Starting phenix.real_space_refine on Tue Jul 7 07:29:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w1p_43729/07_2026/8w1p_43729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w1p_43729/07_2026/8w1p_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_43729/07_2026/8w1p_43729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w1p_43729/07_2026/8w1p_43729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8w1p_43729/07_2026/8w1p_43729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w1p_43729/07_2026/8w1p_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-dev-6108/lib/python3.11/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: 7.52, per 1000 atoms: 0.16 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: 3.98 Conformation dependent library (CDL) restraints added in 921.2 milliseconds 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: 8.03 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: 11.41 Time building geometry restraints manager: 5.52 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=" C1' DT T 16 " pdb=" N1 DT T 16 " ideal model delta sigma weight residual 1.468 1.556 -0.088 1.40e-02 5.10e+03 3.97e+01 bond pdb=" C1' DC N 12 " pdb=" N1 DC N 12 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.46e+01 bond pdb=" C1' DC T 32 " pdb=" N1 DC T 32 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.98e+01 bond pdb=" C1' DT T 41 " pdb=" N1 DT T 41 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.77e+01 bond pdb=" C1' DC T 43 " pdb=" N1 DC T 43 " ideal model delta sigma weight residual 1.468 1.542 -0.074 1.40e-02 5.10e+03 2.76e+01 ... (remaining 47090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 80286 1.82 - 3.64: 4270 3.64 - 5.47: 550 5.47 - 7.29: 32 7.29 - 9.11: 3 Bond angle restraints: 85141 Sorted by residual: angle pdb=" O5' DA T 36 " pdb=" C5' DA T 36 " pdb=" C4' DA T 36 " ideal model delta sigma weight residual 109.40 115.45 -6.05 8.00e-01 1.56e+00 5.72e+01 angle pdb=" O4' DG T 38 " pdb=" C1' DG T 38 " pdb=" N9 DG T 38 " ideal model delta sigma weight residual 108.00 113.25 -5.25 7.00e-01 2.04e+00 5.63e+01 angle pdb=" O4' DG T 12 " pdb=" C1' DG T 12 " pdb=" N9 DG T 12 " ideal model delta sigma weight residual 108.00 103.45 4.55 7.00e-01 2.04e+00 4.23e+01 angle pdb=" N1 C R 29 " pdb=" C2 C R 29 " pdb=" O2 C R 29 " ideal model delta sigma weight residual 118.90 122.66 -3.76 6.00e-01 2.78e+00 3.94e+01 angle pdb=" C2 C R 46 " pdb=" N1 C R 46 " pdb=" C6 C R 46 " ideal model delta sigma weight residual 120.30 117.95 2.35 4.00e-01 6.25e+00 3.45e+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: 2991 0.064 - 0.127: 595 0.127 - 0.191: 129 0.191 - 0.254: 7 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: 0.010 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.670 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 48.830 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.007 0.088 24499 Z= 0.365 Angle : 0.946 7.230 33562 Z= 0.614 Chirality : 0.055 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 are 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/Z covalent geometry : bond 0.00671 / 0.37 (24499) covalent geometry : angle 0.94579 / 0.61 (33562) hydrogen bonds : bond 0.15097 / 10.36 ( 768) hydrogen bonds : angle 6.41449 / 4.52 ( 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 : 1.218 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: 0.8399 (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: 0.4068 time to fit residues: 288.6877 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 : 1.196 ------------------------------------------------------------------------------- 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... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN A 256 ASN A 317 HIS B 75 ASN B 77 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 H 166 ASN I 76 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.130954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092628 restraints weight = 90961.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.095719 restraints weight = 51806.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.097654 restraints weight = 37162.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098805 restraints weight = 30571.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099591 restraints weight = 27100.722| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 24499 Z= 0.308 Angle : 0.715 7.089 33562 Z= 0.411 Chirality : 0.048 0.319 3726 Planarity : 0.005 0.054 3921 Dihedral : 18.245 176.154 4298 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.43 % Allowed : 7.37 % 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 are not related in a simple way. whole: -0.45 (0.15), residues: 2636 helix: 0.21 (0.17), residues: 805 sheet: -0.22 (0.24), residues: 416 loop : -0.55 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 204 TYR 0.038 0.002 TYR G 231 PHE 0.016 0.002 PHE F 131 TRP 0.012 0.002 TRP D 33 HIS 0.010 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.31 (24499) covalent geometry : angle 0.71453 / 0.41 (33562) hydrogen bonds : bond 0.06211 / 4.17 ( 768) hydrogen bonds : angle 5.68644 / 4.01 ( 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 293 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 1.120 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 79 SER cc_start: 0.8726 (OUTLIER) cc_final: 0.8439 (p) REVERT: B 288 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6952 (pp) REVERT: B 315 ASP cc_start: 0.8143 (m-30) cc_final: 0.7901 (t0) REVERT: C 331 LYS cc_start: 0.8903 (mmtt) cc_final: 0.8453 (tptm) REVERT: E 169 TYR cc_start: 0.8077 (m-80) cc_final: 0.7001 (m-80) REVERT: E 269 THR cc_start: 0.8733 (t) cc_final: 0.8479 (p) REVERT: F 183 VAL cc_start: 0.9047 (t) cc_final: 0.8594 (m) REVERT: F 320 MET cc_start: 0.6776 (mmt) cc_final: 0.6259 (mmt) REVERT: G 2 ARG cc_start: 0.8015 (tmm-80) cc_final: 0.7725 (tmm-80) REVERT: G 61 MET cc_start: 0.6786 (tpp) cc_final: 0.6490 (tpp) REVERT: G 282 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7987 (mp0) REVERT: G 321 MET cc_start: 0.7453 (mtp) cc_final: 0.7127 (mtp) REVERT: H 51 ARG cc_start: 0.6985 (mtp-110) cc_final: 0.6706 (ttm170) REVERT: H 106 MET cc_start: 0.6897 (ttm) cc_final: 0.6660 (ttm) REVERT: I 1 MET cc_start: 0.8149 (tpp) cc_final: 0.7867 (tpp) outliers start: 34 outliers final: 24 residues processed: 285 average time/residue: 0.3881 time to fit residues: 171.5720 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 : 1.335 ------------------------------------------------------------------------------- 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 108 SER 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 51 ASP Chi-restraints excluded: chain D residue 104 GLU 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 33 VAL 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: 1.9990 chunk 133 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN C 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094824 restraints weight = 90066.