Starting phenix.real_space_refine on Thu Sep 26 09:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_9324_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_9324.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_9324.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_9324_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n26_9324/09_2024/6n26_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-5461/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: 5.17, per 1000 atoms: 0.39 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 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: 1.24 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: 3.30 Time building geometry restraints manager: 3.31 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: 6878 9.16 - 18.32: 803 18.32 - 27.48: 101 27.48 - 36.63: 91 36.63 - 45.79: 35 Dihedral angle restraints: 7908 sinusoidal: 3173 harmonic: 4735 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 185 " pdb=" CB CYS A 185 " ideal model delta sinusoidal sigma weight residual -86.00 -118.51 32.51 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N ASP D 104 " pdb=" CA ASP D 104 " ideal model delta harmonic sigma weight residual 180.00 -163.38 -16.62 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA PRO A 103 " pdb=" C PRO A 103 " pdb=" N ASP A 104 " pdb=" CA ASP A 104 " ideal model delta harmonic sigma weight residual -180.00 -163.39 -16.61 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 7905 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: 2.05 - 2.62: 72 2.62 - 3.19: 11049 3.19 - 3.76: 19847 3.76 - 4.33: 30114 4.33 - 4.90: 47478 Nonbonded interactions: 108560 Sorted by model distance: nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 185 " model vdw 2.048 3.760 nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 185 " model vdw 2.048 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 185 " model vdw 2.048 3.760 nonbonded pdb=" SG CYS B 135 " pdb=" SG CYS B 185 " model vdw 2.049 3.760 nonbonded pdb=" OD2 ASP B 104 " pdb=" NH2 ARG C 218 " model vdw 2.277 3.120 ... (remaining 108555 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- 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 13570 Z= 0.492 Angle : 0.830 8.585 18455 Z= 0.442 Chirality : 0.051 0.188 2030 Planarity : 0.006 0.051 2285 Dihedral : 9.204 45.792 4845 Min Nonbonded Distance : 2.048 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 1.485 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: 1.2351 time to fit residues: 520.8520 Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 296 ASN B 316 GLN B 339 ASN C 190 ASN C 256 GLN C 293 GLN C 308 ASN C 339 ASN D 96 GLN D 256 GLN D 293 GLN D 339 ASN E 58 GLN E 190 ASN E 256 GLN E 339 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13570 Z= 0.201 Angle : 0.642 10.211 18455 Z= 0.333 Chirality : 0.040 0.164 2030 Planarity : 0.006 0.041 2285 Dihedral : 4.583 29.583 1765 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.77 % Allowed : 9.62 % Favored : 87.61 % 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: -2.96 (0.18), residues: 1575 helix: -1.51 (0.13), residues: 1170 sheet: None (None), residues: 0 loop : -2.85 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 287 HIS 0.006 0.001 HIS C 156 PHE 0.025 0.002 PHE E 272 TYR 0.015 0.001 TYR A 236 ARG 0.005 0.001 ARG D 218 *********************** 