Starting phenix.real_space_refine on Wed Jul 30 21:08:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n26_9324/07_2025/6n26_9324_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n26_9324/07_2025/6n26_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_9324/07_2025/6n26_9324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n26_9324/07_2025/6n26_9324.map" model { file = "/net/cci-nas-00/data/ceres_data/6n26_9324/07_2025/6n26_9324_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n26_9324/07_2025/6n26_9324_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, E, D Time building chain proxies: 5.71, per 1000 atoms: 0.43 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 C 135 " - pdb=" SG CYS C 185 " distance=2.05 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.05 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.05 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 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: 3.09 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.34 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: 4.29 Time building geometry restraints manager: 3.81 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 0.160 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 30.020 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:19.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.064 0.004 TRP E 287 HIS 0.006 0.002 HIS A 168 PHE 0.021 0.003 PHE A 17 TYR 0.042 0.003 TYR A 236 ARG 0.006 0.001 ARG C 105 Details of bonding type rmsd hydrogen bonds : bond 0.32134 ( 752) hydrogen bonds : angle 9.45198 ( 2241) SS BOND : bond 0.01724 ( 5) SS BOND : angle 3.90762 ( 10) covalent geometry : bond 0.00783 (13570) covalent geometry : angle 0.83033 (18455) *********************** 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 : 1.375 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8693 (tttt) cc_final: 0.8193 (tppp) REVERT: A 46 ILE cc_start: 0.8854 (mt) cc_final: 0.8598 (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: 0.7283 (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: 0.8165 (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: 0.7186 (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: 0.8352 (mm) REVERT: E 88 LEU cc_start: 0.8534 (mt) cc_final: 0.8325 (mt) REVERT: E 92 ARG cc_start: 0.7647 (tmt90) cc_final: 0.7214 (tpt170) REVERT: E 253 ILE cc_start: 0.8670 (mt) cc_final: 0.8450 (mt) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 1.3006 time to fit residues: 547.6477 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 : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 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 190 ASN 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 = 0.3621 r_free = 0.3621 target = 0.120622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096352 restraints weight = 22278.367| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.02 r_work: 0.3117 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13575 Z= 0.166 Angle : 0.660 10.364 18465 Z= 0.340 Chirality : 0.042 0.196 2030 Planarity : 0.006 0.042 2285 Dihedral : 4.721 30.581 1765 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.91 % Allowed : 9.20 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.17), residues: 1575 helix: -1.56 (0.13), residues: 1170 sheet: None (None), residues: 0 loop : -2.88 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 287 HIS 0.004 0.001 HIS E 326 PHE 0.026 0.002 PHE E 272 TYR 0.016 0.001 TYR A 236 ARG 0.004 0.001 ARG D 218 Details of bonding type rmsd hydrogen bonds : bond 0.06982 ( 752) hydrogen bonds : angle 4.50873 ( 2241) SS BOND : bond 0.01855 ( 5) SS BOND : angle 3.98437 ( 10) covalent geometry : bond 0.00369 (13570) covalent geometry : angle 0.65326 (18455) *********************** 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: 42 poor density : 229 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8674 (tttt) cc_final: 0.7992 (tppp) REVERT: A 46 ILE cc_start: 0.9009 (mt) cc_final: 0.8681 (mm) REVERT: A 53 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 92 ARG cc_start: 0.8444 (tmt90) cc_final: 0.7348 (mmt90) REVERT: A 328 ASP cc_start: 0.7814 (p0) cc_final: 0.7249 (t70) REVERT: B 30 LYS cc_start: 0.8949 (tttt) cc_final: 0.8265 (tptt) REVERT: B 92 ARG cc_start: 0.8284 (tmt90) cc_final: 0.7626 (mmt90) REVERT: B 323 ASP cc_start: 0.8597 (t0) cc_final: 0.8301 (t0) REVERT: B 328 ASP cc_start: 0.7696 (p0) cc_final: 0.7458 (t0) REVERT: C 