Starting phenix.real_space_refine on Wed Mar 4 10:05:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324.map" model { file = "/net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n26_9324/03_2026/6n26_9324_neut.cif" } resolution = 3.0 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= 0.163 sd= 2.106 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8710 2.51 5 N 2145 2.21 5 O 2270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13190 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2638 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.06, per 1000 atoms: 0.16 Number of scatterers: 13190 At special positions: 0 Unit cell: (94.656, 94.656, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2270 8.00 N 2145 7.00 C 8710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.05 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.05 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.05 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 423.3 milliseconds 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.501A pdb=" N PHE A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 removed outlier: 4.020A pdb=" N VAL A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 97 " --> pdb=" O TRP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 144 removed outlier: 3.507A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 154 through 160 Processing helix chain 'A' and resid 164 through 174 removed outlier: 3.950A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 228 removed outlier: 3.504A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS A 262 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.999A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.746A pdb=" N LEU B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL B 81 " --> pdb=" O PRO B 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR B 97 " --> pdb=" O TRP B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.997A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL C 81 " --> pdb=" O PRO C 77 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'C' and resid 154 through 160 Processing helix chain 'C' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 197 removed outlier: 4.073A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.888A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS C 262 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.500A pdb=" N PHE D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 removed outlier: 4.020A pdb=" N VAL D 81 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR D 97 " --> pdb=" O TRP D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 154 through 160 Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 181 No H-bonds generated for 'chain 'D' and resid 179 through 181' Processing helix chain 'D' and resid 182 through 197 removed outlier: 4.074A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 228 removed outlier: 3.503A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.889A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.533A pdb=" N LYS D 262 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 removed outlier: 3.960A pdb=" N GLN D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 306 through 322 Processing helix chain 'E' and resid 27 through 32 removed outlier: 3.998A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 53 removed outlier: 3.745A pdb=" N LEU E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.514A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 99 removed outlier: 4.019A pdb=" N VAL E 81 " --> pdb=" O PRO E 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR E 97 " --> pdb=" O TRP E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.856A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 144 removed outlier: 3.506A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 151 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 164 through 174 removed outlier: 3.949A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 172 " --> pdb=" O HIS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 182 through 197 removed outlier: 4.073A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 228 removed outlier: 3.504A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN E 215 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.888A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.534A pdb=" N LYS E 262 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 285 removed outlier: 3.961A pdb=" N GLN E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 295 Processing helix chain 'E' and resid 306 through 322 752 hydrogen bonds defined for protein. 