Starting phenix.real_space_refine on Wed Aug 27 02:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w1p_43729/08_2025/8w1p_43729.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.062 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: 6 Type Number sf(0) Gaussians P 105 5.49 5 S 115 5.16 5 C 14796 2.51 5 N 3997 2.21 5 O 4756 1.98 5 H 22596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46365 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5270 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 309} Chain: "B" Number of atoms: 5247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5247 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "C" Number of atoms: 5248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5248 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 15, 'TRANS': 308} Chain: "D" Number of atoms: 5232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 5232 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 15, 'TRANS': 307} Chain: "E" Number of atoms: 4938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4938 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 1 Chain: "F" Number of atoms: 4795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4795 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "G" Number of atoms: 5442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5442 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain: "H" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 4004 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "I" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2823 Classifications: {'peptide': 172} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "N" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 415 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "R" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1939 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 23, 'rna3p_pyr': 14} Link IDs: {'rna2p': 23, 'rna3p': 37} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1012 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Time building chain proxies: 8.83, per 1000 atoms: 0.19 Number of scatterers: 46365 At special positions: 0 Unit cell: (117.796, 149.048, 169.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 115 16.00 P 105 15.00 O 4756 8.00 N 3997 7.00 C 14796 6.00 H 22596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.23 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 31 sheets defined 37.8% alpha, 9.1% beta 34 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 8.21 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 63 through 71 removed outlier: 4.539A pdb=" N LYS A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.576A pdb=" N MET A 106 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 129 Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 145 through 153 removed outlier: 6.326A pdb=" N ARG A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.579A pdb=" N PHE A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.542A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 removed outlier: 3.870A pdb=" N LYS A 295 " --> pdb=" O PRO A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'B' and resid 36 through 40 Processing helix chain 'B' and resid 63 through 71 removed outlier: 4.236A pdb=" N LYS B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 111 through 129 Processing helix chain 'B' and resid 131 through 144 removed outlier: 4.025A pdb=" N ARG B 137 " --> pdb=" O THR B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 6.221A pdb=" N ARG B 150 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.607A pdb=" N GLN B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.524A pdb=" N ILE B 254 " --> pdb=" O HIS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.443A pdb=" N THR B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 295 removed outlier: 4.026A pdb=" N LYS B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 292 through 295' Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'C' and resid 36 through 40 Processing helix chain 'C' and resid 63 through 71 removed outlier: 4.072A pdb=" N LYS C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 104 No H-bonds generated for 'chain 'C' and resid 102 through 104' Processing helix chain 'C' and resid 111 through 130 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 6.426A pdb=" N ARG C 150 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 153 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.682A pdb=" N GLN C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.473A pdb=" N THR C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 295 removed outlier: 3.808A pdb=" N LYS C 295 " --> pdb=" O PRO C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 295' Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 63 through 71 removed outlier: 4.107A pdb=" N LYS D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 153 removed outlier: 6.578A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.715A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 292 through 295 removed outlier: 3.866A pdb=" N LYS D 295 " --> pdb=" O PRO D 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 292 through 295' Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 131 through 144 