 (t0) cc_final: 0.8479 (t0) REVERT: C 297 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8550 (mtp-110) REVERT: C 301 MET cc_start: 0.8720 (mtm) cc_final: 0.8465 (mpp) REVERT: E 200 GLN cc_start: 0.8834 (mt0) cc_final: 0.8587 (mm110) REVERT: E 256 ASP cc_start: 0.8806 (t0) cc_final: 0.8458 (t0) REVERT: E 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8551 (ttp80) REVERT: E 301 MET cc_start: 0.8748 (mtm) cc_final: 0.8453 (mpp) REVERT: G 297 ARG cc_start: 0.9064 (ttp80) cc_final: 0.8650 (ttp80) REVERT: G 301 MET cc_start: 0.8748 (mtm) cc_final: 0.8472 (mpp) REVERT: G 309 GLN cc_start: 0.8270 (mp10) cc_final: 0.7851 (mp10) REVERT: I 6 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8639 (tptp) REVERT: I 256 ASP cc_start: 0.8804 (t0) cc_final: 0.8495 (t0) REVERT: I 297 ARG cc_start: 0.9043 (ttp80) cc_final: 0.8656 (ttp80) REVERT: I 301 MET cc_start: 0.8740 (mtm) cc_final: 0.8461 (mpp) REVERT: K 200 GLN cc_start: 0.8840 (mt0) cc_final: 0.8582 (mm110) REVERT: K 256 ASP cc_start: 0.8805 (t0) cc_final: 0.8461 (t0) REVERT: K 297 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8704 (ttp80) REVERT: K 301 MET cc_start: 0.8773 (mtm) cc_final: 0.8432 (mpp) REVERT: M 297 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8710 (ttp80) REVERT: M 301 MET cc_start: 0.8740 (mtm) cc_final: 0.8414 (mpp) REVERT: O 256 ASP cc_start: 0.8779 (t0) cc_final: 0.8463 (t0) REVERT: O 274 LYS cc_start: 0.8852 (ttpp) cc_final: 0.8616 (tttt) REVERT: O 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8567 (mtp-110) REVERT: O 301 MET cc_start: 0.8735 (mtm) cc_final: 0.8448 (mpp) REVERT: Q 256 ASP cc_start: 0.8809 (t0) cc_final: 0.8041 (t0) REVERT: Q 274 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8592 (tttt) REVERT: Q 297 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8605 (mtp-110) REVERT: Q 301 MET cc_start: 0.8748 (mtm) cc_final: 0.8434 (mpp) REVERT: Q 322 MET cc_start: 0.8134 (mmm) cc_final: 0.7924 (tpt) REVERT: S 200 GLN cc_start: 0.8814 (mt0) cc_final: 0.8595 (mm110) REVERT: S 256 ASP cc_start: 0.8806 (t0) cc_final: 0.8509 (t0) REVERT: S 274 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8621 (tttt) REVERT: S 297 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8484 (mtp-110) REVERT: S 301 MET cc_start: 0.8745 (mtm) cc_final: 0.8431 (mpp) REVERT: U 199 TYR cc_start: 0.8401 (m-10) cc_final: 0.7898 (m-10) REVERT: U 200 GLN cc_start: 0.8805 (mt0) cc_final: 0.8544 (mm110) REVERT: U 256 ASP cc_start: 0.8798 (t0) cc_final: 0.7972 (t0) REVERT: U 297 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8562 (mtp-110) REVERT: U 301 MET cc_start: 0.8741 (mtm) cc_final: 0.8470 (mpp) REVERT: W 161 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8157 (tm-30) REVERT: W 199 TYR cc_start: 0.8437 (m-10) cc_final: 0.8095 (m-80) REVERT: W 256 ASP cc_start: 0.8805 (t0) cc_final: 0.7986 (t0) REVERT: W 297 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8602 (mtp-110) REVERT: W 301 MET cc_start: 0.8774 (mtm) cc_final: 0.8465 (mpp) REVERT: W 309 GLN cc_start: 0.8182 (mp10) cc_final: 0.7895 (mp10) REVERT: Y 256 ASP cc_start: 0.8773 (t0) cc_final: 0.8456 (t0) REVERT: Y 297 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8683 (ttp80) REVERT: Y 301 MET cc_start: 0.8782 (mtm) cc_final: 0.8391 (mpp) outliers start: 59 outliers final: 26 residues processed: 964 average time/residue: 0.2720 time to fit residues: 420.7980 Evaluate side-chains 835 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 809 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 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 185 TYR Chi-restraints excluded: chain Y residue 185 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 134 optimal weight: 2.9990 chunk 250 optimal weight: 0.8980 chunk 416 optimal weight: 7.9990 chunk 408 optimal weight: 0.0670 chunk 272 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 434 optimal weight: 1.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 HIS A 212 GLN C 212 GLN E 87 HIS E 212 GLN G 87 HIS G 212 GLN I 87 HIS I 212 GLN K 212 GLN M 212 GLN O 87 HIS O 212 GLN Q 87 HIS Q 212 GLN 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.099549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084694 restraints weight = 104974.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087636 restraints weight = 55762.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.089717 restraints weight = 36371.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.091207 restraints weight = 26485.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092276 restraints weight = 20689.929| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41132 Z= 0.137 Angle : 0.657 8.897 55952 Z= 0.323 Chirality : 0.050 0.378 6240 Planarity : 0.007 0.132 7059 Dihedral : 8.601 133.493 6396 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.93 % Allowed : 16.86 % Favored : 80.20 % 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: -0.49 (0.12), residues: 4836 helix: 0.22 (0.10), residues: 2951 sheet: -0.72 (0.46), residues: 156 loop : -1.09 (0.13), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 230 TYR 0.018 0.001 TYR G 251 PHE 0.014 0.001 PHE Y 270 TRP 0.012 0.002 TRP S 281 HIS 0.002 0.000 HIS O 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (41093) covalent geometry : angle 0.65671 / 0.32 (55952) hydrogen bonds : bond 0.04156 / 2.76 ( 2197) hydrogen bonds : angle 4.59284 / 3.25 ( 6279) Misc. bond : bond 0.00356 / 0.25 ( 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 993 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 874 time to evaluate : 1.689 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 256 ASP cc_start: 0.8786 (t0) cc_final: 0.8020 (t0) REVERT: A 274 LYS cc_start: 0.8864 (ttpp) cc_final: 0.8645 (tttt) REVERT: A 297 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8716 (mtp-110) REVERT: A 301 MET cc_start: 0.8673 (mtm) cc_final: 0.8416 (mpp) REVERT: A 309 GLN cc_start: 0.8374 (mp10) cc_final: 0.8070 (mp10) REVERT: A 322 MET cc_start: 0.8297 (tpt) cc_final: 0.8028 (tpt) REVERT: C 10 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7953 (ttp-110) REVERT: C 199 TYR cc_start: 0.8397 (m-80) cc_final: 0.7977 (m-80) REVERT: C 256 ASP cc_start: 0.8764 (t0) cc_final: 0.8171 (t0) REVERT: C 289 PHE cc_start: 0.8359 (m-80) cc_final: 0.8078 (m-10) REVERT: C 297 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8518 (mtp-110) REVERT: C 311 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6755 (mtm110) REVERT: C 322 MET cc_start: 0.8214 (mmm) cc_final: 0.8011 (tpt) REVERT: E 161 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 199 TYR cc_start: 0.8361 (m-80) cc_final: 0.7913 (m-10) REVERT: E 256 ASP cc_start: 0.8761 (t0) cc_final: 0.7966 (t0) REVERT: E 297 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8554 (mtp-110) REVERT: E 301 MET cc_start: 0.8639 (mtm) cc_final: 0.8424 (mpp) REVERT: G 200 GLN cc_start: 0.8809 (mt0) cc_final: 0.8479 (mm110) REVERT: G 289 PHE cc_start: 0.8389 (m-80) cc_final: 0.8182 (m-10) REVERT: G 297 ARG cc_start: 0.9109 (ttp80) cc_final: 0.8587 (mtp-110) REVERT: G 301 MET cc_start: 0.8647 (mtm) cc_final: 0.8437 (mpp) REVERT: G 309 GLN cc_start: 0.8392 (mp10) cc_final: 0.8075 (mp10) REVERT: I 253 MET cc_start: 0.7843 (tpt) cc_final: 0.7109 (tpt) REVERT: I 274 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8650 (tttt) REVERT: I 289 PHE cc_start: 0.8389 (m-80) cc_final: 0.8125 (m-10) REVERT: I 297 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8575 (mtp-110) REVERT: K 200 GLN cc_start: 0.8792 (mt0) cc_final: 0.8558 (mm110) REVERT: K 256 