2241 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4029 1.34 - 1.47: 3738 1.47 - 1.59: 5703 1.59 - 1.71: 0 1.71 - 1.84: 100 Bond restraints: 13570 Sorted by residual: bond pdb=" CB MET D 107 " pdb=" CG MET D 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.49e+00 bond pdb=" CB MET C 107 " pdb=" CG MET C 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.46e+00 bond pdb=" CB MET A 107 " pdb=" CG MET A 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" CB MET B 107 " pdb=" CG MET B 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" CB MET E 107 " pdb=" CG MET E 107 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.42e+00 ... (remaining 13565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 17574 1.72 - 3.43: 751 3.43 - 5.15: 95 5.15 - 6.87: 15 6.87 - 8.58: 20 Bond angle restraints: 18455 Sorted by residual: angle pdb=" CA TRP C 287 " pdb=" CB TRP C 287 " pdb=" CG TRP C 287 " ideal model delta sigma weight residual 113.60 121.18 -7.58 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP B 287 " pdb=" CB TRP B 287 " pdb=" CG TRP B 287 " ideal model delta sigma weight residual 113.60 121.18 -7.58 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP A 287 " pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 113.60 121.17 -7.57 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP D 287 " pdb=" CB TRP D 287 " pdb=" CG TRP D 287 " ideal model delta sigma weight residual 113.60 121.17 -7.57 1.90e+00 2.77e-01 1.59e+01 angle pdb=" CA TRP E 287 " pdb=" CB TRP E 287 " pdb=" CG TRP E 287 " ideal model delta sigma weight residual 113.60 121.15 -7.55 1.90e+00 2.77e-01 1.58e+01 ... (remaining 18450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.16: 6882 9.16 - 18.32: 803 18.32 - 27.48: 105 27.48 - 36.63: 95 36.63 - 45.79: 35 Dihedral angle restraints: 7920 sinusoidal: 3185 harmonic: 4735 Sorted by residual: dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " pdb=" CB CYS E 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.55 32.55 1 1.00e+01 1.00e-02 1.51e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " pdb=" CB CYS C 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.52 32.52 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " pdb=" CB CYS D 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.51 32.51 1 1.00e+01 1.00e-02 1.50e+01 ... (remaining 7917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1022 0.038 - 0.075: 769 0.075 - 0.113: 188 0.113 - 0.150: 41 0.150 - 0.188: 10 Chirality restraints: 2030 Sorted by residual: chirality pdb=" CA ILE A 232 " pdb=" N ILE A 232 " pdb=" C ILE A 232 " pdb=" CB ILE A 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE D 232 " pdb=" N ILE D 232 " pdb=" C ILE D 232 " pdb=" CB ILE D 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2027 not shown) Planarity restraints: 2285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.032 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 287 " -0.032 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP E 287 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 287 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP E 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 287 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 287 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 287 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 287 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 287 " 0.031 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP C 287 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 287 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 287 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 287 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 287 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 287 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 287 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 287 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 287 " 0.003 2.00e-02 2.50e+03 ... (remaining 2282 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3827 2.80 - 3.33: 11764 3.33 - 3.85: 21311 3.85 - 4.38: 27095 4.38 - 4.90: 44551 Nonbonded interactions: 108548 Sorted by model distance: nonbonded pdb=" OD2 ASP B 104 " pdb=" NH2 ARG C 218 " model vdw 2.277 3.120 nonbonded pdb=" O LEU C 20 " pdb=" NE2 GLN D 238 " model vdw 2.327 3.120 nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.363 3.120 nonbonded pdb=" N PHE B 17 " pdb=" OE2 GLU C 292 " model vdw 2.367 3.120 nonbonded pdb=" NE ARG D 105 " pdb=" OE1 GLU D 213 " model vdw 2.387 3.120 ... (remaining 108543 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.008 0.061 13575 Z= 0.332 Angle : 0.835 8.585 18465 Z= 0.444 Chirality : 0.051 0.188 2030 Planarity : 0.006 0.051 2285 Dihedral : 9.204 45.792 4845 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: -6.12 (0.12), residues: 1575 helix: -4.06 (0.07), residues: 1145 sheet: None (None), residues: 0 loop : -3.25 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 105 TYR 0.042 0.003 TYR A 236 PHE 0.021 0.003 PHE A 17 TRP 0.064 0.004 TRP E 287 HIS 0.006 0.002 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00783 (13570) covalent geometry : angle 0.83033 (18455) SS BOND : bond 0.01724 ( 5) SS BOND : angle 3.90762 ( 10) hydrogen bonds : bond 0.32134 ( 752) hydrogen bonds : angle 9.45198 ( 2241) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8692 (tttt) cc_final: 0.8192 (tppp) REVERT: A 46 ILE cc_start: 0.8854 (mt) cc_final: 0.8597 (mm) REVERT: A 92 ARG cc_start: 0.7766 (tmt90) cc_final: 0.7327 (tpt170) REVERT: A 308 ASN cc_start: 0.7630 (m-40) cc_final: 0.7364 (m-40) REVERT: B 30 LYS cc_start: 0.8876 (tttt) cc_final: 0.8367 (tptm) REVERT: B 46 ILE cc_start: 