Processing helix chain 'E' and resid 145 through 153 removed outlier: 6.478A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 186 through 201 Processing helix chain 'E' and resid 250 through 260 Processing helix chain 'E' and resid 265 through 270 removed outlier: 4.185A pdb=" N THR E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 306 Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.747A pdb=" N TYR E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.695A pdb=" N PHE F 43 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 104 Processing helix chain 'F' and resid 111 through 129 Processing helix chain 'F' and resid 131 through 144 Processing helix chain 'F' and resid 145 through 153 removed outlier: 6.553A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 186 through 201 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.657A pdb=" N ILE F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.795A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 295 removed outlier: 3.840A pdb=" N LYS F 295 " --> pdb=" O PRO F 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 292 through 295' Processing helix chain 'F' and resid 296 through 306 Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'G' and resid 2 through 10 Processing helix chain 'G' and resid 14 through 30 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 82 through 85 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.824A pdb=" N GLY G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 123 through 133 Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 199 through 205 Processing helix chain 'G' and resid 216 through 220 Processing helix chain 'G' and resid 222 through 228 Processing helix chain 'G' and resid 251 through 253 No H-bonds generated for 'chain 'G' and resid 251 through 253' Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 280 through 292 Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.598A pdb=" N GLY G 311 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'H' and resid 28 through 46 removed outlier: 3.755A pdb=" N PHE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 130 removed outlier: 4.016A pdb=" N GLU H 130 " --> pdb=" O LYS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 169 Processing helix chain 'H' and resid 174 through 186 Processing helix chain 'H' and resid 235 through 239 Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.574A pdb=" N ILE I 19 " --> pdb=" O SER I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 35 Processing helix chain 'I' and resid 64 through 71 removed outlier: 3.584A pdb=" N LEU I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 77 removed outlier: 3.592A pdb=" N HIS I 76 " --> pdb=" O CYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 124 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 27 current: chain 'A' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 45 through 46 current: chain 'A' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 167 through 168 current: chain 'A' and resid 246 through 249 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.282A pdb=" N CYS A 82 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 27 current: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 167 through 168 current: chain 'B' and resid 246 through 249 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 49 through 57 Processing sheet with id=AA8, first strand: chain 'C' and resid 106 through 109 removed outlier: 3.620A pdb=" N SER C 108 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 27 current: chain 'C' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 45 through 46 current: chain 'C' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 168 current: chain 'C' and resid 246 through 249 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.312A pdb=" N CYS C 82 " --> pdb=" O VAL C 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 54 through 57 Processing sheet with id=AB3, first strand: chain 'C' and resid 260 through 262 Processing sheet with id=AB4, first strand: chain 'D' and resid 106 through 109 removed outlier: 3.675A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 27 current: chain 'D' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 46 current: chain 'D' and resid 167 through 173 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 167 through 173 current: chain 'D' and resid 246 through 249 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.266A pdb=" N CYS D 82 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 54 through 56 Processing sheet with id=AB8, first strand: chain 'E' and resid 106 through 108 removed outlier: 6.799A pdb=" N SER E 20 " --> pdb=" O TYR E 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 27 current: chain 'E' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 46 current: chain 'E' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 168 current: chain 'E' and resid 246 through 249 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 50 through 54 removed outlier: 4.282A pdb=" N CYS E 82 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 106 through 109 removed outlier: 3.509A pdb=" N SER F 108 " --> pdb=" O SER F 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 25 through 27 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 27 current: chain 