ASP cc_start: 0.8794 (t0) cc_final: 0.8469 (t0) REVERT: K 274 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8634 (tttt) REVERT: K 297 ARG cc_start: 0.9072 (ttp80) cc_final: 0.8635 (mtp-110) REVERT: K 301 MET cc_start: 0.8682 (mtm) cc_final: 0.8433 (mpp) REVERT: M 256 ASP cc_start: 0.8527 (t0) cc_final: 0.8281 (t0) REVERT: M 297 ARG cc_start: 0.9012 (ttp80) cc_final: 0.8603 (mtp-110) REVERT: M 301 MET cc_start: 0.8651 (mtm) cc_final: 0.8405 (mpp) REVERT: O 161 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7609 (tm-30) REVERT: O 256 ASP cc_start: 0.8754 (t0) cc_final: 0.8041 (t0) REVERT: O 274 LYS cc_start: 0.8871 (ttpp) cc_final: 0.8662 (tttt) REVERT: O 297 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8564 (mtp-110) REVERT: O 301 MET cc_start: 0.8642 (mtm) cc_final: 0.8425 (mpp) REVERT: Q 274 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8638 (tttt) REVERT: Q 297 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8626 (mtp-110) REVERT: Q 301 MET cc_start: 0.8644 (mtm) cc_final: 0.8418 (mpp) REVERT: Q 322 MET cc_start: 0.8218 (mmm) cc_final: 0.8010 (tpt) REVERT: S 161 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7499 (tm-30) REVERT: S 253 MET cc_start: 0.7884 (tpt) cc_final: 0.6058 (tpt) REVERT: S 256 ASP cc_start: 0.8803 (t0) cc_final: 0.8044 (t0) REVERT: S 274 LYS cc_start: 0.8869 (ttpp) cc_final: 0.8637 (tttt) REVERT: S 289 PHE cc_start: 0.8385 (m-80) cc_final: 0.8174 (m-10) REVERT: S 297 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8535 (mtp-110) REVERT: S 301 MET cc_start: 0.8656 (mtm) cc_final: 0.8415 (mpp) REVERT: U 161 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7641 (tm-30) REVERT: U 200 GLN cc_start: 0.8741 (mt0) cc_final: 0.8536 (mm110) REVERT: U 256 ASP cc_start: 0.8784 (t0) cc_final: 0.7989 (t0) REVERT: U 274 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8633 (tttt) REVERT: U 297 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8572 (mtp-110) REVERT: U 322 MET cc_start: 0.8243 (mmm) cc_final: 0.7988 (tpt) REVERT: W 161 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8099 (tm-30) REVERT: W 274 LYS cc_start: 0.8875 (ttpp) cc_final: 0.8649 (tttt) REVERT: W 297 ARG cc_start: 0.9060 (ttp80) cc_final: 0.8539 (mtp-110) REVERT: W 301 MET cc_start: 0.8643 (mtm) cc_final: 0.8408 (mpp) REVERT: W 309 GLN cc_start: 0.8284 (mp10) cc_final: 0.7984 (mp10) REVERT: W 322 MET cc_start: 0.8197 (mmm) cc_final: 0.7905 (tpt) REVERT: Y 253 MET cc_start: 0.7789 (tpt) cc_final: 0.6236 (tpt) REVERT: Y 256 ASP cc_start: 0.8770 (t0) cc_final: 0.7946 (t0) REVERT: Y 274 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8627 (tttt) REVERT: Y 289 PHE cc_start: 0.8424 (m-80) cc_final: 0.8140 (m-10) REVERT: Y 297 ARG cc_start: 0.9024 (ttp80) cc_final: 0.8547 (mtp-110) REVERT: Y 301 MET cc_start: 0.8653 (mtm) cc_final: 0.8394 (mpp) REVERT: Y 322 MET cc_start: 0.8206 (mmm) cc_final: 0.7962 (tpt) outliers start: 119 outliers final: 60 residues processed: 936 average time/residue: 0.2787 time to fit residues: 414.9015 Evaluate side-chains 865 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 805 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 157 CYS 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 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 304 ARG Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain G residue 157 CYS 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 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 157 CYS Chi-restraints excluded: chain K residue 185 TYR 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 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 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 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 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 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 304 ARG Chi-restraints excluded: chain W residue 339 VAL Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR 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: 4.9990 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 0.0570 chunk 470 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 336 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 440 optimal weight: 2.9990 chunk 461 optimal weight: 0.6980 chunk 448 optimal weight: 5.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 63 ASN A 263 ASN C 18 GLN C 63 ASN E 63 ASN E 263 ASN G 18 GLN G 63 ASN G 263 ASN I 18 GLN I 63 ASN K 18 GLN K 63 ASN K 263 ASN M 18 GLN M 63 ASN O 18 GLN O 63 ASN O 263 ASN Q 63 ASN Q 263 ASN S 18 GLN S 63 ASN S 263 ASN U 63 ASN U 263 ASN W 63 ASN W 263 ASN Y 63 ASN Y 263 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.097147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.081874 restraints weight = 104238.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.084964 restraints weight = 53701.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.087113 restraints weight = 34422.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088616 restraints weight = 24880.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089774 restraints weight = 19391.625| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 41132 Z= 0.174 Angle : 0.782 14.906 55952 Z= 0.381 Chirality : 0.053 0.524 6240 Planarity : 0.007 0.132 7059 Dihedral : 8.674 132.181 6396 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.16 % Allowed : 18.29 % Favored : 78.55 % Cbeta Deviations : 0.09 % 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: -0.32 (0.12), residues: 4836 helix: 0.31 (0.10), residues: 2964 sheet: -0.57 (0.46), residues: 156 loop : -0.95 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 230 TYR 0.018 0.001 TYR Q 250 PHE 0.034 0.002 PHE M 289 TRP 0.045 0.003 TRP K 281 HIS 0.002 0.000 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (41093) covalent geometry : angle 0.78227 / 0.38 (55952) hydrogen bonds : bond 0.04269 / 2.83 ( 2197) hydrogen bonds : angle 4.61171 / 3.25 ( 6279) Misc. bond : bond 0.00332 / 0.23 ( 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 930 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 802 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 200 GLN cc_start: 0.8769 (mt0) cc_final: 0.8548 (mm110) REVERT: A 274 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8560 (tttt) REVERT: A 297 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8714 (mtp-110) REVERT: A 301 MET cc_start: 0.8646 (mtm) cc_final: 0.8405 (mpp) REVERT: A 322 MET cc_start: 0.8337 (tpt) cc_final: 0.8067 (tpt) REVERT: C 161 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 165 ASP cc_start: 0.8003 (m-30) cc_final: 0.7668 (m-30) REVERT: C 199 TYR cc_start: 0.8384 (m-80) cc_final: 0.8080 (m-80) REVERT: C 200 GLN cc_start: 0.8816 (mt0) cc_final: 0.8601 (mm110) REVERT: C 256 ASP cc_start: 0.8743 (t0) cc_final: 0.8168 (t0) REVERT: C 297 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8715 (mtp-110) REVERT: C 301 MET cc_start: 0.8797 (mpp) cc_final: 0.8230 (mpp) REVERT: C 322 MET cc_start: 0.8285 (mmm) cc_final: 0.8048 (tpt) REVERT: E 161 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7615 (tm-30) REVERT: E 274 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8540 (tttt) REVERT: E 297 ARG cc_start: 0.9092 (ttp80) cc_final: 0.8621 (mtp-110) REVERT: G 200 GLN cc_start: 0.8790 (mt0) cc_final: 0.8472 (mm110) REVERT: G 297 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8620 (mtp-110) REVERT: I 161 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7673 (tm-30) REVERT: I 256 ASP cc_start: 0.8633 (t0) cc_final: 0.8333 (t0) REVERT: I 274 LYS cc_start: 