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 272 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 1.721 Fit side-chains REVERT: A 30 LYS cc_start: 0.8644 (tttt) cc_final: 0.8049 (tppp) REVERT: A 46 ILE cc_start: 0.8944 (mt) cc_final: 0.8611 (mm) REVERT: A 53 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 92 ARG cc_start: 0.7952 (tmt90) cc_final: 0.7246 (mmt90) REVERT: A 328 ASP cc_start: 0.7324 (p0) cc_final: 0.6999 (t70) REVERT: B 30 LYS cc_start: 0.8848 (tttt) cc_final: 0.8312 (tptt) REVERT: B 92 ARG cc_start: 0.7769 (tmt90) cc_final: 0.7477 (mmt90) REVERT: B 323 ASP cc_start: 0.8037 (t0) cc_final: 0.7786 (t0) REVERT: C 41 SER cc_start: 0.8437 (m) cc_final: 0.8112 (p) REVERT: C 46 ILE cc_start: 0.8573 (mt) cc_final: 0.8225 (mm) REVERT: C 92 ARG cc_start: 0.7673 (tmt90) cc_final: 0.7092 (mmt90) REVERT: C 97 TYR cc_start: 0.6999 (t80) cc_final: 0.6798 (t80) REVERT: C 149 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8133 (ptpt) REVERT: C 249 LEU cc_start: 0.8664 (tp) cc_final: 0.8083 (mm) REVERT: C 328 ASP cc_start: 0.7118 (t70) cc_final: 0.6888 (p0) REVERT: D 30 LYS cc_start: 0.8566 (tttt) cc_final: 0.8210 (mmmm) REVERT: D 46 ILE cc_start: 0.8775 (mt) cc_final: 0.8481 (mm) REVERT: D 92 ARG cc_start: 0.7664 (tmt90) cc_final: 0.7250 (mmt90) REVERT: E 30 LYS cc_start: 0.8656 (tttt) cc_final: 0.8305 (tptm) REVERT: E 46 ILE cc_start: 0.8755 (mt) cc_final: 0.8442 (mm) REVERT: E 92 ARG cc_start: 0.7813 (tmt90) cc_final: 0.7234 (mmt90) REVERT: E 262 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6820 (mptp) REVERT: E 295 ILE cc_start: 0.8583 (tt) cc_final: 0.8337 (OUTLIER) REVERT: E 328 ASP cc_start: 0.7292 (p0) cc_final: 0.7062 (t0) outliers start: 40 outliers final: 13 residues processed: 257 average time/residue: 0.9525 time to fit residues: 273.1770 Evaluate side-chains 203 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN B 190 ASN C 256 GLN D 256 GLN E 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13570 Z= 0.165 Angle : 0.538 9.575 18455 Z= 0.274 Chirality : 0.038 0.146 2030 Planarity : 0.004 0.038 2285 Dihedral : 4.118 25.237 1765 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.28 % Allowed : 11.97 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.51 (0.19), residues: 1575 helix: -0.35 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -2.90 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 287 HIS 0.002 0.000 HIS E 326 PHE 0.028 0.002 PHE E 80 TYR 0.010 0.001 TYR D 225 ARG 0.004 0.000 ARG C 59 *********************** 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 237 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8648 (tttt) cc_final: 0.8073 (tppp) REVERT: A 46 ILE cc_start: 0.8946 (mt) cc_final: 0.8588 (mm) REVERT: A 53 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 92 ARG cc_start: 0.7826 (tmt90) cc_final: 0.7224 (mmt90) REVERT: B 30 LYS cc_start: 0.8860 (tttt) cc_final: 0.8347 (tptt) REVERT: B 92 ARG cc_start: 0.7664 (tmt90) cc_final: 0.7255 (mmt90) REVERT: B 323 ASP cc_start: 0.7925 (t0) cc_final: 0.7609 (t0) REVERT: C 41 SER cc_start: 0.8478 (m) cc_final: 0.8161 (p) REVERT: C 46 ILE cc_start: 0.8652 (mt) cc_final: 0.8311 (mm) REVERT: C 92 ARG cc_start: 0.7674 (tmt90) cc_final: 0.7115 (mmt90) REVERT: C 249 LEU cc_start: 0.8715 (tp) cc_final: 0.8156 (mm) REVERT: C 323 ASP cc_start: 0.7882 (t0) cc_final: 0.7661 (t0) REVERT: C 328 ASP cc_start: 0.7135 (t70) cc_final: 