'F' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 45 through 46 current: chain 'F' and resid 167 through 168 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 167 through 168 current: chain 'F' and resid 246 through 249 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 82 through 83 removed outlier: 4.256A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 34 through 36 Processing sheet with id=AC6, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'G' and resid 147 through 153 removed outlier: 4.359A pdb=" N LYS G 147 " --> pdb=" O ILE G 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 156 through 162 current: chain 'H' and resid 101 through 113 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 101 through 113 current: chain 'H' and resid 137 through 141 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 137 through 141 current: chain 'H' and resid 215 through 229 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 215 through 229 current: chain 'H' and resid 249 through 254 Processing sheet with id=AC8, first strand: chain 'G' and resid 183 through 185 removed outlier: 8.178A pdb=" N VAL H 24 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N PHE G 211 " --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 244 through 245 Processing sheet with id=AD1, first strand: chain 'G' and resid 300 through 304 Processing sheet with id=AD2, first strand: chain 'H' and resid 66 through 68 Processing sheet with id=AD3, first strand: chain 'I' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 8 current: chain 'I' and resid 57 through 62 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 98 through 101 removed outlier: 3.786A pdb=" N LEU I 98 " --> pdb=" O THR I 162 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA I 142 " --> pdb=" O LEU I 159 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 11.48 Time building geometry restraints manager: 5.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22549 1.02 - 1.22: 54 1.22 - 1.42: 10253 1.42 - 1.62: 14053 1.62 - 1.82: 186 Bond restraints: 47095 Sorted by residual: bond pdb=" CA PHE B 131 " pdb=" C PHE B 131 " ideal model delta sigma weight residual 1.522 1.591 -0.069 1.72e-02 3.38e+03 1.61e+01 bond pdb=" C1' DT T 16 " pdb=" N1 DT T 16 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" C3' U R 54 " pdb=" C2' U R 54 " ideal model delta sigma weight residual 1.525 1.557 -0.032 1.50e-02 4.44e+03 4.45e+00 bond pdb=" CB ILE B 322 " pdb=" CG2 ILE B 322 " ideal model delta sigma weight residual 1.521 1.588 -0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB ILE D 118 " pdb=" CG2 ILE D 118 " ideal model delta sigma weight residual 1.521 1.588 -0.067 3.30e-02 9.18e+02 4.11e+00 ... (remaining 47090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 80330 1.82 - 3.64: 4247 3.64 - 5.47: 531 5.47 - 7.29: 30 7.29 - 9.11: 3 Bond angle restraints: 85141 Sorted by residual: angle pdb=" C4' DA T 23 " pdb=" C3' DA T 23 " pdb=" O3' DA T 23 " ideal model delta sigma weight residual 110.00 116.93 -6.93 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" O3' U R 1 " ideal model delta sigma weight residual 109.40 115.97 -6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" C3' U R 1 " pdb=" O3' U R 1 " pdb=" P U R 2 " ideal model delta sigma weight residual 120.20 126.39 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" C3' DA T 23 " pdb=" O3' DA T 23 " pdb=" P DT T 24 " ideal model delta sigma weight residual 120.20 126.14 -5.94 1.50e+00 4.44e-01 1.57e+01 angle pdb=" O4' U R 19 " pdb=" C1' U R 19 " pdb=" N1 U R 19 " ideal model delta sigma weight residual 108.20 114.01 -5.81 1.50e+00 4.44e-01 1.50e+01 ... (remaining 85136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 21168 35.89 - 71.78: 828 71.78 - 107.67: 52 107.67 - 143.56: 10 143.56 - 179.45: 4 Dihedral angle restraints: 22062 sinusoidal: 12708 harmonic: 9354 Sorted by residual: dihedral pdb=" C5' U R 54 " pdb=" C4' U R 54 " pdb=" C3' U R 54 " pdb=" O3' U R 54 " ideal model delta sinusoidal sigma weight residual 147.00 92.31 54.69 1 8.00e+00 1.56e-02 6.33e+01 dihedral pdb=" O4' A R 38 " pdb=" C2' A R 38 " pdb=" C1' A R 38 " pdb=" C3' A R 38 " ideal model delta sinusoidal sigma weight residual -35.00 18.15 -53.15 1 8.00e+00 1.56e-02 6.00e+01 dihedral pdb=" C4' A R 38 " pdb=" C3' A R 38 " pdb=" C2' A R 38 " pdb=" C1' A R 38 " ideal model delta sinusoidal sigma weight residual -35.00 17.78 -52.78 1 8.00e+00 1.56e-02 5.93e+01 ... (remaining 22059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3037 0.064 - 0.127: 567 0.127 - 0.191: 112 0.191 - 0.254: 6 0.254 - 0.318: 4 Chirality restraints: 3726 Sorted by residual: chirality pdb=" C3' A R 38 " pdb=" C4' A R 38 " pdb=" O3' A R 38 " pdb=" C2' A R 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C3' G R 33 " pdb=" C4' G R 33 " pdb=" O3' G R 33 " pdb=" C2' G R 33 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C3' U R 44 " pdb=" C4' U R 44 " pdb=" O3' U R 44 " pdb=" C2' U R 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3723 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 291 " 0.517 9.50e-02 1.11e+02 1.73e-01 3.30e+01 pdb=" NE ARG B 291 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 291 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 291 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 