0.8781 (ttpp) cc_final: 0.8546 (tttt) REVERT: I 297 ARG cc_start: 0.9143 (ttp80) cc_final: 0.8721 (mtp-110) REVERT: I 301 MET cc_start: 0.8764 (mpp) cc_final: 0.8238 (mpp) REVERT: K 200 GLN cc_start: 0.8774 (mt0) cc_final: 0.8563 (mm110) REVERT: K 256 ASP cc_start: 0.8752 (t0) cc_final: 0.8389 (t0) REVERT: K 297 ARG cc_start: 0.9105 (ttp80) cc_final: 0.8622 (mtp-110) REVERT: M 256 ASP cc_start: 0.8574 (t0) cc_final: 0.8336 (t0) REVERT: M 297 ARG cc_start: 0.9054 (ttp80) cc_final: 0.8649 (mtp-110) REVERT: M 301 MET cc_start: 0.8619 (mtm) cc_final: 0.8393 (mpp) REVERT: O 161 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7598 (tm-30) REVERT: O 274 LYS cc_start: 0.8772 (ttpp) cc_final: 0.8570 (tttt) REVERT: O 297 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8543 (mtm110) REVERT: Q 274 LYS cc_start: 0.8752 (ttpp) cc_final: 0.8539 (tttt) REVERT: Q 297 ARG cc_start: 0.9093 (ttp80) cc_final: 0.8629 (mtp-110) REVERT: Q 309 GLN cc_start: 0.8335 (mp10) cc_final: 0.7981 (mp10) REVERT: Q 322 MET cc_start: 0.8300 (mmm) cc_final: 0.8068 (tpt) REVERT: S 161 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7600 (tm-30) REVERT: S 274 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8521 (tttt) REVERT: S 297 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8600 (mtp-110) REVERT: U 161 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7547 (tm-30) REVERT: U 200 GLN cc_start: 0.8774 (mt0) cc_final: 0.8499 (mm110) REVERT: U 274 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8533 (tttt) REVERT: U 297 ARG cc_start: 0.9138 (ttp80) cc_final: 0.8738 (mtp-110) REVERT: U 301 MET cc_start: 0.8783 (mpp) cc_final: 0.8245 (mpp) REVERT: W 161 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8129 (tm-30) REVERT: W 256 ASP cc_start: 0.8581 (t0) cc_final: 0.8304 (t0) REVERT: W 274 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8548 (tttt) REVERT: W 297 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8596 (mtp-110) REVERT: W 322 MET cc_start: 0.8223 (mmm) cc_final: 0.7967 (tpt) REVERT: Y 161 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7679 (tm-30) REVERT: Y 274 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8535 (tttt) REVERT: Y 297 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8601 (mtp-110) REVERT: Y 301 MET cc_start: 0.8618 (mtm) cc_final: 0.8391 (mpp) REVERT: Y 322 MET cc_start: 0.8250 (mmm) cc_final: 0.8000 (tpt) outliers start: 128 outliers final: 78 residues processed: 863 average time/residue: 0.2716 time to fit residues: 374.4719 Evaluate side-chains 833 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 755 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 157 CYS 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 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 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 170 VAL Chi-restraints excluded: chain E residue 185 TYR 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 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 253 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 170 VAL 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 185 TYR 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 157 CYS Chi-restraints excluded: chain O residue 185 TYR 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 157 CYS 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 304 ARG Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 157 CYS Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 279 THR Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 157 CYS Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 289 PHE Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU 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: 5.9990 chunk 91 optimal weight: 1.9990 chunk 415 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 443 optimal weight: 7.9990 chunk 168 optimal weight: 8.9990 chunk 319 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 357 optimal weight: 7.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN C 63 ASN C 263 ASN E 63 ASN G 263 ASN I 263 ASN K 263 ASN M 87 HIS M 263 ASN O 263 ASN Q 63 ASN S 63 ASN Y 263 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.098216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.082796 restraints weight = 105001.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085821 restraints weight = 56546.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087936 restraints weight = 37126.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.089471 restraints weight = 27252.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090616 restraints weight = 21387.401| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 41132 Z= 0.152 Angle : 0.793 25.784 55952 Z= 0.389 Chirality : 0.050 0.433 6240 Planarity : 0.007 0.134 7059 Dihedral : 8.695 131.450 6396 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.16 % Allowed : 19.65 % Favored : 77.19 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.09 (0.12), residues: 4836 helix: 0.47 (0.10), residues: 2964 sheet: -0.30 (0.47), residues: 156 loop : -0.82 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 230 TYR 0.017 0.001 TYR Q 250 PHE 0.031 0.002 PHE Y 289 TRP 0.031 0.002 TRP K 281 HIS 0.002 0.000 HIS Q 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (41093) covalent geometry : angle 0.79323 / 0.39 (55952) hydrogen bonds : bond 0.04120 / 2.74 ( 2197) hydrogen bonds : angle 4.55520 / 3.22 ( 6279) Misc. bond : bond 0.00541 / 0.37 ( 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 915 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 787 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLN cc_start: 0.8765 (mt0) cc_final: 0.8499 (mm110) REVERT: A 274 LYS cc_start: 0.8774 (ttpp) cc_final: 0.8547 (tttt) REVERT: A 297 ARG cc_start: 0.9110 (ttp80) cc_final: 0.8681 (mtp-110) REVERT: A 301 MET cc_start: 0.8605 (mtm) cc_final: 0.8398 (mpp) REVERT: A 322 MET cc_start: 0.8280 (tpt) cc_final: 0.8062 (tpt) REVERT: C 161 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 199 TYR cc_start: 0.8360 (m-80) cc_final: 0.8114 (m-80) REVERT: C 253 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.6954 (tpt) REVERT: C 256 ASP cc_start: 0.8727 (t0) cc_final: 0.8154 (t0) REVERT: C 297 ARG cc_start: 0.9158 (ttp80) cc_final: 0.8896 (mtp-110) REVERT: C 322 MET cc_start: 0.8268 (mmm) cc_final: 0.8029 (tpt) REVERT: E 161 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7485 (tm-30) REVERT: E 274 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8534 (tttt) REVERT: G 200 GLN cc_start: 0.8756 (mt0) cc_final: 0.8443 (mm110) REVERT: G 297 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8880 (mtp-110) REVERT: I 161 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7657 (tm-30) REVERT: I 256 ASP cc_start: 0.8625 (t0) cc_final: 0.8323 (t0) REVERT: I 274 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8524 (tttt) REVERT: I 297 ARG cc_start: 0.9166 (ttp80) cc_final: 0.8952 (mtp-110) REVERT: K 6 LYS cc_start: 0.8936 (tptp) cc_final: 0.8598 (tptp) REVERT: K 161 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7544 (tm-30) REVERT: K 165 ASP cc_start: 0.8004 (m-30) cc_final: 0.7692 (m-30) REVERT: K 253 MET cc_start: 0.7804 (tpt) cc_final: 0.7477 (tpt) REVERT: K 256 ASP cc_start: 0.8722 (t0) cc_final: 0.8400 (t0) REVERT: K 274 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8626 (tttt) REVERT: K 297 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8671 (mtp-110) REVERT: K 301 MET cc_start: 0.8778 (mpp) cc_final: 0.8250 (mpp) REVERT: K 322 MET cc_start: 0.8246 (mmm) cc_final: 0.8040 (tpt) REVERT: M 256 ASP cc_start: 0.8582 (t0) cc_final: 0.8365 (t0) REVERT: M 274 LYS cc_start: 0.8669 (ttpp) cc_final: 0.8463 (tttt) REVERT: M 297 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8632 (mtp-110) REVERT: M 301 MET cc_start: 0.8593 (mtm) cc_final: 0.8359 (mpp) REVERT: O 161 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7507 (tm-30) REVERT: O 274 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8554 (tttt) REVERT: O 297 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8854 (mtp-110) REVERT: Q 297 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8875 (mtp-110) REVERT: Q 322 MET cc_start: 0.8271 (mmm) cc_final: 0.8050 (tpt) REVERT: S 161 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7540 (tm-30) REVERT: S 297 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8829 (mtp-110) REVERT: S 301 MET cc_start: 0.8753 (mpp) cc_final: 0.8424 (mpp) REVERT: S 322 MET cc_start: 0.8274 (mmm) cc_final: 0.8021 (tpt) REVERT: U 161 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7545 (tm-30) REVERT: U 200 GLN cc_start: 0.8756 (mt0) cc_final: 0.8487 (mm110) REVERT: W 161 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8028 (tm-30) REVERT: W 256 ASP cc_start: 0.8599 (t0) cc_final: 0.8311 (t0) REVERT: W 274 LYS cc_start: 0.8776 (ttpp) cc_final: 0.8548 (tttt) REVERT: W 297 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8871 (mtp-110) REVERT: W 322 MET cc_start: 0.8236 (mmm) cc_final: 0.7979 (tpt) REVERT: Y 161 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7701 (tm-30) REVERT: Y 274 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8548 (tttt) REVERT: Y 297 ARG cc_start: 0.9025 (ttp80) cc_final: 0.8575 (mtp-110) REVERT: Y 301 MET cc_start: 0.8596 (mtm) cc_final: 0.8392 (mpp) outliers start: 128 outliers final: 96 residues processed: 857 average time/residue: 0.2588 time to fit residues: 355.9700 Evaluate side-chains 847 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 750 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 157 CYS 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 157 CYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 MET Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 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 263 ASN Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 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 157 CYS Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU 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 157 CYS Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 253 MET Chi-restraints excluded: chain O residue 263 ASN 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 84 MET 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 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 157 CYS Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU 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 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 U residue 347 MET Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 157 CYS Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 157 CYS Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU 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: 1.9990 chunk 307 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 265 optimal weight: 0.3980 chunk 326 optimal weight: 5.9990 chunk 452 optimal weight: 0.8980 chunk 436 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 63 ASN C 263 ASN E 63 ASN I 63 ASN M 63 ASN O 63 ASN Y 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083917 restraints weight = 104964.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086982 restraints weight = 56225.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089138 restraints weight = 36742.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090690 restraints weight = 26816.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.091844 restraints weight = 20969.153| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 41132 Z= 0.141 Angle : 0.762 23.785 55952 Z= 0.368 Chirality : 0.048 0.368 6240 Planarity : 0.007 0.128 7059 Dihedral : 8.604 130.838 6396 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.98 % Allowed : 20.64 % Favored : 76.38 % Cbeta Deviations : 0.13 % 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: 0.05 (0.12), residues: 4836 helix: 0.58 (0.10), residues: 2964 sheet: 0.03 (0.43), residues: 182 loop : -0.81 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 230 TYR 0.017 0.001 TYR Q 250 PHE 0.025 0.002 PHE Y 289 TRP 0.034 0.002 TRP I 281 HIS 0.002 0.000 HIS S 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (41093) covalent geometry : angle 0.76177 / 0.37 (55952) hydrogen bonds : bond 0.03873 / 2.57 ( 2197) hydrogen bonds : angle 4.42182 / 3.12 ( 6279) Misc. bond : bond 0.00566 / 0.41 ( 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 901 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 780 time to evaluate : 1.589 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 200 GLN cc_start: 0.8775 (mt0) cc_final: 0.8484 (mm110) REVERT: A 297 ARG cc_start: 0.9098 (ttp80) cc_final: 0.8677 (mtp-110) REVERT: C 1 MET cc_start: 0.5862 (mmm) cc_final: 0.5463 (mmp) REVERT: C 161 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 165 ASP cc_start: 0.8020 (m-30) cc_final: 0.7443 (m-30) REVERT: C 253 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6949 (tpt) REVERT: C 256 ASP cc_start: 0.8688 (t0) cc_final: 0.8212 (t0) REVERT: C 297 ARG cc_start: 0.9159 (ttp80) cc_final: 0.8597 (mtp-110) REVERT: C 301 MET cc_start: 0.8775 (mpp) cc_final: 0.8262 (mpp) REVERT: C 322 MET cc_start: 0.8272 (mmm) cc_final: 0.8036 (tpt) REVERT: E 1 MET cc_start: 0.6069 (mmm) cc_final: 0.5783 (mmp) REVERT: E 10 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.8009 (mtm110) REVERT: E 14 GLU cc_start: 0.9147 (tp30) cc_final: 0.8775 (mp0) REVERT: E 161 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7524 (tm-30) REVERT: G 161 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7514 (tm-30) REVERT: G 165 ASP cc_start: 0.7767 (m-30) cc_final: 0.7329 (m-30) REVERT: G 200 GLN cc_start: 0.8777 (mt0) cc_final: 0.8436 (mm110) REVERT: I 1 MET cc_start: 0.5860 (mmm) cc_final: 0.5524 (mmp) REVERT: I 161 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7599 (tm-30) REVERT: I 256 ASP cc_start: 0.8637 (t0) cc_final: 0.8336 (t0) REVERT: I 274 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8503 (tttt) REVERT: I 297 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8933 (mtp-110) REVERT: K 161 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7511 (tm-30) REVERT: K 165 ASP cc_start: 0.8021 (m-30) cc_final: 0.7590 (m-30) REVERT: K 256 ASP cc_start: 0.8699 (t0) cc_final: 0.7983 (t0) REVERT: K 297 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8927 (mtp-110) REVERT: K 322 MET cc_start: 0.8262 (mmm) cc_final: 0.8038 (tpt) REVERT: M 256 ASP cc_start: 0.8628 (t0) cc_final: 0.8392 (t0) REVERT: M 297 ARG cc_start: 0.9049 (ttp80) cc_final: 0.8595 (mtm110) REVERT: M 301 MET cc_start: 0.8557 (mtm) cc_final: 0.8337 (mpp) REVERT: O 161 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7492 (tm-30) REVERT: O 274 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8532 (tttt) REVERT: O 297 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8805 (mtm110) REVERT: Q 322 MET cc_start: 0.8277 (mmm) cc_final: 0.8056 (tpt) REVERT: S 161 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7494 (tm-30) REVERT: S 322 MET cc_start: 0.8281 (mmm) cc_final: 0.7978 (tpt) REVERT: U 161 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7523 (tm-30) REVERT: U 200 GLN cc_start: 