0.9001 (mt) cc_final: 0.8758 (mm) REVERT: B 92 ARG cc_start: 0.7781 (tmt90) cc_final: 0.7529 (mmt180) REVERT: B 203 ASP cc_start: 0.7720 (m-30) cc_final: 0.7282 (m-30) REVERT: B 289 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8273 (mmmt) REVERT: B 308 ASN cc_start: 0.7603 (m-40) cc_final: 0.7246 (m-40) REVERT: C 41 SER cc_start: 0.8392 (m) cc_final: 0.8049 (p) REVERT: C 46 ILE cc_start: 0.8469 (mt) cc_final: 0.8166 (mm) REVERT: C 54 LEU cc_start: 0.8157 (mt) cc_final: 0.7898 (mt) REVERT: C 88 LEU cc_start: 0.8473 (mt) cc_final: 0.8270 (mt) REVERT: C 92 ARG cc_start: 0.7723 (tmt90) cc_final: 0.7219 (tpt170) REVERT: C 259 ASP cc_start: 0.7913 (t0) cc_final: 0.7682 (t0) REVERT: C 328 ASP cc_start: 0.7187 (t70) cc_final: 0.6875 (p0) REVERT: D 30 LYS cc_start: 0.8598 (tttt) cc_final: 0.8151 (mmtm) REVERT: D 46 ILE cc_start: 0.8745 (mt) cc_final: 0.8522 (mm) REVERT: D 54 LEU cc_start: 0.8637 (mt) cc_final: 0.8424 (mt) REVERT: D 70 ASN cc_start: 0.9036 (t0) cc_final: 0.8796 (t0) REVERT: D 92 ARG cc_start: 0.7729 (tmt90) cc_final: 0.7340 (mmt90) REVERT: D 308 ASN cc_start: 0.7383 (m-40) cc_final: 0.6825 (p0) REVERT: E 30 LYS cc_start: 0.8549 (tttt) cc_final: 0.8326 (mmtp) REVERT: E 46 ILE cc_start: 0.8656 (mt) cc_final: 0.8353 (mm) REVERT: E 88 LEU cc_start: 0.8534 (mt) cc_final: 0.8326 (mt) REVERT: E 92 ARG cc_start: 0.7647 (tmt90) cc_final: 0.7214 (tpt170) REVERT: E 253 ILE cc_start: 0.8671 (mt) cc_final: 0.8450 (mt) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.6165 time to fit residues: 258.9608 Evaluate side-chains 200 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 316 GLN A 339 ASN B 19 GLN B 96 GLN B 256 GLN B 316 GLN B 339 ASN C 190 ASN C 256 GLN C 293 GLN C 308 ASN C 339 ASN D 96 GLN D 256 GLN D 293 GLN D 339 ASN E 58 GLN E 256 GLN E 339 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.097568 restraints weight = 22335.852| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.00 r_work: 0.3135 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13575 Z= 0.163 Angle : 0.653 10.258 18465 Z= 0.338 Chirality : 0.041 0.198 2030 Planarity : 0.006 0.042 2285 Dihedral : 4.714 29.790 1765 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.49 % Allowed : 9.41 % Favored : 88.10 % 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: -3.12 (0.17), residues: 1575 helix: -1.63 (0.12), residues: 1175 sheet: None (None), residues: 0 loop : -2.91 (0.26), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 122 TYR 0.014 0.001 TYR A 236 PHE 0.025 0.002 PHE E 272 TRP 0.027 0.002 TRP B 287 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00360 (13570) covalent geometry : angle 0.64664 (18455) SS BOND : bond 0.02235 ( 5) SS BOND : angle 3.95243 ( 10) hydrogen bonds : bond 0.07477 ( 752) hydrogen bonds : angle 4.57692 ( 2241) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.518 Fit side-chains REVERT: A 30 LYS cc_start: 0.8678 (tttt) cc_final: 0.7981 (tppp) REVERT: A 46 ILE cc_start: 0.9013 (mt) cc_final: 0.8680 (mm) REVERT: A 53 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8070 (mt) REVERT: A 92 ARG cc_start: 0.8425 (tmt90) cc_final: 0.7353 (mmt90) REVERT: A 328 ASP cc_start: 0.7820 (p0) cc_final: 0.7238 (t70) REVERT: B 30 LYS cc_start: 0.8947 (tttt) cc_final: 0.8271 (tptt) REVERT: B 92 ARG cc_start: 0.8296 (tmt90) cc_final: 0.7666 (mmt90) REVERT: B 323 ASP cc_start: 0.8582 (t0) cc_final: 0.8239 (t0) REVERT: B 328 ASP cc_start: 0.7640 (p0) cc_final: 0.7398 (t0) REVERT: C 41 SER cc_start: 0.8532 (m) cc_final: 0.8177 (p) REVERT: C 46 ILE cc_start: 0.8687 (mt) cc_final: 0.8336 (mm) REVERT: C 92 ARG cc_start: 0.8107 (tmt90) cc_final: 0.7243 (mmt90) REVERT: C 97 TYR cc_start: 0.7316 (t80) cc_final: 0.6944 (t80) REVERT: C 107 MET cc_start: 0.8921 (ttp) cc_final: 0.8601 (ttp) REVERT: C 149 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8337 (ptpt) REVERT: C 159 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7798 (mtt90) REVERT: C 249 LEU cc_start: 0.8787 (tp) cc_final: 0.8209 (mm) REVERT: C 323 ASP cc_start: 0.8353 (t0) cc_final: 0.8066 (t0) REVERT: C 325 MET cc_start: 0.8967 (mtp) cc_final: 0.8703 (mtm) REVERT: C 328 ASP cc_start: 0.7549 (t70) cc_final: 0.6997 (p0) REVERT: D 30 LYS cc_start: 0.8675 (tttt) cc_final: 0.8221 (tptm) REVERT: D 46 ILE cc_start: 0.8900 (mt) cc_final: 0.8605 (mm) REVERT: D 70 ASN cc_start: 0.9144 (t0) cc_final: 0.8924 (t0) REVERT: D 92 ARG cc_start: 0.8196 (tmt90) cc_final: 0.7456 (mmt90) REVERT: E 30 LYS cc_start: 0.8764 (tttt) cc_final: 0.8295 (tptm) REVERT: E 46 ILE cc_start: 0.8847 (mt) cc_final: 0.8539 (mm) REVERT: E 92 ARG cc_start: 0.8378 (tmt90) cc_final: 0.7422 (mmt90) REVERT: E 262 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6890 (mptp) REVERT: E 295 ILE cc_start: 0.8690 (tt) cc_final: 0.8403 (OUTLIER) REVERT: E 328 ASP cc_start: 0.7831 (p0) cc_final: 0.7270 (t0) outliers start: 36 outliers final: 14 residues processed: 258 average time/residue: 0.4674 time to fit residues: 133.9601 Evaluate side-chains 203 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 48 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN B 296 ASN C 256 GLN D 256 GLN E 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096809 