291 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG B 291 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 291 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 291 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 291 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 150 " 0.332 9.50e-02 1.11e+02 1.13e-01 2.21e+01 pdb=" NE ARG E 150 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG E 150 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 150 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 150 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG E 150 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 150 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG E 150 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 150 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 115 " 0.175 9.50e-02 1.11e+02 6.36e-02 1.82e+01 pdb=" NE ARG F 115 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 115 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 115 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG F 115 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG F 115 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 115 " -0.033 2.00e-02 2.50e+03 pdb="HH21 ARG F 115 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 115 " 0.046 2.00e-02 2.50e+03 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4829 2.26 - 2.84: 101921 2.84 - 3.43: 118632 3.43 - 4.01: 168246 4.01 - 4.60: 260113 Nonbonded interactions: 653741 Sorted by model distance: nonbonded pdb=" HH TYR I 143 " pdb=" OP1 U R 44 " model vdw 1.669 2.450 nonbonded pdb=" H ILE F 97 " pdb=" O ILE F 209 " model vdw 1.676 2.450 nonbonded pdb=" HG1 THR I 42 " pdb=" O VAL I 97 " model vdw 1.694 2.450 nonbonded pdb=" H ILE E 97 " pdb=" O ILE E 209 " model vdw 1.702 2.450 nonbonded pdb=" H ILE B 97 " pdb=" O ILE B 209 " model vdw 1.703 2.450 ... (remaining 653736 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' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'B' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'C' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 332)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 50.340 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 : 0.006 0.069 24499 Z= 0.281 Angle : 0.936 6.930 33562 Z= 0.539 Chirality : 0.053 0.318 3726 Planarity : 0.009 0.223 3921 Dihedral : 16.666 179.449 9731 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.29 % Allowed : 2.44 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 2636 helix: -0.49 (0.16), residues: 800 sheet: 0.51 (0.25), residues: 406 loop : -0.52 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG D 204 TYR 0.018 0.004 TYR G 140 PHE 0.031 0.003 PHE A 200 TRP 0.021 0.003 TRP D 33 HIS 0.016 0.002 HIS H 215 Details of bonding type rmsd covalent geometry : bond 0.00647 (24499) covalent geometry : angle 0.93602 (33562) hydrogen bonds : bond 0.15097 ( 768) hydrogen bonds : angle 6.41449 ( 1984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 465 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7012 (t80) cc_final: 0.6762 (t80) REVERT: A 174 SER cc_start: 0.9457 (p) cc_final: 0.9129 (t) REVERT: B 78 LYS cc_start: 0.6289 (mttt) cc_final: 0.6075 (tppt) REVERT: B 224 TYR cc_start: 0.8778 (m-80) cc_final: 0.8063 (m-80) REVERT: B 288 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6617 (pp) REVERT: C 304 MET cc_start: 0.8201 (ttp) cc_final: 0.7851 (ttp) REVERT: C 331 LYS cc_start: 0.9030 (mmtt) cc_final: 0.8808 (tptp) REVERT: D 304 MET cc_start: 0.8569 (ttp) cc_final: 0.8343 (ttp) REVERT: E 78 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7827 (mttp) REVERT: E 169 TYR cc_start: 0.8174 (m-80) cc_final: 0.7338 (m-80) REVERT: E 269 THR cc_start: 0.8914 (t) cc_final: 0.8697 (p) REVERT: E 320 MET cc_start: 0.8013 (mmt) cc_final: 0.7686 (mmp) REVERT: F 40 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.8111 (ptt90) REVERT: F 183 VAL cc_start: 0.8837 (t) cc_final: 0.8330 (m) REVERT: F 320 MET cc_start: 0.6856 (mmt) cc_final: 0.6213 (mmt) REVERT: G 94 MET cc_start: 0.6350 (mtt) cc_final: 0.6030 (mtt) REVERT: H 140 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7832 (ttm-80) REVERT: H 156 TYR cc_start: 0.8010 (t80) cc_final: 0.7786 (t80) REVERT: H 158 TYR cc_start: 0.7999 (m-80) cc_final: 0.7716 (m-80) REVERT: I 1 MET cc_start: 0.8463 (tpp) cc_final: 0.8146 (tpp) REVERT: I 137 GLN cc_start: 0.8723 (mt0) cc_final: 0.8319 (tm-30) REVERT: I 153 GLN cc_start: 0.5380 (mm-40) cc_final: 0.5136 (mm-40) outliers start: 7 outliers final: 0 residues processed: 470 average time/residue: 0.4499 time to fit residues: 315.2910 Evaluate side-chains 248 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS A 252 GLN A 256 ASN A 317 HIS B 75 ASN B 77 GLN B 195 GLN C 250 HIS C 252 GLN C 256 ASN D 256 ASN D 317 HIS D 333 GLN E 250 HIS E 317 HIS F 317 HIS H 17 ASN H 20 ASN I 76 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094530 restraints weight = 91393.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094354 restraints weight = 71948.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095674 restraints weight = 60120.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096557 restraints weight = 49440.