0.8739 (mt0) cc_final: 0.8497 (mm110) REVERT: U 301 MET cc_start: 0.8731 (mpp) cc_final: 0.8224 (mpp) REVERT: W 6 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8632 (tptp) REVERT: W 161 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8106 (tm-30) REVERT: W 256 ASP cc_start: 0.8611 (t0) cc_final: 0.8353 (t0) REVERT: W 297 ARG cc_start: 0.9103 (ttp80) cc_final: 0.8877 (mtp-110) REVERT: W 322 MET cc_start: 0.8251 (mmm) cc_final: 0.7998 (tpt) REVERT: Y 161 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7691 (tm-30) REVERT: Y 200 GLN cc_start: 0.8812 (mt0) cc_final: 0.8574 (mm110) REVERT: Y 274 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8525 (tttt) REVERT: Y 297 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8581 (mtp-110) outliers start: 121 outliers final: 98 residues processed: 843 average time/residue: 0.2670 time to fit residues: 363.2619 Evaluate side-chains 838 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 739 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 84 MET 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 253 MET 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 4 VAL 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 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 253 MET Chi-restraints excluded: chain G residue 280 LYS Chi-restraints excluded: chain G residue 304 ARG Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 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 84 MET 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 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 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 253 MET Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain U residue 347 MET Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 84 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 15 GLN 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 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: 0.8980 chunk 246 optimal weight: 0.0870 chunk 206 optimal weight: 0.8980 chunk 443 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 0.7980 chunk 473 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 388 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 GLN C 212 GLN E 63 ASN G 212 GLN K 87 HIS M 63 ASN Q 63 ASN S 63 ASN S 87 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.100904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085176 restraints weight = 104062.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.088281 restraints weight = 55391.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090485 restraints weight = 36231.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092045 restraints weight = 26510.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093219 restraints weight = 20733.508| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41132 Z= 0.133 Angle : 0.750 20.069 55952 Z= 0.362 Chirality : 0.047 0.340 6240 Planarity : 0.007 0.130 7059 Dihedral : 8.458 129.959 6396 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.93 % Allowed : 21.55 % Favored : 75.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 4836 helix: 0.67 (0.10), residues: 2964 sheet: 0.16 (0.43), residues: 182 loop : -0.68 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 230 TYR 0.013 0.001 TYR Q 250 PHE 0.024 0.001 PHE Y 289 TRP 0.045 0.002 TRP Y 281 HIS 0.003 0.000 HIS K 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (41093) covalent geometry : angle 0.75021 / 0.36 (55952) hydrogen bonds : bond 0.03771 / 2.50 ( 2197) hydrogen bonds : angle 4.36861 / 3.10 ( 6279) Misc. bond : bond 0.00590 / 0.38 ( 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 890 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 771 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: A 161 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 165 ASP cc_start: 0.8220 (m-30) cc_final: 0.7810 (m-30) REVERT: A 200 GLN cc_start: 0.8778 (mt0) cc_final: 0.8437 (mm110) REVERT: A 297 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8863 (mtp-110) REVERT: C 1 MET cc_start: 0.5877 (mmm) cc_final: 0.5571 (mmp) REVERT: C 161 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 256 ASP cc_start: 0.8636 (t0) cc_final: 0.8357 (t0) REVERT: C 297 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8892 (mtp-110) REVERT: C 322 MET cc_start: 0.8276 (mmm) cc_final: 0.8073 (tpt) REVERT: E 1 MET cc_start: 0.6191 (mmm) cc_final: 0.5975 (mmp) REVERT: E 10 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.8022 (mtm110) REVERT: E 14 GLU cc_start: 0.9158 (tp30) cc_final: 0.8765 (mp0) REVERT: E 161 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7558 (tm-30) REVERT: E 301 MET cc_start: 0.8687 (mtm) cc_final: 0.8333 (mpp) REVERT: G 161 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7478 (tm-30) REVERT: G 165 ASP cc_start: 0.7807 (m-30) cc_final: 0.7279 (m-30) REVERT: G 200 GLN cc_start: 0.8785 (mt0) cc_final: 0.8436 (mm110) REVERT: I 161 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7516 (tm-30) REVERT: I 165 ASP cc_start: 0.8084 (m-30) cc_final: 0.7442 (m-30) REVERT: I 256 ASP cc_start: 0.8645 (t0) cc_final: 0.8366 (t0) REVERT: I 297 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8837 (mtp-110) REVERT: K 6 LYS cc_start: 0.8927 (tptp) cc_final: 0.8598 (tptp) REVERT: K 161 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7480 (tm-30) REVERT: K 165 ASP cc_start: 0.8037 (m-30) cc_final: 0.7523 (m-30) REVERT: K 297 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8597 (mtp-110) REVERT: K 301 MET cc_start: 0.8669 (mtm) cc_final: 0.8371 (mpp) REVERT: M 256 ASP cc_start: 0.8627 (t0) cc_final: 0.8415 (t0) REVERT: M 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8569 (mtm110) REVERT: M 301 MET cc_start: 0.8535 (mtm) cc_final: 0.8283 (mpp) REVERT: O 161 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7585 (tm-30) REVERT: O 200 GLN cc_start: 0.8775 (mt0) cc_final: 0.8482 (mm110) REVERT: O 297 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8565 (mtm110) REVERT: O 301 MET cc_start: 0.8737 (mpp) cc_final: 0.8201 (mpp) REVERT: S 161 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7674 (tm-30) REVERT: U 161 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7612 (tm-30) REVERT: U 200 GLN cc_start: 0.8737 (mt0) cc_final: 0.8459 (mm110) REVERT: U 322 MET cc_start: 0.8213 (tpt) cc_final: 0.7948 (tpt) REVERT: W 6 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8625 (tptp) REVERT: W 161 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8129 (tm-30) REVERT: W 256 ASP cc_start: 0.8615 (t0) cc_final: 0.8360 (t0) REVERT: W 297 ARG cc_start: 0.9048 (ttp80) cc_final: 0.8698 (mtp-110) REVERT: W 301 MET cc_start: 0.8596 (mtm) cc_final: 0.8329 (mpp) REVERT: Y 161 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7655 (tm-30) REVERT: Y 200 GLN cc_start: 0.8831 (mt0) cc_final: 0.8568 (mm110) outliers start: 119 outliers final: 93 residues processed: 836 average time/residue: 0.2706 time to fit residues: 363.9035 Evaluate side-chains 830 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 737 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 ARG Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 173 GLN 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 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 99 ILE 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 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 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 304 ARG Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 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 