restraints weight = 22387.748| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.01 r_work: 0.3126 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13575 Z= 0.124 Angle : 0.546 9.968 18465 Z= 0.279 Chirality : 0.039 0.172 2030 Planarity : 0.004 0.039 2285 Dihedral : 4.248 26.092 1765 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.21 % Allowed : 12.32 % Favored : 85.47 % 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: -1.73 (0.19), residues: 1575 helix: -0.53 (0.13), residues: 1200 sheet: None (None), residues: 0 loop : -2.89 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 59 TYR 0.011 0.001 TYR D 225 PHE 0.022 0.001 PHE B 80 TRP 0.023 0.001 TRP B 229 HIS 0.002 0.000 HIS E 326 Details of bonding type rmsd covalent geometry : bond 0.00270 (13570) covalent geometry : angle 0.54279 (18455) SS BOND : bond 0.01281 ( 5) SS BOND : angle 2.60851 ( 10) hydrogen bonds : bond 0.05466 ( 752) hydrogen bonds : angle 4.10090 ( 2241) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.365 Fit side-chains REVERT: A 30 LYS cc_start: 0.8661 (tttt) cc_final: 0.7983 (tppp) REVERT: A 46 ILE cc_start: 0.9025 (mt) cc_final: 0.8666 (mm) REVERT: A 53 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 92 ARG cc_start: 0.8334 (tmt90) cc_final: 0.7246 (tpt170) REVERT: A 328 ASP cc_start: 0.7715 (p0) cc_final: 0.7505 (t70) REVERT: B 30 LYS cc_start: 0.8970 (tttt) cc_final: 0.8309 (tptt) REVERT: B 92 ARG cc_start: 0.8195 (tmt90) cc_final: 0.7477 (mmt90) REVERT: B 97 TYR cc_start: 0.7592 (t80) cc_final: 0.7384 (t80) REVERT: B 323 ASP cc_start: 0.8511 (t0) cc_final: 0.8100 (t0) REVERT: C 41 SER cc_start: 0.8595 (m) cc_final: 0.8254 (p) REVERT: C 46 ILE cc_start: 0.8772 (mt) cc_final: 0.8420 (mm) REVERT: C 92 ARG cc_start: 0.8039 (tmt90) cc_final: 0.7211 (mmt90) REVERT: C 97 TYR cc_start: 0.7311 (t80) cc_final: 0.6858 (t80) REVERT: C 249 LEU cc_start: 0.8772 (tp) cc_final: 0.8171 (mm) REVERT: C 323 ASP cc_start: 0.8313 (t0) cc_final: 0.8081 (t0) REVERT: C 325 MET cc_start: 0.8965 (mtp) cc_final: 0.8750 (mtm) REVERT: C 328 ASP cc_start: 0.7579 (t70) cc_final: 0.7024 (p0) REVERT: D 30 LYS cc_start: 0.8706 (tttt) cc_final: 0.8187 (mmtp) REVERT: D 46 ILE cc_start: 0.8897 (mt) cc_final: 0.8565 (mm) REVERT: D 92 ARG cc_start: 0.8117 (tmt90) cc_final: 0.7401 (mmt90) REVERT: E 30 LYS cc_start: 0.8784 (tttt) cc_final: 0.8286 (tptm) REVERT: E 46 ILE cc_start: 0.8882 (mt) cc_final: 0.8578 (mm) REVERT: E 64 LYS cc_start: 0.8985 (mttt) cc_final: 0.8777 (mttt) REVERT: E 92 ARG cc_start: 0.8408 (tmt90) cc_final: 0.7348 (mmt-90) REVERT: E 203 ASP cc_start: 0.8629 (m-30) cc_final: 0.8422 (m-30) REVERT: E 262 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6946 (mptp) REVERT: E 295 ILE cc_start: 0.8722 (tt) cc_final: 0.8433 (mt) REVERT: E 328 ASP cc_start: 0.7771 (p0) cc_final: 0.7484 (t0) outliers start: 32 outliers final: 12 residues processed: 225 average time/residue: 0.4690 time to fit residues: 117.1682 Evaluate side-chains 192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 256 GLN A 326 HIS B 19 GLN D 256 GLN E 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093916 restraints weight = 22655.276| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.03 r_work: 0.3076 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13575 Z= 0.165 Angle : 0.580 9.374 18465 Z= 0.292 Chirality : 0.041 0.213 2030 Planarity : 0.004 0.039 2285 Dihedral : 4.275 33.757 1765 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.91 % Allowed : 13.01 % Favored : 84.08 % Cbeta Deviations : 0.00 % 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: -0.87 (0.20), residues: 1575 helix: 0.13 (0.14), residues: 1185 sheet: None (None), residues: 0 loop : -2.60 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 218 TYR 0.018 0.001 TYR E 225 PHE 0.031 0.002 PHE E 80 TRP 0.022 0.002 TRP B 287 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00387 (13570) covalent geometry : angle 0.57534 (18455) SS BOND : bond 0.01505 ( 5) SS BOND : angle 3.08460 ( 10) hydrogen bonds : bond 0.05479 ( 752) hydrogen bonds : angle 4.03820 ( 2241) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8701 (tttt) cc_final: 0.8011 (tppp) REVERT: A 46 ILE cc_start: 0.9052 (mt) cc_final: 0.8843 (mt) REVERT: A 53 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7994 (mt) REVERT: A 91 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8844 (m) REVERT: A 92 ARG cc_start: 0.8363 (tmt90) cc_final: 0.7415 (mmt90) REVERT: B 30 LYS cc_start: 0.8982 (tttt) cc_final: 0.8354 (tptt) REVERT: B 67 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8850 (mp) REVERT: B 92 ARG cc_start: 0.8239 (tmt90) cc_final: 0.7489 (mmt90) REVERT: B 323 ASP cc_start: 0.8543 (t0) cc_final: 0.8162 (t0) REVERT: C 41 SER cc_start: 0.8589 (m) cc_final: 0.8243 (p) REVERT: C 46 ILE cc_start: 0.8873 (mt) cc_final: 0.8550 (mm) REVERT: C 92 ARG cc_start: 0.8139 (tmt90) cc_final: 0.7288 (mmt90) REVERT: C 97 TYR cc_start: 0.7377 (t80) cc_final: 0.6938 (t80) REVERT: C 107 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8635 (ttp) REVERT: C 249 LEU cc_start: 0.8857 (tp) cc_final: 0.8230 (mm) REVERT: C 323 ASP cc_start: 0.8487 (t0) cc_final: 0.8264 (t0) REVERT: C 328 ASP cc_start: 0.7660 (t70) cc_final: 0.7022 (p0) REVERT: D 30 LYS cc_start: 0.8723 (tttt) cc_final: 0.8278 (tptm) REVERT: D 46 ILE cc_start: 0.8907 (mt) cc_final: 0.8603 (mm) REVERT: D 92 ARG cc_start: 0.8221 (tmt90) cc_final: 0.7398 (mmt90) REVERT: D 259 ASP cc_start: 0.8342 (t0) cc_final: 0.8057 (t0) REVERT: D 325 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8507 (mtp) REVERT: D 328 ASP cc_start: 0.7483 (t70) cc_final: 0.6972 (p0) REVERT: E 30 LYS cc_start: 0.8820 (tttt) cc_final: 0.8226 (tttt) REVERT: E 46 ILE cc_start: 0.8972 (mt) cc_final: 0.8697 (mm) REVERT: E 92 ARG cc_start: 0.8373 (tmt90) cc_final: 0.7388 (mmt-90) REVERT: E 149 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8103 (ptpt) REVERT: E 203 ASP cc_start: 0.8682 (m-30) cc_final: 0.8354 (m-30) REVERT: E 262 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7049 (mptp) outliers start: 42 outliers final: 22 residues processed: 213 average time/residue: 0.4881 time to fit residues: 115.3752 Evaluate side-chains 192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 149 optimal weight: 0.0000 chunk 124 optimal weight: 0.0040 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN C 256 GLN D 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.127114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105725 restraints weight = 22732.272| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.82 r_work: 0.3309 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13575 Z= 0.123 Angle : 0.533 9.989 18465 Z= 0.267 Chirality : 0.039 0.226 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.090 31.151 1765 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.70 % Allowed : 13.84 % Favored : 83.46 % Cbeta Deviations : 0.00 % 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: -0.38 (0.20), residues: 1575 helix: 0.43 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : -2.40 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 218 TYR 0.013 0.001 TYR E 225 PHE 0.032 0.001 PHE B 80 TRP 0.021 0.001 TRP B 229 HIS 0.001 0.000 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00281 (13570) covalent geometry : angle 0.52826 (18455) SS BOND : bond 0.01468 ( 5) SS BOND : angle 3.07189 ( 10) hydrogen bonds : bond 0.04829 ( 752) hydrogen bonds : angle 3.88321 ( 2241) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 0.534 Fit side-chains REVERT: A 30 LYS cc_start: 0.8718 (tttt) cc_final: 0.8162 (tppp) REVERT: A 46 ILE cc_start: 0.8998 (mt) cc_final: 0.8758 (mm) REVERT: A 53 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7950 (mt) REVERT: A 92 ARG cc_start: 0.8420 (tmt90) cc_final: 0.7640 (mmt90) REVERT: B 30 LYS cc_start: 0.8940 (tttt) cc_final: 0.8440 (tptt) REVERT: B 67 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8923 (mp) REVERT: B 92 ARG cc_start: 0.8348 (tmt90) cc_final: 0.7790 (mmt90) REVERT: B 154 MET cc_start: 0.8305 (mmm) cc_final: 0.7749 (mmm) REVERT: B 323 ASP cc_start: 0.8369 (t0) cc_final: 0.8003 (t0) REVERT: C 30 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8260 (mmtp) REVERT: C 41 SER cc_start: 0.8711 (m) cc_final: 0.8412 (p) REVERT: C 46 ILE cc_start: 0.8840 (mt) cc_final: 0.8529 (mm) REVERT: C 92 ARG cc_start: 0.8374 (tmt90) cc_final: 0.7713 (mmt90) REVERT: C 97 TYR cc_start: 0.7442 (t80) cc_final: 0.7210 (t80) REVERT: C 249 LEU cc_start: 0.8848 (tp) cc_final: 0.8253 (mm) REVERT: C 328 ASP cc_start: 0.7478 (t70) cc_final: 0.7093 (p0) REVERT: D 30 LYS cc_start: 0.8709 (tttt) cc_final: 0.8356 (tptm) REVERT: D 46 ILE cc_start: 0.8838 (mt) cc_final: 0.8588 (mm) REVERT: D 92 ARG cc_start: 0.8379 (tmt90) cc_final: 0.7677 (mmt90) REVERT: D 325 MET cc_start: 0.8981 (mtp) cc_final: 0.8548 (mtp) REVERT: E 30 LYS cc_start: 0.8745 (tttt) cc_final: 0.8270 (tttt) REVERT: E 46 ILE cc_start: 0.8914 (mt) cc_final: 0.8638 (mm) REVERT: E 92 ARG cc_start: 0.8468 (tmt90) cc_final: 0.7680 (mmt-90) REVERT: E 149 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8082 (ptpt) REVERT: E 203 ASP cc_start: 0.8490 (m-30) cc_final: 0.8234 (m-30) REVERT: E 262 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.7062 (mptp) outliers start: 39 outliers final: 17 residues processed: 201 average time/residue: 0.4624 time to fit residues: 103.0376 Evaluate side-chains 188 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN D 256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105666 restraints weight = 22647.372| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.82 r_work: 0.3308 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13575 Z= 0.125 Angle : 0.539 10.095 18465 Z= 0.268 Chirality : 0.039 0.244 2030 Planarity : 0.004 0.037 2285 Dihedral : 3.990 29.596 1765 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.08 % Allowed : 15.09 % Favored : 82.84 % 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: -0.10 (0.21), residues: 1575 helix: 0.62 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 218 TYR 0.012 0.001 TYR A 225 PHE 0.029 0.001 PHE A 278 TRP 0.024 0.001 TRP B 229 HIS 0.002 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00291 (13570) covalent geometry : angle 0.53563 (18455) SS BOND : bond 0.01260 ( 5) SS BOND : angle 2.78558 ( 