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096664 restraints weight = 43212.766| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 24499 Z= 0.317 Angle : 0.704 6.895 33562 Z= 0.397 Chirality : 0.047 0.259 3726 Planarity : 0.005 0.045 3921 Dihedral : 18.226 171.327 4298 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 7.46 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 2636 helix: 0.28 (0.17), residues: 809 sheet: -0.29 (0.24), residues: 416 loop : -0.56 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 291 TYR 0.021 0.002 TYR E 206 PHE 0.022 0.002 PHE E 273 TRP 0.015 0.002 TRP D 33 HIS 0.012 0.002 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00724 (24499) covalent geometry : angle 0.70406 (33562) hydrogen bonds : bond 0.05381 ( 768) hydrogen bonds : angle 5.58268 ( 1984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 288 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.7004 (pp) REVERT: C 331 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8357 (tptm) REVERT: E 269 THR cc_start: 0.8618 (t) cc_final: 0.8364 (p) REVERT: F 183 VAL cc_start: 0.8945 (t) cc_final: 0.8585 (m) REVERT: G 61 MET cc_start: 0.6782 (tpp) cc_final: 0.6440 (tpp) REVERT: G 261 GLU cc_start: 0.7867 (tp30) cc_final: 0.7603 (tp30) REVERT: G 310 GLN cc_start: 0.7325 (mm-40) cc_final: 0.6927 (mp10) REVERT: H 51 ARG cc_start: 0.6882 (mtp-110) cc_final: 0.6620 (ttm-80) REVERT: H 140 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7820 (ttt180) outliers start: 32 outliers final: 24 residues processed: 270 average time/residue: 0.4217 time to fit residues: 175.3499 Evaluate side-chains 233 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 121 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN F 250 HIS G 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094842 restraints weight = 90312.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.097848 restraints weight = 52388.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099756 restraints weight = 37964.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100828 restraints weight = 31378.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101420 restraints weight = 27991.931| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24499 Z= 0.141 Angle : 0.579 8.352 33562 Z= 0.322 Chirality : 0.042 0.260 3726 Planarity : 0.004 0.047 3921 Dihedral : 18.091 169.640 4298 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.93 % Allowed : 9.44 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2636 helix: 0.82 (0.18), residues: 801 sheet: -0.49 (0.23), residues: 437 loop : -0.45 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 329 TYR 0.014 0.001 TYR F 265 PHE 0.015 0.001 PHE E 273 TRP 0.010 0.001 TRP D 33 HIS 0.007 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00316 (24499) covalent geometry : angle 0.57908 (33562) hydrogen bonds : bond 0.04361 ( 768) hydrogen bonds : angle 5.05214 ( 1984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8460 (mm-40) REVERT: B 288 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7177 (pp) REVERT: C 14 SER cc_start: 0.8308 (t) cc_final: 0.7932 (m) REVERT: C 331 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8481 (tptm) REVERT: E 221 MET cc_start: 0.8367 (mmt) cc_final: 0.8085 (mmp) REVERT: E 269 THR cc_start: 0.8589 (t) cc_final: 0.8274 (p) REVERT: F 183 VAL cc_start: 0.8964 (t) cc_final: 0.8562 (m) REVERT: G 61 MET cc_start: 0.6517 (tpp) cc_final: 0.6201 (tpp) REVERT: G 321 MET cc_start: 0.7778 (mtp) cc_final: 0.7409 (mtp) REVERT: H 5 TYR cc_start: 0.7764 (m-80) cc_final: 0.7307 (m-10) REVERT: H 140 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7849 (ttt180) REVERT: H 156 TYR cc_start: 0.8036 (t80) cc_final: 0.7834 (t80) REVERT: I 1 MET cc_start: 0.7812 (tpp) cc_final: 0.7179 (tpp) outliers start: 22 outliers final: 16 residues processed: 254 average time/residue: 0.3772 time to fit residues: 152.9452 Evaluate side-chains 219 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 75 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 185 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 227 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 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN C 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.127967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.091812 restraints weight = 91861.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093221 restraints weight = 68719.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.094522 restraints weight = 49089.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094693 restraints weight = 41004.