41 SER cc_start: 0.8542 (m) cc_final: 0.8188 (p) REVERT: C 46 ILE cc_start: 0.8716 (mt) cc_final: 0.8370 (mm) REVERT: C 92 ARG cc_start: 0.8121 (tmt90) cc_final: 0.7227 (mmt90) REVERT: C 97 TYR cc_start: 0.7356 (t80) cc_final: 0.6962 (t80) REVERT: C 149 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8355 (ptpt) REVERT: C 159 ARG cc_start: 0.8129 (mtt90) cc_final: 0.7805 (mtt90) REVERT: C 249 LEU cc_start: 0.8801 (tp) cc_final: 0.8210 (mm) REVERT: C 323 ASP cc_start: 0.8363 (t0) cc_final: 0.8107 (t0) REVERT: C 325 MET cc_start: 0.8978 (mtp) cc_final: 0.8704 (mtm) REVERT: C 328 ASP cc_start: 0.7537 (t70) cc_final: 0.6962 (p0) REVERT: D 30 LYS cc_start: 0.8697 (tttt) cc_final: 0.8200 (mmmm) REVERT: D 46 ILE cc_start: 0.8906 (mt) cc_final: 0.8602 (mm) REVERT: D 70 ASN cc_start: 0.9140 (t0) cc_final: 0.8933 (t0) REVERT: D 92 ARG cc_start: 0.8223 (tmt90) cc_final: 0.7450 (mmt90) REVERT: E 30 LYS cc_start: 0.8779 (tttt) cc_final: 0.8296 (tptm) REVERT: E 46 ILE cc_start: 0.8865 (mt) cc_final: 0.8565 (mm) REVERT: E 92 ARG cc_start: 0.8314 (tmt90) cc_final: 0.7403 (mmt90) REVERT: E 262 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6942 (mptp) REVERT: E 295 ILE cc_start: 0.8692 (tt) cc_final: 0.8413 (OUTLIER) REVERT: E 328 ASP cc_start: 0.7852 (p0) cc_final: 0.7294 (t0) outliers start: 42 outliers final: 16 residues processed: 259 average time/residue: 1.1868 time to fit residues: 343.7383 Evaluate side-chains 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 241 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 140 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN A 326 HIS B 19 GLN B 296 ASN C 256 GLN D 256 GLN E 339 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093955 restraints weight = 22318.506| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.99 r_work: 0.3074 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13575 Z= 0.160 Angle : 0.587 9.276 18465 Z= 0.297 Chirality : 0.041 0.200 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.280 26.031 1765 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.49 % Allowed : 11.97 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1575 helix: -0.43 (0.13), residues: 1200 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 287 HIS 0.003 0.001 HIS A 326 PHE 0.023 0.002 PHE B 80 TYR 0.018 0.001 TYR D 225 ARG 0.004 0.001 ARG C 59 Details of bonding type rmsd hydrogen bonds : bond 0.05771 ( 752) hydrogen bonds : angle 4.12315 ( 2241) SS BOND : bond 0.01420 ( 5) SS BOND : angle 3.19440 ( 10) covalent geometry : bond 0.00371 (13570) covalent geometry : angle 0.58207 (18455) *********************** 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 229 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 2.035 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8693 (tttt) cc_final: 0.8011 (tppp) REVERT: A 46 ILE cc_start: 0.9021 (mt) cc_final: 0.8661 (mm) REVERT: A 53 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8018 (mt) REVERT: A 92 ARG cc_start: 0.8367 (tmt90) cc_final: 0.7341 (mmt90) REVERT: B 30 LYS cc_start: 0.8998 (tttt) cc_final: 0.8360 (tptt) REVERT: B 92 ARG cc_start: 0.8201 (tmt90) cc_final: 0.7441 (mmt90) REVERT: B 97 TYR cc_start: 0.7607 (t80) cc_final: 0.7402 (t80) REVERT: C 30 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8134 (mmtp) REVERT: C 41 SER cc_start: 0.8735 (m) cc_final: 0.8402 (p) REVERT: C 46 ILE cc_start: 0.8863 (mt) cc_final: 0.8531 (mm) REVERT: C 92 ARG cc_start: 0.8168 (tmt90) cc_final: 0.7257 (mmt90) REVERT: C 97 TYR cc_start: 0.7367 (t80) cc_final: 0.6938 (t80) REVERT: C 107 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8639 (ttp) REVERT: C 154 MET cc_start: 0.8570 (mmm) cc_final: 0.8353 (mmm) REVERT: C 249 LEU cc_start: 0.8838 (tp) cc_final: 0.8240 (mm) REVERT: C 323 ASP cc_start: 0.8435 (t0) cc_final: 0.8138 (t0) REVERT: C 325 MET cc_start: 0.8992 (mtp) cc_final: 0.8771 (mtm) REVERT: D 30 LYS cc_start: 0.8748 (tttt) cc_final: 0.8267 (mmmm) REVERT: D 46 ILE cc_start: 0.8906 (mt) cc_final: 0.8590 (mm) REVERT: D 70 ASN cc_start: 0.9162 (t0) cc_final: 0.8950 (t0) REVERT: D 92 ARG cc_start: 0.8205 (tmt90) cc_final: 0.7388 (mmt90) REVERT: D 107 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8788 (ttp) REVERT: D 259 ASP cc_start: 0.8310 (t0) cc_final: 0.8092 (t0) REVERT: D 325 MET cc_start: 0.9097 (mtp) cc_final: 0.8451 (mtp) REVERT: D 328 ASP cc_start: 0.7463 (t70) cc_final: 0.6967 (p0) REVERT: E 30 LYS cc_start: 0.8817 (tttt) cc_final: 0.8280 (tptm) REVERT: E 46 ILE cc_start: 0.8901 (mt) cc_final: 0.8619 (mm) REVERT: E 92 ARG cc_start: 0.8263 (tmt90) cc_final: 0.7369 (mmt-90) REVERT: E 203 ASP cc_start: 0.8661 (m-30) cc_final: 0.8369 (m-30) REVERT: E 262 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7055 (mptp) REVERT: E 328 ASP cc_start: 0.7805 (p0) cc_final: 0.7467 (t0) outliers start: 36 outliers final: 14 residues processed: 216 average time/residue: 1.7186 time to fit residues: 420.9157 Evaluate side-chains 186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 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 107 MET 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 Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 316 GLN B 19 GLN C 256 GLN D 256 GLN E 326 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090882 restraints weight = 22282.359| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.97 r_work: 0.3026 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 13575 Z= 0.239 Angle : 0.658 9.011 18465 Z= 0.331 Chirality : 0.044 0.208 2030 Planarity : 0.005 0.042 2285 Dihedral : 4.424 34.370 1765 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.53 % Allowed : 13.15 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1575 helix: 0.03 (0.14), residues: 1175 sheet: None (None), residues: 0 loop : -2.63 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 229 HIS 0.004 0.001 HIS B 326 PHE 0.025 0.002 PHE E 80 TYR 0.027 0.002 TYR E 225 ARG 0.003 0.001 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.06103 ( 752) hydrogen bonds : angle 4.21540 ( 2241) SS BOND : bond 0.01977 ( 5) SS BOND : angle 3.35766 ( 10) covalent geometry : bond 0.00568 (13570) covalent geometry : angle 0.65401 (18455) *********************** 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 218 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 167 time to evaluate : 2.862 Fit side-chains REVERT: A 30 LYS cc_start: 0.8724 (tttt) cc_final: 0.8049 (mmtp) REVERT: A 46 ILE cc_start: 0.9092 (mt) cc_final: 0.8764 (mp) REVERT: A 92 ARG cc_start: 0.8420 (tmt90) cc_final: 0.7367 (mmt90) REVERT: B 30 LYS cc_start: 0.8971 (tttt) cc_final: 0.8306 (tptt) REVERT: B 67 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8859 (mp) REVERT: B 92 ARG cc_start: 0.8242 (tmt90) cc_final: 0.7570 (mmt90) REVERT: B 154 MET cc_start: 0.8546 (mmm) cc_final: 0.7959 (mmm) REVERT: B 202 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: C 41 SER cc_start: 0.8857 (m) cc_final: 0.8508 (p) REVERT: C 46 ILE cc_start: 0.9037 (mt) cc_final: 0.8709 (mm) REVERT: C 92 ARG cc_start: 0.8343 (tmt90) cc_final: 0.7429 (mmt90) REVERT: C 107 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8781 (ttp) REVERT: C 323 ASP cc_start: 0.8571 (t0) cc_final: 0.8249 (t0) REVERT: C 325 MET cc_start: 0.9035 (mtp) cc_final: 0.8806 (mtm) REVERT: C 328 ASP cc_start: 0.7740 (t70) cc_final: 0.7055 (p0) REVERT: D 30 LYS cc_start: 0.8761 (tttt) cc_final: 0.8204 (mmtp) REVERT: D 46 ILE cc_start: 0.8908 (mt) cc_final: 0.8675 (mm) REVERT: D 92 ARG cc_start: 0.8272 (tmt90) cc_final: 0.7391 (mmt90) REVERT: D 107 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8805 (ttp) REVERT: D 328 ASP cc_start: 0.7650 (t70) cc_final: 0.7028 (p0) REVERT: E 30 LYS cc_start: 0.8791 (tttt) cc_final: 0.8216 (tptt) REVERT: E 46 ILE cc_start: 0.9048 (mt) cc_final: 0.8749 (mm) REVERT: E 92 ARG cc_start: 0.8270 (tmt90) cc_final: 0.7422 (mmt90) REVERT: E 129 MET cc_start: 0.9134 (mmm) cc_final: 0.8932 (mmp) REVERT: E 149 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8199 (ptpt) REVERT: E 203 ASP cc_start: 0.8672 (m-30) cc_final: 0.8356 (m-30) REVERT: E 262 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7288 (mptp) REVERT: E 328 ASP cc_start: 0.7787 (p0) cc_final: 0.7479 (t70) outliers start: 51 outliers final: 25 residues processed: 205 average time/residue: 1.5120 time to fit residues: 344.1312 Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU 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 91 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 202 ARG 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 107 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 241 THR 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 34 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 141 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 C 256 GLN D 256 GLN D 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.093018 restraints weight = 