10) hydrogen bonds : bond 0.04722 ( 752) hydrogen bonds : angle 3.86370 ( 2241) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.520 Fit side-chains REVERT: A 30 LYS cc_start: 0.8720 (tttt) cc_final: 0.8167 (tppp) REVERT: A 41 SER cc_start: 0.8837 (m) cc_final: 0.8557 (p) REVERT: A 53 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 61 MET cc_start: 0.8542 (ttm) cc_final: 0.8336 (ttt) REVERT: A 92 ARG cc_start: 0.8422 (tmt90) cc_final: 0.7633 (mmt90) REVERT: A 120 TYR cc_start: 0.8792 (t80) cc_final: 0.8545 (t80) REVERT: B 30 LYS cc_start: 0.8908 (tttt) cc_final: 0.8381 (tptt) REVERT: B 67 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8916 (mp) REVERT: B 92 ARG cc_start: 0.8410 (tmt90) cc_final: 0.7811 (mmt90) REVERT: B 323 ASP cc_start: 0.8417 (t0) cc_final: 0.8161 (t0) REVERT: C 41 SER cc_start: 0.8769 (m) cc_final: 0.8428 (p) REVERT: C 46 ILE cc_start: 0.8878 (mt) cc_final: 0.8566 (mm) REVERT: C 92 ARG cc_start: 0.8443 (tmt90) cc_final: 0.7743 (mmt90) REVERT: C 107 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8548 (ttp) REVERT: C 249 LEU cc_start: 0.8888 (tp) cc_final: 0.8279 (mm) REVERT: C 323 ASP cc_start: 0.8364 (t0) cc_final: 0.8104 (t0) REVERT: C 328 ASP cc_start: 0.7491 (t70) cc_final: 0.7104 (p0) REVERT: D 30 LYS cc_start: 0.8718 (tttt) cc_final: 0.8323 (tptm) REVERT: D 46 ILE cc_start: 0.8874 (mt) cc_final: 0.8617 (mm) REVERT: D 92 ARG cc_start: 0.8406 (tmt90) cc_final: 0.7725 (mmt90) REVERT: D 305 PHE cc_start: 0.5523 (m-80) cc_final: 0.5311 (m-80) REVERT: D 325 MET cc_start: 0.8970 (mtp) cc_final: 0.8583 (mtp) REVERT: D 328 ASP cc_start: 0.7564 (t70) cc_final: 0.7160 (p0) REVERT: E 30 LYS cc_start: 0.8747 (tttt) cc_final: 0.8284 (tttt) REVERT: E 41 SER cc_start: 0.8716 (m) cc_final: 0.8470 (p) REVERT: E 46 ILE cc_start: 0.8933 (mt) cc_final: 0.8707 (mm) REVERT: E 92 ARG cc_start: 0.8390 (tmt90) cc_final: 0.7744 (mmt90) REVERT: E 149 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8160 (ptpt) REVERT: E 203 ASP cc_start: 0.8481 (m-30) cc_final: 0.8197 (m-30) REVERT: E 262 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7134 (mptp) outliers start: 30 outliers final: 19 residues processed: 207 average time/residue: 0.4619 time to fit residues: 105.7749 Evaluate side-chains 191 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 256 GLN B 19 GLN D 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.094173 restraints weight = 22319.084| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.97 r_work: 0.3079 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13575 Z= 0.143 Angle : 0.563 11.403 18465 Z= 0.277 Chirality : 0.041 0.303 2030 Planarity : 0.004 0.037 2285 Dihedral : 3.997 29.297 1765 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.35 % Allowed : 15.99 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1575 helix: 0.71 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 218 TYR 0.016 0.001 TYR E 225 PHE 0.033 0.002 PHE B 80 TRP 0.024 0.001 TRP B 229 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00335 (13570) covalent geometry : angle 0.55906 (18455) SS BOND : bond 0.01377 ( 5) SS BOND : angle 3.05680 ( 10) hydrogen bonds : bond 0.04881 ( 752) hydrogen bonds : angle 3.89002 ( 2241) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.504 Fit side-chains REVERT: A 30 LYS cc_start: 0.8687 (tttt) cc_final: 0.8010 (tppp) REVERT: A 41 SER cc_start: 0.8850 (m) cc_final: 0.8492 (p) REVERT: A 92 ARG cc_start: 0.8273 (tmt90) cc_final: 0.7289 (mmt90) REVERT: B 30 LYS cc_start: 0.8866 (tttt) cc_final: 0.8270 (tptt) REVERT: B 67 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8796 (mp) REVERT: B 92 ARG cc_start: 0.8224 (tmt90) cc_final: 0.7415 (mmt90) REVERT: B 97 TYR cc_start: 0.7618 (t80) cc_final: 0.7357 (t80) REVERT: B 323 ASP cc_start: 0.8561 (t0) cc_final: 0.8335 (t0) REVERT: C 41 SER cc_start: 0.8828 (m) cc_final: 0.8471 (p) REVERT: C 46 ILE cc_start: 0.9027 (mt) cc_final: 0.8727 (mm) REVERT: C 92 ARG cc_start: 0.8154 (tmt90) cc_final: 0.7312 (mmt90) REVERT: C 107 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8627 (ttp) REVERT: C 323 ASP cc_start: 0.8477 (t0) cc_final: 0.8213 (t0) REVERT: C 328 ASP cc_start: 0.7748 (t70) cc_final: 0.7097 (p0) REVERT: D 30 LYS cc_start: 0.8748 (tttt) cc_final: 0.8184 (tptm) REVERT: D 46 ILE cc_start: 0.8900 (mt) cc_final: 0.8634 (mm) REVERT: D 92 ARG cc_start: 0.8223 (tmt90) cc_final: 0.7331 (mmt90) REVERT: D 325 MET cc_start: 0.9103 (mtp) cc_final: 0.8643 (mtp) REVERT: D 328 ASP cc_start: 0.7590 (t70) cc_final: 0.7034 (p0) REVERT: E 30 LYS cc_start: 0.8768 (tttt) cc_final: 0.8285 (tptt) REVERT: E 41 SER cc_start: 0.8831 (m) cc_final: 0.8543 (p) REVERT: E 46 ILE cc_start: 0.8712 (mt) cc_final: 0.8424 (tt) REVERT: E 92 ARG cc_start: 0.8286 (tmt90) cc_final: 0.7483 (mmt90) REVERT: E 149 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8066 (ptpt) REVERT: E 262 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7196 (mptp) outliers start: 34 outliers final: 20 residues processed: 197 average time/residue: 0.4372 time to fit residues: 96.0860 Evaluate side-chains 190 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 45 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.094686 