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.094908 restraints weight = 40150.592| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24499 Z= 0.264 Angle : 0.624 6.490 33562 Z= 0.347 Chirality : 0.044 0.227 3726 Planarity : 0.004 0.050 3921 Dihedral : 17.998 170.485 4298 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.94 % Allowed : 9.31 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2636 helix: 0.67 (0.18), residues: 804 sheet: -0.86 (0.23), residues: 424 loop : -0.74 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 259 TYR 0.024 0.002 TYR E 271 PHE 0.018 0.002 PHE E 273 TRP 0.015 0.001 TRP D 33 HIS 0.007 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00604 (24499) covalent geometry : angle 0.62410 (33562) hydrogen bonds : bond 0.04604 ( 768) hydrogen bonds : angle 5.12278 ( 1984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8509 (mm-40) REVERT: B 288 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7347 (pp) REVERT: C 14 SER cc_start: 0.8489 (t) cc_final: 0.8186 (p) REVERT: E 269 THR cc_start: 0.8684 (t) cc_final: 0.8395 (p) REVERT: F 183 VAL cc_start: 0.8961 (t) cc_final: 0.8612 (m) REVERT: G 310 GLN cc_start: 0.6980 (mm-40) cc_final: 0.6680 (mm-40) REVERT: G 317 LYS cc_start: 0.8433 (mttt) cc_final: 0.8201 (mtmt) REVERT: H 140 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8007 (ttt180) outliers start: 46 outliers final: 35 residues processed: 248 average time/residue: 0.3754 time to fit residues: 148.9923 Evaluate side-chains 232 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 72 optimal weight: 0.7980 chunk 231 optimal weight: 4.9990 chunk 127 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 ASN C 333 GLN D 195 GLN E 34 GLN E 333 GLN I 135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.131129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.090347 restraints weight = 93156.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.094681 restraints weight = 41123.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.097323 restraints weight = 25994.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098906 restraints weight = 19968.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099807 restraints weight = 17131.292| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24499 Z= 0.116 Angle : 0.526 5.060 33562 Z= 0.289 Chirality : 0.040 0.219 3726 Planarity : 0.003 0.041 3921 Dihedral : 17.915 170.883 4298 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.35 % Allowed : 10.16 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2636 helix: 1.10 (0.18), residues: 809 sheet: -0.87 (0.23), residues: 408 loop : -0.58 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.010 0.001 TYR E 271 PHE 0.011 0.001 PHE D 231 TRP 0.008 0.001 TRP D 33 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00260 (24499) covalent geometry : angle 0.52600 (33562) hydrogen bonds : bond 0.03646 ( 768) hydrogen bonds : angle 4.67309 ( 1984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8749 (t) cc_final: 0.8272 (p) REVERT: E 221 MET cc_start: 0.8436 (mmt) cc_final: 0.8158 (mmt) REVERT: E 269 THR cc_start: 0.8814 (t) cc_final: 0.8503 (p) REVERT: F 183 VAL cc_start: 0.8865 (t) cc_final: 0.8436 (m) REVERT: G 310 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6493 (mm-40) REVERT: G 317 LYS cc_start: 0.8476 (mttt) cc_final: 0.8104 (mtmt) REVERT: G 321 MET cc_start: 0.7630 (mtp) cc_final: 0.7128 (mtp) REVERT: H 140 ARG cc_start: 0.8589 (ttp80) cc_final: 0.7892 (ttt180) REVERT: I 1 MET cc_start: 0.8027 (tpp) cc_final: 0.7628 (tpp) REVERT: I 23 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7072 (p0) REVERT: I 137 GLN cc_start: 0.8693 (mt0) cc_final: 0.8353 (tm-30) outliers start: 32 outliers final: 24 residues processed: 236 average time/residue: 0.3741 time to fit residues: 141.4422 Evaluate side-chains 225 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 62 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 113 optimal weight: 0.0370 chunk 254 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 269 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 29 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 140 ASN D 255 ASN I 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.130615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089723 restraints weight = 93775.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093993 restraints weight = 41604.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096655 restraints weight = 26460.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.098248 restraints weight = 20325.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099199 restraints weight = 17399.051| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24499 Z= 0.153 Angle : 0.524 5.338 33562 Z= 0.288 Chirality : 0.041 0.224 3726 Planarity : 0.003 0.040 3921 Dihedral : 17.846 171.471 4296 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.56 % Allowed : 10.16 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2636 helix: 1.20 (0.18), residues: 809 sheet: -0.93 (0.23), residues: 415 loop : -0.57 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 291 TYR 0.012 0.001 TYR H 142 PHE 0.014 0.001 PHE E 273 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00349 (24499) covalent geometry : angle 0.52377 (33562) hydrogen bonds : bond 0.03677 ( 768) hydrogen bonds : angle 4.64756 ( 1984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8767 (t) cc_final: 0.8295 (p) REVERT: C 43 PHE cc_start: 0.8262 (t80) cc_final: 0.7970 (t80) REVERT: E 269 THR cc_start: 0.8845 (t) cc_final: 0.8487 (p) REVERT: F 183 VAL cc_start: 0.8886 (t) cc_final: 0.8525 (m) REVERT: F 194 GLN cc_start: 0.8570 (tp40) cc_final: 0.8346 (tp40) REVERT: G 310 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6370 (mm-40) REVERT: G 317 LYS cc_start: 0.8466 (mttt) cc_final: 0.8103 (mtmt) REVERT: G 321 MET cc_start: 0.7605 (mtp) cc_final: 0.7121 (mtp) REVERT: H 140 ARG cc_start: 0.8605 (ttp80) cc_final: 0.7930 (ttt180) REVERT: I 1 MET cc_start: 0.7996 (tpp) cc_final: 0.7665 (tpp) REVERT: I 23 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7107 (p0) outliers start: 37 outliers final: 33 residues processed: 236 average time/residue: 0.3793 time to fit residues: 143.0365 Evaluate side-chains 239 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 127 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 196 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 chunk 254 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.087779 restraints weight = 94231.