22313.266| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.98 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13575 Z= 0.143 Angle : 0.561 9.771 18465 Z= 0.280 Chirality : 0.040 0.195 2030 Planarity : 0.004 0.043 2285 Dihedral : 4.170 31.401 1765 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 14.74 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1575 helix: 0.42 (0.14), residues: 1185 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 229 HIS 0.002 0.000 HIS C 178 PHE 0.029 0.001 PHE B 80 TYR 0.015 0.001 TYR A 97 ARG 0.004 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.05131 ( 752) hydrogen bonds : angle 3.97340 ( 2241) SS BOND : bond 0.01448 ( 5) SS BOND : angle 2.82126 ( 10) covalent geometry : bond 0.00333 (13570) covalent geometry : angle 0.55731 (18455) *********************** 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 217 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8708 (tttt) cc_final: 0.8071 (tppp) REVERT: A 46 ILE cc_start: 0.9067 (mt) cc_final: 0.8829 (mt) REVERT: A 92 ARG cc_start: 0.8329 (tmt90) cc_final: 0.7326 (mmt90) REVERT: B 30 LYS cc_start: 0.8914 (tttt) cc_final: 0.8177 (mmtp) REVERT: B 67 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8873 (mp) REVERT: B 92 ARG cc_start: 0.8143 (tmt90) cc_final: 0.7380 (mmt90) REVERT: B 154 MET cc_start: 0.8524 (mmm) cc_final: 0.7872 (mmm) REVERT: B 202 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: B 323 ASP cc_start: 0.8548 (t0) cc_final: 0.8228 (t0) REVERT: C 41 SER cc_start: 0.8827 (m) cc_final: 0.8467 (p) REVERT: C 46 ILE cc_start: 0.9056 (mt) cc_final: 0.8703 (mm) REVERT: C 92 ARG cc_start: 0.8286 (tmt90) cc_final: 0.7364 (mmt90) REVERT: C 97 TYR cc_start: 0.7496 (t80) cc_final: 0.7127 (t80) REVERT: C 323 ASP cc_start: 0.8566 (t0) cc_final: 0.8329 (t0) REVERT: C 334 LYS cc_start: 0.8781 (mttt) cc_final: 0.8566 (mttm) REVERT: D 30 LYS cc_start: 0.8796 (tttt) cc_final: 0.8224 (tptm) REVERT: D 46 ILE cc_start: 0.8895 (mt) cc_final: 0.8651 (mm) REVERT: D 92 ARG cc_start: 0.8206 (tmt90) cc_final: 0.7318 (mmt90) REVERT: D 107 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8752 (ttp) REVERT: D 259 ASP cc_start: 0.8410 (t0) cc_final: 0.8196 (t0) REVERT: E 30 LYS cc_start: 0.8756 (tttt) cc_final: 0.8212 (tptt) REVERT: E 46 ILE cc_start: 0.9022 (mt) cc_final: 0.8762 (mm) REVERT: E 92 ARG cc_start: 0.8282 (tmt90) cc_final: 0.7451 (mmt90) REVERT: E 149 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8196 (ptpt) REVERT: E 203 ASP cc_start: 0.8620 (m-30) cc_final: 0.8297 (m-30) REVERT: E 262 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7282 (mptp) outliers start: 33 outliers final: 19 residues processed: 208 average time/residue: 1.0321 time to fit residues: 238.8252 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 : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER 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 91 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 75 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 107 MET Chi-restraints excluded: chain D residue 234 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.102348 restraints weight = 22740.227| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.83 r_work: 0.3267 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13575 Z= 0.177 Angle : 0.590 9.920 18465 Z= 0.293 Chirality : 0.042 0.235 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.147 30.425 1765 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.91 % Allowed : 15.43 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1575 helix: 0.56 (0.14), residues: 1185 sheet: None (None), residues: 0 loop : -2.29 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 229 HIS 0.003 0.001 HIS B 326 PHE 0.029 0.002 PHE D 278 TYR 0.018 0.001 TYR E 225 ARG 0.003 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 752) hydrogen bonds : angle 4.00730 ( 2241) SS BOND : bond 0.01490 ( 5) SS BOND : angle 3.04085 ( 10) covalent geometry : bond 0.00419 (13570) covalent geometry : angle 0.58544 (18455) *********************** 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 218 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 1.425 Fit side-chains REVERT: A 30 LYS cc_start: 0.8675 (tttt) cc_final: 0.8160 (tppp) REVERT: A 41 SER cc_start: 0.8874 (m) cc_final: 0.8579 (p) REVERT: A 46 ILE cc_start: 0.9059 (mt) cc_final: 0.8840 (mt) REVERT: A 92 ARG cc_start: 0.8495 (tmt90) cc_final: 0.7673 (mmt90) REVERT: B 30 LYS cc_start: 0.8863 (tttt) cc_final: 