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU 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 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 253 MET Chi-restraints excluded: chain U residue 267 THR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 76 LEU Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 185 TYR Chi-restraints excluded: chain W residue 253 MET Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain Y residue 99 ILE Chi-restraints excluded: chain Y residue 185 TYR Chi-restraints excluded: chain Y residue 246 LEU Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 304 ARG Chi-restraints excluded: chain Y residue 334 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 463 optimal weight: 5.9990 chunk 332 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 465 optimal weight: 6.9990 chunk 329 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 338 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 GLN C 63 ASN C 263 ASN E 63 ASN E 263 ASN G 63 ASN K 263 ASN U 263 ASN W 263 ASN Y 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.079795 restraints weight = 109165.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082661 restraints weight = 60077.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084668 restraints weight = 40156.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.086104 restraints weight = 29895.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087206 restraints weight = 23865.998| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 41132 Z= 0.229 Angle : 0.860 26.447 55952 Z= 0.425 Chirality : 0.052 0.291 6240 Planarity : 0.007 0.131 7059 Dihedral : 8.859 134.370 6396 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 3.30 % Allowed : 22.19 % Favored : 74.51 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4836 helix: 0.21 (0.09), residues: 2964 sheet: 0.05 (0.50), residues: 156 loop : -0.72 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 230 TYR 0.018 0.002 TYR U 303 PHE 0.022 0.002 PHE C 289 TRP 0.033 0.003 TRP W 281 HIS 0.002 0.001 HIS O 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (41093) covalent geometry : angle 0.85964 / 0.42 (55952) hydrogen bonds : bond 0.04490 / 2.98 ( 2197) hydrogen bonds : angle 4.69713 / 3.32 ( 6279) Misc. bond : bond 0.00533 / 0.36 ( 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 910 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 776 time to evaluate : 1.675 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: A 200 GLN cc_start: 0.8864 (mt0) cc_final: 0.8522 (mm110) REVERT: A 297 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8766 (mtp-110) REVERT: A 301 MET cc_start: 0.8702 (mtm) cc_final: 0.8325 (mpp) REVERT: C 1 MET cc_start: 0.6061 (mmm) cc_final: 0.5545 (mmp) REVERT: C 161 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 165 ASP cc_start: 0.7999 (m-30) cc_final: 0.7660 (m-30) REVERT: C 200 GLN cc_start: 0.8818 (mt0) cc_final: 0.8548 (mm110) REVERT: C 256 ASP cc_start: 0.8620 (t0) cc_final: 0.8348 (t0) REVERT: C 274 LYS cc_start: 0.8652 (tttt) cc_final: 0.8307 (ttpp) REVERT: C 297 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8931 (mtp-110) REVERT: C 322 MET cc_start: 0.8351 (mmm) cc_final: 0.8010 (tpt) REVERT: E 1 MET cc_start: 0.6382 (mmm) cc_final: 0.6098 (mmp) REVERT: E 161 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7645 (tm-30) REVERT: E 301 MET cc_start: 0.8738 (mtm) cc_final: 0.8457 (mpp) REVERT: G 6 LYS cc_start: 0.9058 (tmtt) cc_final: 0.8360 (tmtt) REVERT: G 10 ARG cc_start: 0.8108 (ttp-110) cc_final: 0.7672 (ttp80) REVERT: G 161 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7433 (tm-30) REVERT: G 165 ASP cc_start: 0.7850 (m-30) cc_final: 0.7265 (m-30) REVERT: G 200 GLN cc_start: 0.8869 (mt0) cc_final: 0.8497 (mm110) REVERT: I 161 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7607 (tm-30) REVERT: I 256 ASP cc_start: 0.8678 (t0) cc_final: 0.8431 (t0) REVERT: I 297 ARG cc_start: 0.9155 (ttp80) cc_final: 0.8836 (mtm110) REVERT: K 161 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7477 (tm-30) REVERT: K 165 ASP cc_start: 0.7985 (m-30) cc_final: 0.7393 (m-30) REVERT: K 297 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8562 (mtp-110) REVERT: K 301 MET cc_start: 0.8644 (mtm) cc_final: 0.8399 (mpp) REVERT: M 52 LEU cc_start: 0.8632 (tt) cc_final: 0.8418 (tp) REVERT: M 161 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7658 (tm-30) REVERT: M 256 ASP cc_start: 0.8633 (t0) cc_final: 0.8390 (t0) REVERT: M 297 ARG cc_start: 0.9096 (ttp80) cc_final: 0.8597 (mtm110) REVERT: M 301 MET cc_start: 0.8652 (mtm) cc_final: 0.8424 (mpp) REVERT: O 52 LEU cc_start: 0.8630 (tt) cc_final: 0.8406 (tp) REVERT: O 161 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7678 (tm-30) REVERT: O 253 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7457 (tpt) REVERT: O 297 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8851 (mtm110) REVERT: O 308 GLU cc_start: 0.8556 (pm20) cc_final: 0.8336 (pm20) REVERT: Q 161 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7622 (tm-30) REVERT: S 161 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7678 (tm-30) REVERT: U 1 MET cc_start: 0.5883 (mmm) cc_final: 0.5615 (mmp) REVERT: U 161 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7705 (tm-30) REVERT: U 200 GLN cc_start: 0.8841 (mt0) cc_final: 0.8522 (mm110) REVERT: W 161 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8187 (tm-30) REVERT: W 256 ASP cc_start: 0.8672 (t0) cc_final: 0.8375 (t0) REVERT: W 297 ARG cc_start: 0.9107 (ttp80) cc_final: 0.8859 (ttp80) REVERT: Y 161 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7699 (tm-30) outliers start: 134 outliers final: 109 residues processed: 835 average time/residue: 0.2710 time to fit residues: 362.5235 Evaluate side-chains 860 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 750 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL 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 263 ASN Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 88 ILE 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 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 4 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 185 TYR Chi-restraints excluded: chain I residue 246 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain K residue 304 ARG Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 99 ILE Chi-restraints excluded: chain M residue 185 TYR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 267 THR Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 253 MET 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 88 ILE 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 170 VAL Chi-restraints excluded: chain S residue 185 TYR Chi-restraints excluded: chain S residue 246 LEU Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 280 LYS Chi-restraints excluded: chain S residue 304 ARG Chi-restraints excluded: chain S residue 334 SER Chi-restraints excluded: chain U residue 76 LEU Chi-restraints excluded: chain U residue 90 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR 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 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 267 THR Chi-restraints excluded: chain W residue 304 ARG Chi-restraints excluded: chain W residue 334 SER Chi-restraints excluded: chain W residue 339 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 280 LYS 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: 4.9990 chunk 401 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 0.0170 chunk 354 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 360 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 368 optimal weight: 4.9990 chunk 304 optimal weight: 0.