0.6910 (p0) REVERT: D 30 LYS cc_start: 0.8570 (tttt) cc_final: 0.8252 (mmtm) REVERT: D 46 ILE cc_start: 0.8771 (mt) cc_final: 0.8456 (mm) REVERT: D 92 ARG cc_start: 0.7676 (tmt90) cc_final: 0.7235 (mmt90) REVERT: E 30 LYS cc_start: 0.8655 (tttt) cc_final: 0.8293 (tptm) REVERT: E 46 ILE cc_start: 0.8776 (mt) cc_final: 0.8462 (mm) REVERT: E 92 ARG cc_start: 0.7836 (tmt90) cc_final: 0.7138 (mmt-90) REVERT: E 262 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6874 (mptp) REVERT: E 295 ILE cc_start: 0.8597 (tt) cc_final: 0.8289 (mt) outliers start: 33 outliers final: 14 residues processed: 227 average time/residue: 1.0425 time to fit residues: 263.2133 Evaluate side-chains 188 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 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 139 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 10.0000 chunk 94 optimal weight: 0.3980 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 chunk 134 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 256 GLN A 326 HIS B 19 GLN D 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13570 Z= 0.209 Angle : 0.553 10.084 18455 Z= 0.278 Chirality : 0.040 0.175 2030 Planarity : 0.004 0.038 2285 Dihedral : 4.014 34.170 1765 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 13.49 % Favored : 84.22 % 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: -0.55 (0.20), residues: 1575 helix: 0.38 (0.14), residues: 1185 sheet: None (None), residues: 0 loop : -2.56 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 229 HIS 0.002 0.001 HIS E 326 PHE 0.026 0.001 PHE C 278 TYR 0.015 0.001 TYR E 225 ARG 0.004 0.001 ARG B 218 *********************** 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 207 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 1.493 Fit side-chains REVERT: A 30 LYS cc_start: 0.8677 (tttt) cc_final: 0.8101 (tppp) REVERT: A 46 ILE cc_start: 0.8988 (mt) cc_final: 0.8778 (mt) REVERT: A 53 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7779 (mt) REVERT: A 92 ARG cc_start: 0.7721 (tmt90) cc_final: 0.7146 (mmt90) REVERT: A 328 ASP cc_start: 0.7310 (t70) cc_final: 0.6988 (p0) REVERT: B 30 LYS cc_start: 0.8869 (tttt) cc_final: 0.8313 (mmtp) REVERT: B 67 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8798 (mp) REVERT: B 92 ARG cc_start: 0.7655 (tmt90) cc_final: 0.7272 (mmt90) REVERT: C 30 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8170 (mmtp) REVERT: C 41 SER cc_start: 0.8501 (m) cc_final: 0.8182 (p) REVERT: C 46 ILE cc_start: 0.8760 (mt) cc_final: 0.8446 (mm) REVERT: C 92 ARG cc_start: 0.7710 (tmt90) cc_final: 0.7136 (mmt90) REVERT: C 107 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8367 (ttp) REVERT: C 249 LEU cc_start: 0.8779 (tp) cc_final: 0.8167 (mm) REVERT: D 30 LYS cc_start: 0.8620 (tttt) cc_final: 0.8290 (mmmm) REVERT: D 46 ILE cc_start: 0.8780 (mt) cc_final: 0.8493 (mm) REVERT: D 92 ARG cc_start: 0.7768 (tmt90) cc_final: 0.7203 (mmt90) REVERT: D 325 MET cc_start: 0.8948 (mtp) cc_final: 0.8497 (mtm) REVERT: E 30 LYS cc_start: 0.8709 (tttt) cc_final: 0.8225 (tttt) REVERT: E 46 ILE cc_start: 0.8807 (mt) cc_final: 0.8509 (mm) REVERT: E 92 ARG cc_start: 0.7797 (tmt90) cc_final: 0.7242 (mmt-90) REVERT: E 149 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7946 (ptpt) REVERT: E 262 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6939 (mptp) outliers start: 33 outliers final: 19 