0.8241 (mmtp) REVERT: B 46 ILE cc_start: 0.9119 (mt) cc_final: 0.8838 (mp) REVERT: B 67 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8915 (mp) REVERT: B 92 ARG cc_start: 0.8397 (tmt90) cc_final: 0.7775 (mmt90) REVERT: B 154 MET cc_start: 0.8287 (mmm) cc_final: 0.7736 (mmm) REVERT: B 202 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7589 (ttm170) REVERT: C 41 SER cc_start: 0.8832 (m) cc_final: 0.8545 (p) REVERT: C 46 ILE cc_start: 0.9016 (mt) cc_final: 0.8741 (mm) REVERT: C 61 MET cc_start: 0.8384 (ttm) cc_final: 0.8086 (ttt) REVERT: C 92 ARG cc_start: 0.8546 (tmt90) cc_final: 0.7837 (mmt90) REVERT: C 323 ASP cc_start: 0.8503 (t0) cc_final: 0.8260 (t0) REVERT: C 328 ASP cc_start: 0.7628 (t70) cc_final: 0.7182 (p0) REVERT: D 30 LYS cc_start: 0.8783 (tttt) cc_final: 0.8344 (mmtp) REVERT: D 92 ARG cc_start: 0.8415 (tmt90) cc_final: 0.7716 (mmt90) REVERT: D 107 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8725 (ttp) REVERT: D 325 MET cc_start: 0.8942 (mtp) cc_final: 0.8615 (mtp) REVERT: D 328 ASP cc_start: 0.7595 (t70) cc_final: 0.7153 (p0) REVERT: E 30 LYS cc_start: 0.8747 (tttt) cc_final: 0.8305 (tptt) REVERT: E 46 ILE cc_start: 0.9014 (mt) cc_final: 0.8762 (mm) REVERT: E 92 ARG cc_start: 0.8457 (tmt90) cc_final: 0.7778 (mmt90) REVERT: E 149 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8098 (ptpt) REVERT: E 262 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7241 (mptp) outliers start: 42 outliers final: 23 residues processed: 208 average time/residue: 0.9864 time to fit residues: 228.4657 Evaluate side-chains 194 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER 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 91 SER Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 202 ARG 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 136 SER Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 234 LEU 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 88 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093191 restraints weight = 22323.513| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.98 r_work: 0.3060 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4227 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= 0.138 Angle : 0.577 10.335 18465 Z= 0.282 Chirality : 0.041 0.265 2030 Planarity : 0.004 0.039 2285 Dihedral : 4.051 28.281 1765 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.77 % Allowed : 16.33 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.21), residues: 1575 helix: 0.64 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.19 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 229 HIS 0.002 0.000 HIS B 326 PHE 0.032 0.001 PHE B 80 TYR 0.014 0.001 TYR B 225 ARG 0.003 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 752) hydrogen bonds : angle 3.92304 ( 2241) SS BOND : bond 0.01123 ( 5) SS BOND : angle 2.38517 ( 10) covalent geometry : bond 0.00322 (13570) covalent geometry : angle 0.57418 (18455) *********************** 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 219 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8660 (tttt) cc_final: 0.7985 (tppp) REVERT: A 41 SER cc_start: 0.8855 (m) cc_final: 0.8502 (p) REVERT: A 46 ILE cc_start: 0.9083 (mt) cc_final: 0.8822 (mm) REVERT: A 91 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8791 (m) REVERT: A 92 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7276 (mmt90) REVERT: B 30 LYS cc_start: 0.8829 (tttt) cc_final: 0.8119 (mmtp) REVERT: B 67 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 92 ARG cc_start: 0.8166 (tmt90) cc_final: 0.7384 (mmt90) REVERT: B 97 TYR cc_start: 0.7717 (t80) cc_final: 0.7474 (t80) REVERT: B 154 MET cc_start: 0.8509 (mmm) cc_final: 0.7854 (mmm) REVERT: B 202 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7573 (ttm170) REVERT: B 323 ASP cc_start: 0.8550 (t0) cc_final: 0.8230 (t0) REVERT: C 41 SER cc_start: 0.8834 (m) cc_final: 0.8558 (p) REVERT: C 61 MET cc_start: 0.8676 (ttm) cc_final: 0.8355 (ttt) REVERT: C 92 ARG cc_start: 0.8254 (tmt90) cc_final: 0.7345 (mmt90) REVERT: C 107 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8624 (ttp) REVERT: C 323 ASP cc_start: 0.8606 (t0) cc_final: 0.8376 (t0) REVERT: C 328 ASP cc_start: 0.7655 (t70) cc_final: 0.7049 (p0) REVERT: D 30 LYS cc_start: 0.8735 (tttt) cc_final: 0.8131 (mmtm) REVERT: D 92 ARG cc_start: 0.8168 (tmt90) cc_final: 0.7259 (mmt90) REVERT: D 107 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8780 (ttp) REVERT: E 19 