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 263 ASN C 63 ASN C 263 ASN E 63 ASN E 263 ASN G 263 ASN I 263 ASN K 263 ASN M 263 ASN Q 263 ASN W 63 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.099434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083692 restraints weight = 105911.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.086750 restraints weight = 57775.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088869 restraints weight = 38211.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090409 restraints weight = 28179.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091553 restraints weight = 22230.260| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 41132 Z= 0.153 Angle : 0.874 27.043 55952 Z= 0.422 Chirality : 0.049 0.344 6240 Planarity : 0.007 0.126 7059 Dihedral : 8.771 131.119 6396 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Rotamer: Outliers : 2.71 % Allowed : 23.20 % Favored : 74.09 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.12), residues: 4836 helix: 0.60 (0.10), residues: 2938 sheet: 0.30 (0.44), residues: 182 loop : -0.66 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 230 TYR 0.017 0.001 TYR C 199 PHE 0.024 0.002 PHE C 289 TRP 0.034 0.002 TRP E 281 HIS 0.001 0.000 HIS W 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (41093) covalent geometry : angle 0.87357 / 0.42 (55952) hydrogen bonds : bond 0.04085 / 2.68 ( 2197) hydrogen bonds : angle 4.55734 / 3.23 ( 6279) Misc. bond : bond 0.00634 / 0.43 ( 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 865 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 755 time to evaluate : 1.591 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: A 161 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 165 ASP cc_start: 0.8197 (m-30) cc_final: 0.7811 (m-30) REVERT: A 200 GLN cc_start: 0.8808 (mt0) cc_final: 0.8495 (mm110) REVERT: A 297 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8691 (mtp-110) REVERT: A 301 MET cc_start: 0.8633 (mtm) cc_final: 0.8380 (mpp) REVERT: C 1 MET cc_start: 0.5897 (mmm) cc_final: 0.5432 (mmp) REVERT: C 161 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7564 (tm-30) REVERT: C 165 ASP cc_start: 0.7987 (m-30) cc_final: 0.7615 (m-30) REVERT: C 256 ASP cc_start: 0.8598 (t0) cc_final: 0.8396 (t0) REVERT: C 297 ARG cc_start: 0.9194 (ttp80) cc_final: 0.8948 (mtp-110) REVERT: C 322 MET cc_start: 0.8285 (mmm) cc_final: 0.8044 (tpt) REVERT: E 1 MET cc_start: 0.6263 (mmm) cc_final: 0.5960 (mmp) REVERT: E 14 GLU cc_start: 0.9120 (tp30) cc_final: 0.8776 (mp0) REVERT: E 161 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7564 (tm-30) REVERT: E 301 MET cc_start: 0.8676 (mtm) cc_final: 0.8346 (mpp) REVERT: G 161 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7444 (tm-30) REVERT: G 165 ASP cc_start: 0.7838 (m-30) cc_final: 0.7214 (m-30) REVERT: G 200 GLN cc_start: 0.8803 (mt0) cc_final: 0.8453 (mm110) REVERT: G 274 LYS cc_start: 0.8654 (tttt) cc_final: 0.8303 (ttpp) REVERT: G 301 MET cc_start: 0.8712 (mtm) cc_final: 0.8389 (mpp) REVERT: I 161 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7507 (tm-30) REVERT: I 165 ASP cc_start: 0.8087 (m-30) cc_final: 0.7393 (m-30) REVERT: I 256 ASP cc_start: 0.8667 (t0) cc_final: 0.8431 (t0) REVERT: I 297 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8820 (mtm110) REVERT: K 6 LYS cc_start: 0.8943 (tptp) cc_final: 0.8628 (tptp) REVERT: K 161 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7473 (tm-30) REVERT: K 165 ASP cc_start: 0.7995 (m-30) cc_final: 0.7408 (m-30) REVERT: K 297 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8490 (mtp-110) REVERT: M 16 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7848 (mm-30) REVERT: M 51 MET cc_start: 0.7643 (ttm) cc_final: 0.7345 (mtm) REVERT: M 256 ASP cc_start: 0.8597 (t0) cc_final: 0.8378 (t0) REVERT: M 274 LYS cc_start: 0.8627 (tttt) cc_final: 0.8301 (ttpp) REVERT: M 297 ARG cc_start: 0.9038 (ttp80) cc_final: 0.8466 (mtm110) REVERT: O 161 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7610 (tm-30) REVERT: O 200 GLN cc_start: 0.8777 (mt0) cc_final: 0.8497 (mm110) REVERT: O 297 ARG cc_start: 0.9121 (ttp80) cc_final: 0.8566 (mtm110) REVERT: O 301 MET cc_start: 0.8721 (mpp) cc_final: 0.8212 (mpp) REVERT: Q 161 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7584 (tm-30) REVERT: Q 301 MET cc_start: 0.8713 (mtm) cc_final: 0.8401 (mpp) REVERT: S 301 MET cc_start: 0.8750 (mtm) cc_final: 0.8416 (mpp) REVERT: U 1 MET cc_start: 0.5827 (mmm) cc_final: 0.5597 (mmp) REVERT: U 200 GLN cc_start: 0.8763 (mt0) cc_final: 0.8505 (mm110) REVERT: U 322 MET cc_start: 0.8249 (tpt) cc_final: 0.7936 (tpt) REVERT: W 165 ASP cc_start: 0.8429 (m-30) cc_final: 0.8009 (p0) REVERT: W 256 ASP cc_start: 0.8622 (t0) cc_final: 0.8373 (t0) REVERT: W 297 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8794 (mtp-110) REVERT: Y 6 LYS cc_start: 0.8904 (tptp) cc_final: 0.8581 (tptp) REVERT: Y 161 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7708 (tm-30) REVERT: Y 200 GLN cc_start: 0.8828 (mt0) cc_final: 0.8581 (mm110) REVERT: Y 253 MET cc_start: 0.7666 (tpt) cc_final: 0.6009 (tpt) REVERT: Y 256 ASP cc_start: 0.8647 (t0) cc_final: 0.8229 (t0) REVERT: Y 308 GLU cc_start: 0.8568 (pm20) cc_final: 0.8340 (pm20) outliers start: 110 outliers final: 98 residues processed: 820 average time/residue: 0.2551 time to fit residues: 339.1733 Evaluate side-chains 826 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 728 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 263 ASN 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 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 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 263 ASN 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 263 ASN 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 263 ASN Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain K residue 263 ASN 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 90 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 263 ASN Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 263 ASN 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 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 90 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 301 MET Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain U residue 347 MET 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 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 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: 0.9980 chunk 332 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 213 optimal weight: 20.0000 chunk 374 optimal weight: 3.9990 chunk 358 optimal weight: 2.9990 chunk 475 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 314 optimal weight: 0.9990 chunk 247 optimal weight: 6.9990 chunk 412 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN C 63 ASN C 263 ASN E 63 ASN E 263 ASN G 263 ASN I 263 ASN K 263 ASN M 263 ASN O 212 GLN Q 212 GLN Q 263 ASN U 263 ASN Y 212 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083509 restraints weight = 105689.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086550 restraints weight = 57780.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.088683 restraints weight = 38289.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090238 restraints weight = 28272.