residues processed: 199 average time/residue: 1.0022 time to fit residues: 221.8464 Evaluate side-chains 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE 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 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 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 234 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 262 LYS Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 335 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN B 19 GLN C 256 GLN D 256 GLN E 326 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13570 Z= 0.361 Angle : 0.641 9.727 18455 Z= 0.320 Chirality : 0.044 0.199 2030 Planarity : 0.005 0.041 2285 Dihedral : 4.169 33.528 1765 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.39 % Allowed : 13.22 % Favored : 83.39 % 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: -0.47 (0.20), residues: 1575 helix: 0.41 (0.14), residues: 1195 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 229 HIS 0.004 0.001 HIS C 326 PHE 0.029 0.002 PHE A 278 TYR 0.027 0.002 TYR E 225 ARG 0.003 0.001 ARG B 218 *********************** 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 226 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 1.544 Fit side-chains REVERT: A 30 LYS cc_start: 0.8658 (tttt) cc_final: 0.8120 (tppp) REVERT: A 46 ILE cc_start: 0.9001 (mt) cc_final: 0.8694 (mp) REVERT: A 92 ARG cc_start: 0.7929 (tmt90) cc_final: 0.7242 (mmt90) REVERT: A 328 ASP cc_start: 0.7442 (t70) cc_final: 0.6996 (p0) REVERT: B 30 LYS cc_start: 0.8806 (tttt) cc_final: 0.8256 (mmtp) REVERT: B 67 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 92 ARG cc_start: 0.7673 (tmt90) cc_final: 0.7385 (mmt90) REVERT: B 202 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7076 (ttm170) REVERT: C 41 SER cc_start: 0.8709 (m) cc_final: 0.8354 (p) REVERT: C 46 ILE cc_start: 0.8953 (mt) cc_final: 0.8602 (mm) REVERT: C 92 ARG cc_start: 0.7896 (tmt90) cc_final: 0.7319 (mmt90) REVERT: C 107 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8445 (ttp) REVERT: C 323 ASP cc_start: 0.8074 (t0) cc_final: 0.7780 (t0) REVERT: C 328 ASP cc_start: 0.7254 (t70) cc_final: 0.6929 (p0) REVERT: D 30 LYS cc_start: 0.8740 (tttt) cc_final: 0.8300 (mmtp) REVERT: D 46 ILE cc_start: 0.8851 (mt) cc_final: 0.8631 (mm) REVERT: D 92 ARG cc_start: 0.7804 (tmt90) cc_final: 0.7222 (mmt90) REVERT: D 259 ASP cc_start: 0.8211 (t0) cc_final: 0.7966 (t0) REVERT: D 325 MET cc_start: 0.8952 (mtp) cc_final: 0.8602 (mtm) REVERT: E 30 LYS cc_start: 0.8710 (tttt) cc_final: 0.8264 (tptt) REVERT: E 46 ILE cc_start: 0.8934 (mt) cc_final: 0.8667 (mm) REVERT: E 92 ARG cc_start: 0.7780 (tmt90) cc_final: 0.7301 (mmt90) REVERT: E 129 MET cc_start: 0.8992 (mmm) cc_final: 0.8783 (mmp) REVERT: E 149 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8070 (ptpt) REVERT: E 262 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7218 (mptp) outliers start: 49 outliers final: 24 residues processed: 212 average time/residue: 0.9628 time to fit residues: 228.1252 Evaluate side-chains 201 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 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 142 SER Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 249 LEU 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 107 MET 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 100 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13570 