GLN cc_start: 0.7651 (pm20) cc_final: 0.7113 (pt0) REVERT: E 30 LYS cc_start: 0.8743 (tttt) cc_final: 0.8240 (tptt) REVERT: E 41 SER cc_start: 0.8797 (m) cc_final: 0.8495 (p) REVERT: E 46 ILE cc_start: 0.8751 (mt) cc_final: 0.8471 (tt) REVERT: E 92 ARG cc_start: 0.8254 (tmt90) cc_final: 0.7472 (mmt90) REVERT: E 149 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8132 (ptpt) REVERT: E 154 MET cc_start: 0.8638 (mmp) cc_final: 0.8401 (tpp) REVERT: E 262 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7278 (mptp) outliers start: 40 outliers final: 22 residues processed: 205 average time/residue: 1.0221 time to fit residues: 232.9372 Evaluate side-chains 193 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 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 202 ARG 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 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 234 LEU 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 84 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.0370 overall best weight: 3.4066 ------------------------------------------------------------------------------- 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 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 = 0.3578 r_free = 0.3578 target = 0.117126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.092627 restraints weight = 22397.752| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.98 r_work: 0.3054 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13575 Z= 0.149 Angle : 0.590 11.631 18465 Z= 0.287 Chirality : 0.042 0.347 2030 Planarity : 0.004 0.038 2285 Dihedral : 4.033 27.366 1765 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 3.11 % Allowed : 16.96 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1575 helix: 0.70 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 229 HIS 0.003 0.001 HIS B 326 PHE 0.022 0.001 PHE B 278 TYR 0.015 0.001 TYR B 225 ARG 0.003 0.000 ARG C 159 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 752) hydrogen bonds : angle 3.94025 ( 2241) SS BOND : bond 0.01164 ( 5) SS BOND : angle 2.42123 ( 10) covalent geometry : bond 0.00351 (13570) covalent geometry : angle 0.58713 (18455) *********************** 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 215 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8622 (tttt) cc_final: 0.8022 (tppp) REVERT: A 46 ILE cc_start: 0.8871 (mt) cc_final: 0.8636 (mp) REVERT: A 91 SER cc_start: 0.9034 (OUTLIER) cc_final: 0.8790 (m) REVERT: A 92 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7278 (mmt90) REVERT: B 30 LYS cc_start: 0.8790 (tttt) cc_final: 0.8094 (mmtp) REVERT: B 67 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 70 ASN cc_start: 0.8859 (t0) cc_final: 0.8651 (t160) REVERT: B 92 ARG cc_start: 0.8171 (tmt90) cc_final: 0.7389 (mmt90) REVERT: B 97 TYR cc_start: 0.7778 (t80) cc_final: 0.7525 (t80) REVERT: B 154 MET cc_start: 0.8493 (mmm) cc_final: 0.7866 (mmm) REVERT: B 202 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7577 (ttm170) REVERT: C 41 SER cc_start: 0.8834 (m) cc_final: 0.8610 (p) REVERT: C 46 ILE cc_start: 0.8703 (mp) cc_final: 0.8227 (tt) REVERT: C 61 MET cc_start: 0.8684 (ttm) cc_final: 0.8323 (ttt) REVERT: C 92 ARG cc_start: 0.8291 (tmt90) cc_final: 0.7403 (mmt90) REVERT: C 107 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8635 (ttp) REVERT: C 323 ASP cc_start: 0.8602 (t0) cc_final: 0.8358 (t0) REVERT: C 328 ASP cc_start: 0.7731 (t70) cc_final: 0.7049 (p0) REVERT: D 30 LYS cc_start: 0.8764 (tttt) cc_final: 0.8196 (mmtp) REVERT: D 92 ARG cc_start: 0.8186 (tmt90) cc_final: 0.7269 (mmt90) REVERT: D 107 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8814 (ttp) REVERT: D 328 ASP cc_start: 0.7536 (t70) cc_final: 0.6975 (p0) REVERT: E 19 GLN cc_start: 0.7600 (pm20) cc_final: 0.7063 (pt0) REVERT: E 30 LYS cc_start: 0.8755 (tttt) cc_final: 0.8255 (tptt) REVERT: E 41 SER cc_start: 0.8816 (m) cc_final: 0.8513 (p) REVERT: E 46 ILE cc_start: 0.8902 (mt) cc_final: 0.8558 (tt) REVERT: E 92 ARG cc_start: 0.8251 (tmt90) cc_final: 0.7474 (mmt90) REVERT: E 149 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8143 (ptpt) REVERT: E 154 MET cc_start: 0.8639 (mmp) cc_final: 0.8375 (tpp) REVERT: E 262 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7274 (mptp) outliers start: 45 outliers final: 24 residues processed: 198 average time/residue: 1.0524 time to fit residues: 232.8498 Evaluate side-chains 190 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 