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091941 restraints weight = 42295.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094526 restraints weight = 27012.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096104 restraints weight = 20804.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096972 restraints weight = 17848.508| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24499 Z= 0.238 Angle : 0.564 5.677 33562 Z= 0.312 Chirality : 0.042 0.221 3726 Planarity : 0.004 0.044 3921 Dihedral : 17.826 171.432 4296 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.60 % Allowed : 10.32 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2636 helix: 1.03 (0.18), residues: 802 sheet: -1.02 (0.23), residues: 428 loop : -0.68 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.012 0.001 TYR C 169 PHE 0.014 0.002 PHE E 273 TRP 0.012 0.001 TRP D 33 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00552 (24499) covalent geometry : angle 0.56438 (33562) hydrogen bonds : bond 0.04028 ( 768) hydrogen bonds : angle 4.83326 ( 1984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8804 (t) cc_final: 0.8341 (p) REVERT: E 269 THR cc_start: 0.8921 (t) cc_final: 0.8587 (p) REVERT: F 183 VAL cc_start: 0.8900 (t) cc_final: 0.8557 (m) REVERT: F 194 GLN cc_start: 0.8647 (tp40) cc_final: 0.8404 (tp40) REVERT: G 310 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6625 (mm-40) REVERT: G 317 LYS cc_start: 0.8479 (mttt) cc_final: 0.8160 (mtmt) REVERT: G 321 MET cc_start: 0.7599 (mtp) cc_final: 0.7127 (mtp) REVERT: H 140 ARG cc_start: 0.8613 (ttp80) cc_final: 0.7944 (ttt180) REVERT: I 1 MET cc_start: 0.7950 (tpp) cc_final: 0.7679 (tpp) REVERT: I 23 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7125 (p0) outliers start: 38 outliers final: 35 residues processed: 233 average time/residue: 0.4018 time to fit residues: 147.0432 Evaluate side-chains 235 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 248 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN C 333 GLN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089666 restraints weight = 94054.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.093950 restraints weight = 41935.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096581 restraints weight = 26634.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098179 restraints weight = 20505.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099039 restraints weight = 17567.736| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24499 Z= 0.139 Angle : 0.514 6.138 33562 Z= 0.282 Chirality : 0.040 0.215 3726 Planarity : 0.003 0.039 3921 Dihedral : 17.803 171.483 4296 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.56 % Allowed : 10.37 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2636 helix: 1.23 (0.18), residues: 809 sheet: -1.07 (0.23), residues: 420 loop : -0.60 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.012 0.001 TYR H 142 PHE 0.013 0.001 PHE E 273 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00319 (24499) covalent geometry : angle 0.51380 (33562) hydrogen bonds : bond 0.03614 ( 768) hydrogen bonds : angle 4.60706 ( 1984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8787 (t) cc_final: 0.8323 (p) REVERT: D 157 ILE cc_start: 0.8946 (mt) cc_final: 0.8716 (mm) REVERT: E 269 THR cc_start: 0.8904 (t) cc_final: 0.8570 (p) REVERT: F 183 VAL cc_start: 0.8863 (t) cc_final: 0.8509 (m) REVERT: F 194 GLN cc_start: 0.8601 (tp40) cc_final: 0.8362 (tp40) REVERT: G 310 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6443 (mm-40) REVERT: G 317 LYS cc_start: 0.8465 (mttt) cc_final: 0.8127 (mtmt) REVERT: G 321 MET cc_start: 0.7546 (mtp) cc_final: 0.7108 (mtp) REVERT: H 140 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8029 (ttt180) REVERT: I 23 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7098 (p0) outliers start: 37 outliers final: 30 residues processed: 242 average time/residue: 0.2875 time to fit residues: 110.4972 Evaluate side-chains 236 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 208 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 151 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS C 333 GLN D 252 GLN G 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090054 restraints weight = 93201.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094323 restraints weight = 41589.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.096946 restraints weight = 26461.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098536 restraints weight = 20371.