Z= 0.242 Angle : 0.573 10.434 18455 Z= 0.285 Chirality : 0.041 0.223 2030 Planarity : 0.004 0.040 2285 Dihedral : 4.030 29.978 1765 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.84 % Allowed : 14.60 % Favored : 82.56 % 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: -0.11 (0.20), residues: 1575 helix: 0.66 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 229 HIS 0.002 0.001 HIS B 178 PHE 0.015 0.001 PHE A 278 TYR 0.017 0.001 TYR D 225 ARG 0.003 0.000 ARG B 218 *********************** 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 221 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 180 time to evaluate : 1.670 Fit side-chains REVERT: A 30 LYS cc_start: 0.8611 (tttt) cc_final: 0.8092 (tppp) REVERT: A 46 ILE cc_start: 0.8998 (mt) cc_final: 0.8738 (mm) REVERT: A 92 ARG cc_start: 0.7901 (tmt90) cc_final: 0.7227 (mmt90) REVERT: A 328 ASP cc_start: 0.7398 (t70) cc_final: 0.6988 (p0) REVERT: B 30 LYS cc_start: 0.8750 (tttt) cc_final: 0.8194 (mmtp) REVERT: B 67 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 92 ARG cc_start: 0.7643 (tmt90) cc_final: 0.7233 (mmt90) REVERT: B 202 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7108 (ttm170) REVERT: B 323 ASP cc_start: 0.7994 (t0) cc_final: 0.7714 (t0) REVERT: C 41 SER cc_start: 0.8713 (m) cc_final: 0.8386 (p) REVERT: C 46 ILE cc_start: 0.8964 (mt) cc_final: 0.8672 (mm) REVERT: C 92 ARG cc_start: 0.7925 (tmt90) cc_final: 0.7305 (mmt90) REVERT: C 107 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8374 (ttp) REVERT: C 252 LEU cc_start: 0.8951 (tp) cc_final: 0.8713 (tm) REVERT: C 323 ASP cc_start: 0.8092 (t0) cc_final: 0.7791 (t0) REVERT: C 328 ASP cc_start: 0.7263 (t70) cc_final: 0.6980 (p0) REVERT: D 30 LYS cc_start: 0.8742 (tttt) cc_final: 0.8289 (mmtp) REVERT: D 46 ILE cc_start: 0.8821 (mt) cc_final: 0.8590 (mm) REVERT: D 92 ARG cc_start: 0.7782 (tmt90) cc_final: 0.7169 (mmt90) REVERT: D 325 MET cc_start: 0.8882 (mtp) cc_final: 0.8517 (mtm) REVERT: E 30 LYS cc_start: 0.8641 (tttt) cc_final: 0.8227 (tptt) REVERT: E 46 ILE cc_start: 0.8958 (mt) cc_final: 0.8696 (mm) REVERT: E 92 ARG cc_start: 0.7778 (tmt90) cc_final: 0.7251 (mmt90) REVERT: E 129 MET cc_start: 0.8941 (mmm) cc_final: 0.8721 (mmp) REVERT: E 149 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7918 (ptpt) REVERT: E 262 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7229 (mptp) outliers start: 41 outliers final: 22 residues processed: 210 average time/residue: 1.0844 time to fit residues: 253.7630 Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 249 LEU 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 273 VAL Chi-restraints excluded: chain C residue 295 ILE 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 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 16 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13570 Z= 0.160 Angle : 0.544 10.833 18455 Z= 0.267 Chirality : 0.040 0.272 2030 Planarity : 0.004 0.039 2285 Dihedral : 3.904 27.303 1765 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.35 % Allowed : 15.64 % Favored : 82.01 % 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: 0.23 (0.21), residues: 1575 helix: 0.86 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 229 HIS 0.001 0.000 HIS C 178 PHE 0.030 0.001 PHE B 80 TYR 0.015 0.001 TYR A 97 ARG 0.009 0.000 ARG E 202 *********************** 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 