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 202 ARG 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 325 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain D residue 234 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 25 optimal weight: 0.0670 chunk 140 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 3.0524 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.117549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.093323 restraints weight = 22162.266| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.96 r_work: 0.3061 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4328 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= 0.141 Angle : 0.591 11.597 18465 Z= 0.286 Chirality : 0.041 0.314 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.022 29.806 1765 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.63 % Allowed : 17.51 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1575 helix: 0.77 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.09 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 229 HIS 0.002 0.000 HIS B 326 PHE 0.035 0.001 PHE B 80 TYR 0.014 0.001 TYR B 225 ARG 0.002 0.000 ARG B 159 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 752) hydrogen bonds : angle 3.91108 ( 2241) SS BOND : bond 0.01181 ( 5) SS BOND : angle 2.30149 ( 10) covalent geometry : bond 0.00330 (13570) covalent geometry : angle 0.58894 (18455) *********************** 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 204 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.735 Fit side-chains REVERT: A 30 LYS cc_start: 0.8618 (tttt) cc_final: 0.8031 (tppp) REVERT: A 46 ILE cc_start: 0.8905 (mt) cc_final: 0.8639 (mp) REVERT: A 91 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8790 (m) REVERT: A 92 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7273 (mmt90) REVERT: B 30 LYS cc_start: 0.8775 (tttt) cc_final: 0.8067 (tttt) REVERT: B 67 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8804 (mp) REVERT: B 70 ASN cc_start: 0.8903 (t0) cc_final: 0.8698 (t160) REVERT: B 92 ARG cc_start: 0.8156 (tmt90) cc_final: 0.7378 (mmt90) REVERT: B 154 MET cc_start: 0.8489 (mmm) cc_final: 0.7854 (mmm) REVERT: B 202 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: B 323 ASP cc_start: 0.8502 (t0) cc_final: 0.8292 (t0) REVERT: C 41 SER cc_start: 0.8922 (m) cc_final: 0.8628 (p) REVERT: C 46 ILE cc_start: 0.8719 (mp) cc_final: 0.8235 (tt) REVERT: C 61 MET cc_start: 0.8692 (ttm) cc_final: 0.8324 (ttt) REVERT: C 92 ARG cc_start: 0.8271 (tmt90) cc_final: 0.7384 (mmt90) REVERT: C 107 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8612 (ttp) REVERT: C 323 ASP cc_start: 0.8596 (t0) cc_final: 0.8360 (t0) REVERT: C 328 ASP cc_start: 0.7738 (t70) cc_final: 0.7055 (p0) REVERT: D 30 LYS cc_start: 0.8748 (tttt) cc_final: 0.8220 (mmtp) REVERT: D 92 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7279 (mmt90) REVERT: D 107 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8827 (ttp) REVERT: D 252 LEU cc_start: 0.8987 (tm) cc_final: 0.8778 (tp) REVERT: E 19 GLN cc_start: 0.7607 (pm20) cc_final: 0.7083 (pt0) REVERT: E 30 LYS cc_start: 0.8746 (tttt) cc_final: 0.8277 (tptt) REVERT: E 41 SER cc_start: 0.8824 (m) cc_final: 0.8520 (p) REVERT: E 46 ILE cc_start: 0.8738 (mt) cc_final: 0.8448 (tt) REVERT: E 92 ARG cc_start: 0.8231 (tmt90) cc_final: 0.7477 (mmt90) REVERT: E 149 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8105 (ptpt) REVERT: E 154 MET cc_start: 0.8617 (mmp) cc_final: 0.8322 (tpp) REVERT: E 262 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (mptp) outliers start: 38 outliers final: 24 residues processed: 189 average time/residue: 1.0845 time to fit residues: 228.2535 Evaluate side-chains 192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 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 202 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 54 LEU 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 325 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 234 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 E 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.115911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092324 restraints weight = 22462.676| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.95 r_work: 0.3042 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13575 Z= 0.195 Angle : 0.643 11.488 18465 Z= 0.312 Chirality : 0.044 0.365 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.206 