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091388 restraints weight = 22300.086| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.4379 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= 0.166 Angle : 0.919 28.727 55952 Z= 0.445 Chirality : 0.049 0.392 6240 Planarity : 0.007 0.126 7059 Dihedral : 8.767 131.058 6396 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.64 % Allowed : 23.64 % Favored : 73.72 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: 0.72 (0.10), residues: 2860 sheet: 0.28 (0.44), residues: 182 loop : -0.67 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 230 TYR 0.049 0.002 TYR Y 199 PHE 0.020 0.002 PHE Q 289 TRP 0.029 0.002 TRP Y 281 HIS 0.001 0.000 HIS K 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (41093) covalent geometry : angle 0.91915 / 0.45 (55952) hydrogen bonds : bond 0.04211 / 2.77 ( 2197) hydrogen bonds : angle 4.60552 / 3.26 ( 6279) Misc. bond : bond 0.00668 / 0.47 ( 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 860 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 753 time to evaluate : 1.561 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: A 200 GLN cc_start: 0.8818 (mt0) cc_final: 0.8499 (mm110) REVERT: A 274 LYS cc_start: 0.8570 (tttt) cc_final: 0.8327 (ttpt) REVERT: A 297 ARG cc_start: 0.9034 (ttp80) cc_final: 0.8665 (mtp-110) REVERT: A 301 MET cc_start: 0.8618 (mtm) cc_final: 0.8363 (mpp) REVERT: C 1 MET cc_start: 0.5887 (mmm) cc_final: 0.5575 (mmp) REVERT: C 132 LEU cc_start: 0.9489 (pt) cc_final: 0.9062 (tp) REVERT: C 161 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 165 ASP cc_start: 0.7959 (m-30) cc_final: 0.7588 (m-30) REVERT: C 297 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8834 (mtm110) REVERT: E 1 MET cc_start: 0.6331 (mmm) cc_final: 0.5949 (mmp) REVERT: E 10 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: E 301 MET cc_start: 0.8670 (mtm) cc_final: 0.8347 (mpp) REVERT: G 161 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7434 (tm-30) REVERT: G 165 ASP cc_start: 0.7811 (m-30) cc_final: 0.7177 (m-30) REVERT: G 200 GLN cc_start: 0.8802 (mt0) cc_final: 0.8453 (mm110) REVERT: G 256 ASP cc_start: 0.8629 (t0) cc_final: 0.8108 (t0) REVERT: I 161 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7493 (tm-30) REVERT: I 165 ASP cc_start: 0.8066 (m-30) cc_final: 0.7364 (m-30) REVERT: I 297 ARG cc_start: 0.9136 (ttp80) cc_final: 0.8827 (mtm110) REVERT: K 6 LYS cc_start: 0.8950 (tptp) cc_final: 0.8597 (tptp) REVERT: K 52 LEU cc_start: 0.8557 (tt) cc_final: 0.8332 (tp) REVERT: K 161 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7466 (tm-30) REVERT: K 165 ASP cc_start: 0.7998 (m-30) cc_final: 0.7443 (m-30) REVERT: M 256 ASP cc_start: 0.8610 (t0) cc_final: 0.8399 (t0) REVERT: M 297 ARG cc_start: 0.9102 (ttp80) cc_final: 0.8751 (mtm110) REVERT: O 161 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7577 (tm-30) REVERT: O 200 GLN cc_start: 0.8778 (mt0) cc_final: 0.8498 (mm110) REVERT: O 297 ARG cc_start: 0.9130 (ttp80) cc_final: 0.8563 (mtm110) REVERT: O 301 MET cc_start: 0.8734 (mpp) cc_final: 0.8189 (mpp) REVERT: O 308 GLU cc_start: 0.8500 (pm20) cc_final: 0.8294 (pm20) REVERT: Q 161 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7601 (tm-30) REVERT: U 1 MET cc_start: 0.5821 (mmm) cc_final: 0.5613 (mmp) REVERT: U 200 GLN cc_start: 0.8777 (mt0) cc_final: 0.8510 (mm110) REVERT: U 322 MET cc_start: 0.8276 (tpt) cc_final: 0.7960 (tpt) REVERT: W 256 ASP cc_start: 0.8642 (t0) cc_final: 0.8383 (t0) REVERT: W 297 ARG cc_start: 0.9042 (ttp80) cc_final: 0.8803 (mtp-110) REVERT: Y 6 LYS cc_start: 0.8882 (tptp) cc_final: 0.8530 (tptp) REVERT: Y 161 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7732 (tm-30) REVERT: Y 200 GLN cc_start: 0.8807 (mt0) cc_final: 0.8540 (mm110) REVERT: Y 308 GLU cc_start: 0.8584 (pm20) cc_final: 0.8365 (pm20) outliers start: 107 outliers final: 97 residues processed: 816 average time/residue: 0.2505 time to fit residues: 333.0213 Evaluate side-chains 832 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 735 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 263 ASN 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 301 MET Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 253 MET Chi-restraints excluded: chain E residue 304 ARG Chi-restraints excluded: chain E residue 334 SER Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 185 TYR Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 263 ASN 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 4 VAL 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 263 ASN Chi-restraints excluded: chain I residue 301 MET Chi-restraints excluded: chain I residue 304 ARG Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 253 MET Chi-restraints excluded: chain K residue 263 ASN 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 90 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 261 ILE Chi-restraints excluded: chain M residue 304 ARG Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain O residue 76 LEU Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain O residue 185 TYR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 304 ARG Chi-restraints excluded: chain O residue 334 SER Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 99 ILE Chi-restraints excluded: chain Q residue 185 TYR Chi-restraints excluded: chain Q residue 246 LEU Chi-restraints excluded: chain Q residue 263 ASN 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 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 90 LEU Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain U residue 185 TYR Chi-restraints excluded: chain U residue 280 LYS Chi-restraints excluded: chain U residue 301 MET Chi-restraints excluded: chain U residue 304 ARG Chi-restraints excluded: chain U residue 334 SER Chi-restraints excluded: chain W residue 4 VAL 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 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 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: 1.9990 chunk 373 optimal weight: 7.9990 chunk 440 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 465 optimal weight: 0.9980 chunk 348 optimal weight: 0.0870 chunk 50 optimal weight: 5.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.099491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083694 restraints weight = 106035.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086734 restraints weight = 57775.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088869 restraints weight = 38222.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090424 restraints weight = 28194.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091538 restraints weight = 22222.081| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 41132 Z= 0.227 Angle : 1.147 59.200 55952 Z= 0.623 Chirality : 0.054 1.524 6240 Planarity : 0.007 0.140 7059 Dihedral : 8.789 131.102 6396 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.65 % Rotamer: Outliers : 2.39 % Allowed : 23.87 % Favored : 73.74 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: 0.24 (0.12), residues: 4836 helix: 0.73 (0.10), residues: 2860 sheet: 0.27 (0.44), residues: 182 loop : -0.66 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 230 TYR 0.051 0.002 TYR G 199 PHE 0.034 0.002 PHE E 289 TRP 0.027 0.002 TRP Y 281 HIS 0.001 0.000 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (41093) covalent geometry : angle 1.14671 / 0.62 (55952) hydrogen bonds : bond 0.04272 / 2.84 ( 2197) hydrogen bonds : angle 4.62286 / 3.28 ( 6279) Misc. bond : bond 0.02190 / 0.94 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10954.02 seconds wall clock time: 188 minutes 42.48 seconds (11322.48 seconds total)