213 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.613 Fit side-chains REVERT: A 30 LYS cc_start: 0.8592 (tttt) cc_final: 0.8116 (mmtp) REVERT: A 46 ILE cc_start: 0.8733 (mt) cc_final: 0.8497 (mp) REVERT: A 92 ARG cc_start: 0.7813 (tmt90) cc_final: 0.7172 (mmt90) REVERT: A 328 ASP cc_start: 0.7362 (t70) cc_final: 0.6991 (p0) REVERT: B 30 LYS cc_start: 0.8738 (tttt) cc_final: 0.8195 (mmtp) REVERT: B 67 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8793 (mp) REVERT: B 92 ARG cc_start: 0.7717 (tmt90) cc_final: 0.7254 (mmt90) REVERT: B 154 MET cc_start: 0.8067 (mmm) cc_final: 0.7622 (mmm) REVERT: B 323 ASP cc_start: 0.7955 (t0) cc_final: 0.7700 (t0) REVERT: C 41 SER cc_start: 0.8733 (m) cc_final: 0.8406 (p) REVERT: C 46 ILE cc_start: 0.8960 (mt) cc_final: 0.8660 (mm) REVERT: C 92 ARG cc_start: 0.7868 (tmt90) cc_final: 0.7260 (mmt90) REVERT: C 323 ASP cc_start: 0.8029 (t0) cc_final: 0.7765 (t0) REVERT: C 328 ASP cc_start: 0.7173 (t70) cc_final: 0.6933 (p0) REVERT: D 30 LYS cc_start: 0.8709 (tttt) cc_final: 0.8306 (mmtp) REVERT: D 46 ILE cc_start: 0.8808 (mt) cc_final: 0.8557 (mm) REVERT: D 92 ARG cc_start: 0.7829 (tmt90) cc_final: 0.7169 (mmt90) REVERT: E 30 LYS cc_start: 0.8655 (tttt) cc_final: 0.8269 (tptt) REVERT: E 41 SER cc_start: 0.8618 (m) cc_final: 0.8308 (p) REVERT: E 46 ILE cc_start: 0.8498 (mt) cc_final: 0.8255 (tt) REVERT: E 92 ARG cc_start: 0.7721 (tmt90) cc_final: 0.7351 (mmt90) REVERT: E 129 MET cc_start: 0.8910 (mmm) cc_final: 0.8664 (mmp) REVERT: E 149 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7916 (ptpt) REVERT: E 262 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7195 (mptp) outliers start: 34 outliers final: 13 residues processed: 201 average time/residue: 1.0335 time to fit residues: 230.7742 Evaluate side-chains 182 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 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 59 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 0.2980 chunk 117 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 19 GLN D 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13570 Z= 0.231 Angle : 0.579 10.796 18455 Z= 0.283 Chirality : 0.041 0.334 2030 Planarity : 0.004 0.040 2285 Dihedral : 3.924 27.040 1765 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.87 % Allowed : 16.61 % Favored : 81.52 % 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: 0.23 (0.21), residues: 1575 helix: 0.90 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -2.17 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 229 HIS 0.003 0.001 HIS D 156 PHE 0.023 0.002 PHE D 278 TYR 0.016 0.001 TYR E 225 ARG 0.009 0.000 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3150 Ramachandran restraints generated. 1575 Oldfield, 0 Emsley, 1575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.467 Fit side-chains REVERT: A 30 LYS cc_start: 0.8571 (tttt) cc_final: 0.8093 (tppp) REVERT: A 46 ILE cc_start: 0.8799 (mt) cc_final: 0.8557 (mp) REVERT: A 92 ARG cc_start: 0.7795 (tmt90) cc_final: 0.7186 (mmt90) REVERT: A 328 ASP cc_start: 0.7357 (t70) cc_final: 0.6979 (p0) REVERT: B 30 LYS cc_start: 0.8768 (tttt) cc_final: 0.8169 (mmtp) REVERT: B 67 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8797 (mp) REVERT: B 92 ARG cc_start: 0.7808 (tmt90) cc_final: 0.7279 (mmt90) REVERT: B 323 ASP cc_start: 0.7958 (t0) cc_final: 0.7737 (t0) REVERT: C 41 SER