34.064 1765 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.63 % Allowed : 17.79 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1575 helix: 0.77 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -2.02 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 229 HIS 0.003 0.001 HIS B 326 PHE 0.020 0.002 PHE E 80 TYR 0.020 0.002 TYR E 225 ARG 0.003 0.000 ARG E 130 Details of bonding type rmsd hydrogen bonds : bond 0.05297 ( 752) hydrogen bonds : angle 4.03170 ( 2241) SS BOND : bond 0.01814 ( 5) SS BOND : angle 3.35894 ( 10) covalent geometry : bond 0.00464 (13570) covalent geometry : angle 0.63796 (18455) ********************** 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 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8612 (tttt) cc_final: 0.8029 (tppp) REVERT: A 46 ILE cc_start: 0.8904 (mt) cc_final: 0.8637 (mp) REVERT: A 92 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7300 (mmt90) REVERT: B 30 LYS cc_start: 0.8767 (tttt) cc_final: 0.8074 (tttt) REVERT: B 67 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 92 ARG cc_start: 0.8206 (tmt90) cc_final: 0.7397 (mmt90) REVERT: B 154 MET cc_start: 0.8525 (mmm) cc_final: 0.7948 (mmm) REVERT: B 202 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7587 (ttm170) REVERT: C 41 SER cc_start: 0.8939 (m) cc_final: 0.8645 (p) REVERT: C 46 ILE cc_start: 0.8797 (mp) cc_final: 0.8316 (tt) REVERT: C 54 LEU cc_start: 0.8408 (mt) cc_final: 0.8166 (tt) REVERT: C 61 MET cc_start: 0.8711 (ttm) cc_final: 0.8353 (ttt) REVERT: C 92 ARG cc_start: 0.8339 (tmt90) cc_final: 0.7431 (mmt90) REVERT: C 97 TYR cc_start: 0.7468 (t80) cc_final: 0.7152 (t80) REVERT: C 107 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8692 (ttp) REVERT: C 328 ASP cc_start: 0.7748 (t70) cc_final: 0.7054 (p0) REVERT: D 92 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7285 (mmt90) REVERT: D 107 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8831 (ttp) REVERT: D 252 LEU cc_start: 0.8939 (tm) cc_final: 0.8731 (tp) REVERT: D 328 ASP cc_start: 0.7601 (t70) cc_final: 0.6974 (p0) REVERT: E 19 GLN cc_start: 0.7643 (pm20) cc_final: 0.7088 (pt0) REVERT: E 30 LYS cc_start: 0.8736 (tttt) cc_final: 0.8281 (tptt) REVERT: E 41 SER cc_start: 0.8846 (m) cc_final: 0.8546 (p) REVERT: E 46 ILE cc_start: 0.8917 (mt) cc_final: 0.8601 (tt) REVERT: E 92 ARG cc_start: 0.8221 (tmt90) cc_final: 0.7301 (mmt90) REVERT: E 149 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8184 (ptpt) REVERT: E 262 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7256 (mptp) REVERT: E 305 PHE cc_start: 0.5761 (m-10) cc_final: 0.5558 (m-80) outliers start: 38 outliers final: 25 residues processed: 184 average time/residue: 1.0283 time to fit residues: 210.5663 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 136 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 202 ARG 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 325 MET Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 69 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 234 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 21 optimal weight: 0.0270 chunk 125 optimal weight: 20.0000 overall best weight: 1.8046 ------------------------------------------------------------------------------- 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 D 316 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.094831 restraints weight = 22440.840| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.97 r_work: 0.3089 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4461 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= 0.119 Angle : 0.579 11.661 18465 Z= 0.279 Chirality : 0.040 0.272 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.065 35.664 1765 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.08 % Allowed : 18.75 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1575 helix: 0.97 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.87 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 229 HIS 0.001 0.000 HIS C 156 PHE 0.036 0.001 PHE B 80 TYR 0.011 0.001 TYR E 225 ARG 0.003 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04568 ( 752) hydrogen bonds : angle 3.88429 ( 2241) SS BOND : bond 0.01103 ( 5) SS BOND : angle 2.36588 ( 10) covalent geometry : bond 0.00267 (13570) covalent geometry : angle 0.57608 (18455) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9448.25 seconds wall clock time: 169 minutes 29.31 seconds (10169.31 seconds total)