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099437 restraints weight = 17460.519| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24499 Z= 0.140 Angle : 0.504 6.071 33562 Z= 0.276 Chirality : 0.040 0.212 3726 Planarity : 0.003 0.040 3921 Dihedral : 17.746 171.621 4296 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.47 % Allowed : 10.62 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.17), residues: 2636 helix: 1.32 (0.18), residues: 821 sheet: -0.96 (0.24), residues: 435 loop : -0.53 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.011 0.001 TYR E 271 PHE 0.013 0.001 PHE E 273 TRP 0.009 0.001 TRP D 33 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00323 (24499) covalent geometry : angle 0.50356 (33562) hydrogen bonds : bond 0.03518 ( 768) hydrogen bonds : angle 4.49737 ( 1984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 218 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 SER cc_start: 0.8792 (t) cc_final: 0.8340 (p) REVERT: D 72 MET cc_start: 0.6825 (mmm) cc_final: 0.6575 (mtm) REVERT: D 157 ILE cc_start: 0.8950 (mt) cc_final: 0.8707 (mm) REVERT: E 269 THR cc_start: 0.8886 (t) cc_final: 0.8542 (p) REVERT: F 183 VAL cc_start: 0.8841 (t) cc_final: 0.8534 (m) REVERT: G 39 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8715 (m) REVERT: G 310 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6402 (mm-40) REVERT: G 317 LYS cc_start: 0.8469 (mttt) cc_final: 0.8131 (mtmt) REVERT: G 321 MET cc_start: 0.7507 (mtp) cc_final: 0.7047 (mtp) REVERT: H 140 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8098 (ttt180) REVERT: I 23 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7144 (p0) outliers start: 35 outliers final: 28 residues processed: 245 average time/residue: 0.2973 time to fit residues: 114.5148 Evaluate side-chains 236 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 144 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN G 246 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.089349 restraints weight = 94058.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093598 restraints weight = 42080.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096209 restraints weight = 26822.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097765 restraints weight = 20650.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098555 restraints weight = 17756.691| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24499 Z= 0.167 Angle : 0.514 5.402 33562 Z= 0.282 Chirality : 0.041 0.208 3726 Planarity : 0.003 0.040 3921 Dihedral : 17.699 171.859 4296 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.35 % Allowed : 10.79 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.17), residues: 2636 helix: 1.31 (0.18), residues: 815 sheet: -1.00 (0.24), residues: 435 loop : -0.53 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 284 TYR 0.011 0.001 TYR I 96 PHE 0.014 0.001 PHE E 273 TRP 0.010 0.001 TRP D 33 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00385 (24499) covalent geometry : angle 0.51399 (33562) hydrogen bonds : bond 0.03650 ( 768) hydrogen bonds : angle 4.54231 ( 1984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8292 (ttmm) REVERT: C 14 SER cc_start: 0.8815 (t) cc_final: 0.8354 (p) REVERT: D 157 ILE cc_start: 0.8939 (mt) cc_final: 0.8676 (mm) REVERT: E 269 THR cc_start: 0.8873 (t) cc_final: 0.8555 (p) REVERT: G 39 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8737 (m) REVERT: G 310 GLN cc_start: 0.6998 (mm-40) cc_final: 0.6474 (mm-40) REVERT: G 317 LYS cc_start: 0.8464 (mttt) cc_final: 0.8120 (mtmt) REVERT: G 321 MET cc_start: 0.7513 (mtp) cc_final: 0.7044 (mtp) REVERT: H 140 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8075 (ttt180) REVERT: I 23 ASP cc_start: 0.7611 (OUTLIER) cc_final: 0.7207 (p0) REVERT: I 107 GLN cc_start: 0.1852 (OUTLIER) cc_final: 0.1511 (tp40) outliers start: 32 outliers final: 28 residues processed: 235 average time/residue: 0.3202 time to fit residues: 120.0003 Evaluate side-chains 234 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 107 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 52 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 254 optimal weight: 0.0670 chunk 216 optimal weight: 8.9990 chunk 171 optimal weight: 0.2980 chunk 49 optimal weight: 2.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090833 restraints weight = 93384.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095154 restraints weight = 41446.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097822 restraints weight = 26230.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099434 restraints weight = 20104.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100349 restraints weight = 17188.083| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24499 Z= 0.116 Angle : 0.484 5.850 33562 Z= 0.264 Chirality : 0.040 0.199 3726 Planarity : 0.003 0.037 3921 Dihedral : 17.641 171.950 4296 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 1.31 % Allowed : 10.91 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.17), residues: 2636 helix: 1.47 (0.18), residues: 821 sheet: -1.00 (0.24), residues: 429 loop : -0.46 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.010 0.001 TYR H 142 PHE 0.013 0.001 PHE E 273 TRP 0.008 0.001 TRP D 33 HIS 0.004 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00266 (24499) covalent geometry : angle 0.48442 (33562) hydrogen bonds : bond 0.03371 ( 768) hydrogen bonds : angle 4.37684 ( 1984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7033.38 seconds wall clock time: 121 minutes 6.64 seconds (7266.64 seconds total)