cc_start: 0.8744 (m) cc_final: 0.8419 (p) REVERT: C 92 ARG cc_start: 0.7889 (tmt90) cc_final: 0.7268 (mmt90) REVERT: C 323 ASP cc_start: 0.8065 (t0) cc_final: 0.7782 (t0) REVERT: C 328 ASP cc_start: 0.7205 (t70) cc_final: 0.6937 (p0) REVERT: D 30 LYS cc_start: 0.8712 (tttt) cc_final: 0.8264 (mmtp) REVERT: D 325 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: E 30 LYS cc_start: 0.8617 (tttt) cc_final: 0.8245 (tptt) REVERT: E 41 SER cc_start: 0.8628 (m) cc_final: 0.8318 (p) REVERT: E 46 ILE cc_start: 0.8700 (mt) cc_final: 0.8390 (tt) REVERT: E 92 ARG cc_start: 0.7717 (tmt90) cc_final: 0.7362 (mmt90) REVERT: E 129 MET cc_start: 0.8959 (mmm) cc_final: 0.8735 (mmp) REVERT: E 149 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7917 (ptpt) outliers start: 27 outliers final: 17 residues processed: 188 average time/residue: 0.9495 time to fit residues: 200.1119 Evaluate side-chains 176 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 142 SER Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 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 143 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13570 Z= 0.156 Angle : 0.552 10.733 18455 Z= 0.267 Chirality : 0.039 0.290 2030 Planarity : 0.004 0.040 2285 Dihedral : 3.828 25.271 1765 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.45 % Allowed : 17.30 % Favored : 81.25 % 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: 0.54 (0.21), residues: 1575 helix: 1.08 (0.15), residues: 1210 sheet: None (None), residues: 0 loop : -2.03 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 229 HIS 0.001 0.000 HIS C 178 PHE 0.034 0.001 PHE B 80 TYR 0.013 0.001 TYR C 97 ARG 0.007 0.000 ARG E 202 *********************** 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 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.461 Fit side-chains REVERT: A 30 LYS cc_start: 0.8562 (tttt) cc_final: 0.8097 (tppp) REVERT: A 46 ILE cc_start: 0.8789 (mt) cc_final: 0.8548 (mp) REVERT: A 92 ARG cc_start: 0.7751 (tmt90) cc_final: 0.7133 (mmt90) REVERT: A 328 ASP cc_start: 0.7321 (t70) cc_final: 0.6976 (p0) REVERT: B 30 LYS cc_start: 0.8715 (tttt) cc_final: 0.8186 (mmtp) REVERT: B 92 ARG cc_start: 0.7711 (tmt90) cc_final: 0.7185 (mmt90) REVERT: B 154 MET cc_start: 0.8055 (mmm) cc_final: 0.7633 (mmm) REVERT: B 323 ASP cc_start: 0.7936 (t0) cc_final: 0.7691 (t0) REVERT: C 41 SER cc_start: 0.8727 (m) cc_final: 0.8464 (p) REVERT: C 46 ILE cc_start: 0.8598 (mp) cc_final: 0.8159 (tt) REVERT: C 92 ARG cc_start: 0.7936 (tmt90) cc_final: 0.7262 (mmt90) REVERT: C 323 ASP cc_start: 0.8036 (t0) cc_final: 0.7793 (t0) REVERT: C 328 ASP cc_start: 0.7292 (t70) cc_final: 0.6978 (p0) REVERT: D 30 LYS cc_start: 0.8685 (tttt) cc_final: 0.8238 (mmtp) REVERT: D 92 ARG cc_start: 0.7907 (tmt90) cc_final: 0.7205 (mmt90) REVERT: D 252 LEU cc_start: 0.8940 (tm) cc_final: 0.8716 (tp) REVERT: D 325 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8454 (mtm) REVERT: E 30 LYS cc_start: 0.8642 (tttt) cc_final: 0.8278 (tptt) REVERT: E 41 SER cc_start: 0.8583 (m) cc_final: 0.8265 (p) REVERT: E 46 ILE cc_start: 0.8586 (mt) cc_final: 0.8306 (tt) REVERT: E 92 ARG cc_start: 0.7673 (tmt90) cc_final: 0.7163 (mmt-90) REVERT: E 149 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7914 (ptpt) outliers start: 21 outliers final: 13 residues processed: 183 average time/residue: 1.0158 time to fit residues: 207.0033 Evaluate