restraints weight = 22268.059| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.00 r_work: 0.3089 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13575 Z= 0.123 Angle : 0.551 11.404 18465 Z= 0.270 Chirality : 0.040 0.318 2030 Planarity : 0.004 0.039 2285 Dihedral : 3.936 27.841 1765 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.87 % Allowed : 16.40 % Favored : 81.73 % 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: 0.21 (0.21), residues: 1575 helix: 0.83 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.10 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 159 TYR 0.013 0.001 TYR E 225 PHE 0.022 0.001 PHE B 278 TRP 0.021 0.001 TRP E 229 HIS 0.003 0.000 HIS D 156 Details of bonding type rmsd covalent geometry : bond 0.00281 (13570) covalent geometry : angle 0.54816 (18455) SS BOND : bond 0.01148 ( 5) SS BOND : angle 2.55254 ( 10) hydrogen bonds : bond 0.04660 ( 752) hydrogen bonds : angle 3.86489 ( 2241) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.423 Fit side-chains REVERT: A 30 LYS cc_start: 0.8662 (tttt) cc_final: 0.7992 (tppp) REVERT: A 41 SER cc_start: 0.8854 (m) cc_final: 0.8514 (p) REVERT: A 92 ARG cc_start: 0.8288 (tmt90) cc_final: 0.7319 (mmt90) REVERT: A 120 TYR cc_start: 0.8864 (t80) cc_final: 0.8612 (t80) REVERT: B 30 LYS cc_start: 0.8853 (tttt) cc_final: 0.8210 (mmtp) REVERT: B 67 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8808 (mp) REVERT: B 92 ARG cc_start: 0.8181 (tmt90) cc_final: 0.7278 (mmt90) REVERT: B 97 TYR cc_start: 0.7626 (t80) cc_final: 0.7402 (t80) REVERT: B 154 MET cc_start: 0.8504 (mmm) cc_final: 0.8259 (mmp) REVERT: B 323 ASP cc_start: 0.8528 (t0) cc_final: 0.8231 (t0) REVERT: C 41 SER cc_start: 0.8814 (m) cc_final: 0.8468 (p) REVERT: C 61 MET cc_start: 0.8566 (ttm) cc_final: 0.8238 (ttt) REVERT: C 92 ARG cc_start: 0.8244 (tmt90) cc_final: 0.7364 (mmt90) REVERT: C 97 TYR cc_start: 0.7359 (t80) cc_final: 0.6985 (t80) REVERT: C 323 ASP cc_start: 0.8472 (t0) cc_final: 0.8197 (t0) REVERT: C 328 ASP cc_start: 0.7759 (t70) cc_final: 0.7117 (p0) REVERT: D 30 LYS cc_start: 0.8768 (tttt) cc_final: 0.8262 (mmtp) REVERT: D 46 ILE cc_start: 0.8902 (mt) cc_final: 0.8636 (mm) REVERT: D 92 ARG cc_start: 0.8246 (tmt90) cc_final: 0.7345 (mmt90) REVERT: D 259 ASP cc_start: 0.8245 (t0) cc_final: 0.8022 (t0) REVERT: D 325 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: E 30 LYS cc_start: 0.8761 (tttt) cc_final: 0.8291 (tptt) REVERT: E 41 SER cc_start: 0.8725 (m) cc_final: 0.8384 (p) REVERT: E 46 ILE cc_start: 0.8710 (mt) cc_final: 0.8413 (tt) REVERT: E 92 ARG cc_start: 0.8192 (tmt90) cc_final: 0.7484 (mmt90) REVERT: E 149 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8089 (ptpt) REVERT: E 262 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7204 (mptp) REVERT: E 323 ASP cc_start: 0.8666 (t0) cc_final: 0.8387 (t0) outliers start: 27 outliers final: 16 residues processed: 188 average time/residue: 0.4612 time to fit residues: 96.0135 Evaluate side-chains 185 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 122 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.118206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093950 restraints weight = 22412.910| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.98 r_work: 0.3073 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13575 Z= 0.150 Angle : 0.575 11.346 18465 Z= 0.281 Chirality : 0.041 0.338 2030 Planarity : 0.004 0.038 2285 Dihedral : 3.964 28.037 1765 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.87 % Allowed : 17.09 % Favored : 81.04 % 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: 0.24 (0.21), residues: 1575 helix: 0.84 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.016 0.001 TYR E 225 PHE 0.034 0.002 PHE B 80 TRP 0.028 0.002 TRP E 229 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00352 (13570) covalent geometry : angle 0.57072 (18455) SS BOND : bond 0.01305 ( 5) SS BOND : angle 2.88701 ( 10) hydrogen bonds : bond 0.04843 ( 752) hydrogen bonds : angle 3.89771 ( 2241) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.380 Fit side-chains REVERT: A 30 LYS cc_start: 0.8619 (tttt) cc_final: 0.8004 (tppp) REVERT: A 41 SER cc_start: 0.8895 (m) cc_final: 0.8543 (p) REVERT: A 92 ARG cc_start: 0.8296 (tmt90) cc_final: 0.7313 (mmt90) REVERT: A 120 TYR cc_start: 0.8867 (t80) cc_final: 0.8598 (t80) REVERT: B 30 LYS cc_start: 0.8825 (tttt) cc_final: 0.8189 (mmtp) REVERT: B 67 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 92 ARG cc_start: 0.8178 (tmt90) cc_final: 0.7313 (mmt90) REVERT: B 97 TYR cc_start: 0.7695 (t80) cc_final: 0.7466 (t80) REVERT: B 323 ASP cc_start: 0.8537 (t0) cc_final: 0.8247 (t0) REVERT: C 41 SER cc_start: 0.8870 (m) cc_final: 0.8513 (p) REVERT: C 46 ILE cc_start: 0.8591 (mp) cc_final: 0.8143 (tt) REVERT: C 61 MET cc_start: 0.8505 (ttm) cc_final: 0.8143 (ttt) REVERT: C 92 ARG cc_start: 0.8304 (tmt90) cc_final: 0.7389 (mmt90) REVERT: C 97 TYR cc_start: 0.7514 (t80) cc_final: 0.7194 (t80) REVERT: C 323 ASP cc_start: 0.8519 (t0) cc_final: 0.8233 (t0) REVERT: C 328 ASP cc_start: 0.7772 (t70) cc_final: 0.7117 (p0) REVERT: D 30 LYS cc_start: 0.8762 (tttt) cc_final: 0.8255 (mmtp) REVERT: D 92 ARG cc_start: 0.8311 (tmt90) cc_final: 0.7369 (mmt90) REVERT: D 325 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8667 (mtp) REVERT: E 30 LYS cc_start: 0.8766 (tttt) cc_final: 0.8290 (tptt) REVERT: E 41 SER cc_start: 0.8812 (m) cc_final: 0.8471 (p) REVERT: E 46 ILE cc_start: 0.8737 (mt) cc_final: 0.8436 (tt) REVERT: E 92 ARG cc_start: 0.8225 (tmt90) cc_final: 0.7523 (mmt90) REVERT: E 149 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8117 (ptpt) REVERT: E 262 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7220 (mptp) outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 0.4627 time to fit residues: 96.6473 Evaluate side-chains 187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.7980 chunk 142 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 190 ASN D 296 ASN D 316 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095353 restraints weight = 22418.666| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.98 r_work: 0.3096 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13575 Z= 0.120 Angle : 0.559 11.503 18465 Z= 0.272 Chirality : 0.040 0.201 2030 Planarity : 0.004 0.038 2285 Dihedral : 3.913 27.081 1765 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.59 % Allowed : 17.58 % Favored : 80.83 % 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: 0.44 (0.21), residues: 1575 helix: 0.98 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -1.95 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.012 0.001 TYR E 225 PHE 0.020 0.001 PHE E 80 TRP 0.023 0.001 TRP D 229 HIS 0.001 0.000 HIS C 178 Details of bonding type rmsd covalent geometry : bond 0.00273 (13570) covalent geometry : angle 0.55666 (18455) SS BOND : bond 0.01020 ( 5) SS BOND : angle 2.36275 ( 10) hydrogen bonds : bond 0.04544 ( 752) hydrogen bonds : angle 3.85525 ( 2241) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.375 Fit side-chains REVERT: A 30 LYS cc_start: 0.8630 (tttt) cc_final: 0.8012 (tppp) REVERT: A 41 SER cc_start: 0.8886 (m) cc_final: 0.8537 (p) REVERT: A 92 ARG cc_start: 0.8274 (tmt90) cc_final: 0.7278 (mmt90) REVERT: A 120 TYR cc_start: 0.8875 (t80) cc_final: 0.8604 (t80) REVERT: B 30 LYS cc_start: 0.8828 (tttt) cc_final: 0.8224 (tptm) REVERT: B 70 ASN cc_start: 0.8849 (t0) cc_final: 0.8640 (t160) REVERT: B 92 ARG cc_start: 0.8171 (tmt90) cc_final: 0.7266 (mmt90) REVERT: B 97 TYR cc_start: 0.7724 (t80) cc_final: 0.7514 (t80) REVERT: B 323 ASP cc_start: 0.8524 (t0) cc_final: 0.8218 (t0) REVERT: C 41 SER cc_start: 0.8820 (m) cc_final: 0.8478 (p) REVERT: C 46 ILE cc_start: 0.8551 (mp) cc_final: 0.8102 (tt) REVERT: C 61 MET cc_start: 0.8504 (ttm) cc_final: 0.8127 (ttt) REVERT: C 92 ARG cc_start: 0.8257 (tmt90) cc_final: 0.7349 (mmt90) REVERT: C 97 TYR cc_start: 0.7727 (t80) cc_final: 0.7453 (t80) REVERT: C 323 ASP cc_start: 0.8525 (t0) cc_final: 0.8253 (t0) REVERT: C 328 ASP cc_start: 0.7804 (t70) cc_final: 0.7128 (p0) REVERT: D 30 LYS cc_start: 0.8740 (tttt) cc_final: 0.8244 (mmtp) REVERT: D 92 ARG cc_start: 0.8251 (tmt90) cc_final: 0.7329 (mmt90) REVERT: D 252 LEU cc_start: 0.8977 (tm) cc_final: 0.8738 (tp) REVERT: D 325 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8657 (mtp) REVERT: D 328 ASP cc_start: 0.7601 (t70) cc_final: 0.7055 (p0) REVERT: E 19 GLN cc_start: 0.7651 (pm20) cc_final: 0.7146 (pt0) REVERT: E 30 LYS cc_start: 0.8749 (tttt) cc_final: 0.8285 (tptt) REVERT: E 41 SER cc_start: 0.8806 (m) cc_final: 0.8509 (p) REVERT: E 46 ILE cc_start: 0.8734 (mt) cc_final: 0.8450 (tt) REVERT: E 64 LYS cc_start: 0.9132 (mttt) cc_final: 0.8760 (mttp) REVERT: E 92 ARG cc_start: 0.8248 (tmt90) cc_final: 0.7397 (mmt90) REVERT: E 149 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8092 (ptpt) REVERT: E 262 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.7221 (mptp) outliers start: 23 outliers final: 15 residues processed: 188 average time/residue: 0.4721 time to fit residues: 98.1193 Evaluate side-chains 181 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN D 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.118479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094257 restraints weight = 22305.134| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.98 r_work: 0.3079 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13575 Z= 0.140 Angle : 0.577 11.387 18465 Z= 0.280 Chirality : 0.040 0.180 2030 Planarity : 0.004 0.038 2285 Dihedral : 3.926 27.648 1765 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.73 % Allowed : 17.51 % Favored : 80.76 % 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: 0.46 (0.21), residues: 1575 helix: 0.99 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -1.92 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.015 0.001 TYR B 225 PHE 0.037 0.001 PHE B 80 TRP 0.023 0.002 TRP A 229 HIS 0.002 0.000 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00327 (13570) covalent geometry : angle 0.57387 (18455) SS BOND : bond 0.01244 ( 5) SS BOND : angle 2.76621 ( 10) hydrogen bonds : bond 0.04723 ( 752) hydrogen bonds : angle 3.87402 ( 2241) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4042.32 seconds wall clock time: 69 minutes 37.46 seconds (4177.46 seconds total)