side-chains 175 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 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 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13570 Z= 0.245 Angle : 0.598 12.100 18455 Z= 0.290 Chirality : 0.042 0.359 2030 Planarity : 0.004 0.041 2285 Dihedral : 3.920 26.394 1765 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.52 % Allowed : 17.65 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.45 (0.21), residues: 1575 helix: 1.04 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -2.04 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 229 HIS 0.002 0.001 HIS B 178 PHE 0.017 0.002 PHE D 278 TYR 0.017 0.001 TYR E 225 ARG 0.008 0.000 ARG E 202 ********************** 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 186 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 30 LYS cc_start: 0.8566 (tttt) cc_final: 0.8091 (tppp) REVERT: A 41 SER cc_start: 0.8747 (m) cc_final: 0.8410 (p) REVERT: A 46 ILE cc_start: 0.8810 (mt) cc_final: 0.8567 (mp) REVERT: A 92 ARG cc_start: 0.7788 (tmt90) cc_final: 0.7161 (mmt90) REVERT: A 328 ASP cc_start: 0.7349 (t70) cc_final: 0.6986 (p0) REVERT: B 30 LYS cc_start: 0.8743 (tttt) cc_final: 0.8156 (mmtp) REVERT: B 92 ARG cc_start: 0.7755 (tmt90) cc_final: 0.7184 (mmt90) REVERT: B 323 ASP cc_start: 0.7960 (t0) cc_final: 0.7754 (t0) REVERT: C 41 SER cc_start: 0.8745 (m) cc_final: 0.8545 (p) REVERT: C 46 ILE cc_start: 0.8649 (mp) cc_final: 0.8212 (tt) REVERT: C 92 ARG cc_start: 0.7926 (tmt90) cc_final: 0.7291 (mmt90) REVERT: C 323 ASP cc_start: 0.8080 (t0) cc_final: 0.7807 (t0) REVERT: C 328 ASP cc_start: 0.7267 (t70) cc_final: 0.6949 (p0) REVERT: D 92 ARG cc_start: 0.7766 (tmt90) cc_final: 0.7160 (mmt90) REVERT: D 252 LEU cc_start: 0.8932 (tm) cc_final: 0.8661 (tp) REVERT: D 325 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8502 (mtm) REVERT: E 30 LYS cc_start: 0.8622 (tttt) cc_final: 0.8283 (tptt) REVERT: E 41 SER cc_start: 0.8692 (m) cc_final: 0.8377 (p) REVERT: E 46 ILE cc_start: 0.8781 (mt) cc_final: 0.8486 (tt) REVERT: E 92 ARG cc_start: 0.7672 (tmt90) cc_final: 0.7133 (mmt180) REVERT: E 149 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7933 (ptpt) outliers start: 22 outliers final: 16 residues processed: 178 average time/residue: 1.0388 time to fit residues: 206.0916 Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 75 LEU 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 273 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 149 LYS Chi-restraints excluded: chain E residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.093676 restraints weight = 22274.202| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.96 r_work: 0.3068 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13570 Z= 0.179 Angle : 0.563 11.870 18455 Z= 0.272 Chirality : 0.040 0.268 2030 Planarity : 0.004 0.041 2285 Dihedral : 3.842 25.419 1765 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.52 % Allowed : 17.58 % 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: 0.79 (0.21), residues: 1575 helix: 1.24 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.64 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 229 HIS 0.001 0.000 HIS B 178 PHE 0.038 0.001 PHE A 80 TYR 0.015 0.001 TYR C 97 ARG 0.008 0.000 ARG E 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.26 seconds wall clock time: 78 minutes 58.12 seconds (4738.12 seconds total)