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098018 restraints weight = 50980.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100025 restraints weight = 36475.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.101243 restraints weight = 29872.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.101914 restraints weight = 26474.024| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24499 Z= 0.137 Angle : 0.591 9.964 33562 Z= 0.340 Chirality : 0.043 0.278 3726 Planarity : 0.004 0.044 3921 Dihedral : 18.153 170.722 4298 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 8.81 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2636 helix: 0.73 (0.18), residues: 801 sheet: -0.38 (0.23), residues: 437 loop : -0.44 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 329 TYR 0.015 0.001 TYR E 206 PHE 0.017 0.001 PHE E 273 TRP 0.008 0.001 TRP D 33 HIS 0.006 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (24499) covalent geometry : angle 0.59066 / 0.34 (33562) hydrogen bonds : bond 0.05045 / 3.35 ( 768) hydrogen bonds : angle 5.24010 / 3.70 ( 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 250 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 1.220 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: B 288 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6938 (pp) REVERT: C 21 PHE cc_start: 0.8825 (m-80) cc_final: 0.8614 (m-80) REVERT: C 331 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8606 (tptm) REVERT: E 169 TYR cc_start: 0.7976 (m-80) cc_final: 0.6956 (m-80) REVERT: E 174 SER cc_start: 0.8721 (p) cc_final: 0.8378 (t) REVERT: E 221 MET cc_start: 0.8432 (mmt) cc_final: 0.8160 (mmp) REVERT: E 269 THR cc_start: 0.8670 (t) cc_final: 0.8401 (p) REVERT: F 183 VAL cc_start: 0.9000 (t) cc_final: 0.8576 (m) REVERT: F 320 MET cc_start: 0.6868 (mmt) cc_final: 0.6225 (mmt) REVERT: G 61 MET cc_start: 0.6565 (tpp) cc_final: 0.6222 (tpp) REVERT: G 310 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6562 (mm-40) REVERT: G 321 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7294 (mtp) REVERT: H 51 ARG cc_start: 0.6907 (mtp-110) cc_final: 0.6557 (ttm170) outliers start: 29 outliers final: 20 residues processed: 242 average time/residue: 0.3608 time to fit residues: 140.5010 Evaluate side-chains 227 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 106 MET 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 124 GLU 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 30 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 321 MET 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 233 LEU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 33 VAL 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: 6.9990 chunk 185 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 ASN A 250 HIS C 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092235 restraints weight = 91085.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.095331 restraints weight = 52062.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097256 restraints weight = 37413.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098451 restraints weight = 30820.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099027 restraints weight = 27373.458| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24499 Z= 0.246 Angle : 0.605 6.931 33562 Z= 0.349 Chirality : 0.044 0.272 3726 Planarity : 0.004 0.049 3921 Dihedral : 18.096 169.456 4298 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.43 % Allowed : 8.85 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2636 helix: 0.67 (0.18), residues: 810 sheet: -0.69 (0.23), residues: 446 loop : -0.59 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.022 0.002 TYR F 265 PHE 0.017 0.002 PHE E 273 TRP 0.012 0.001 TRP D 33 HIS 0.008 0.001 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.25 (24499) covalent geometry : angle 0.60478 / 0.35 (33562) hydrogen bonds : bond 0.04753 / 3.15 ( 768) hydrogen bonds : angle 5.18761 / 3.66 ( 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 244 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.263 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: B 288 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7196 (pp) REVERT: C 14 SER cc_start: 0.8440 (t) cc_final: 0.8053 (m) REVERT: C 331 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8568 (tptm) REVERT: E 269 THR cc_start: 0.8685 (t) cc_final: 0.8406 (p) REVERT: F 183 VAL cc_start: 0.8957 (t) cc_final: 0.8553 (m) REVERT: G 310 GLN cc_start: 0.7040 (mm-40) cc_final: 0.6670 (mm-40) REVERT: G 321 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: I 137 GLN cc_start: 0.8810 (mt0) cc_final: 0.8456 (tm-30) outliers start: 34 outliers final: 25 residues processed: 234 average time/residue: 0.3581 time to fit residues: 135.9006 Evaluate side-chains 225 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 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 E residue 319 VAL 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 144 GLN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 321 MET 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 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: 1.9990 chunk 231 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 263 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 GLN D 252 GLN F 250 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094577 restraints weight = 89877.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097756 restraints weight = 51038.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099652 restraints weight = 36567.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.100908 restraints weight = 29974.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.101584 restraints weight = 26678.094| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24499 Z= 0.121 Angle : 0.531 6.657 33562 Z= 0.302 Chirality : 0.042 0.263 3726 Planarity : 0.003 0.044 3921 Dihedral : 18.028 169.687 4298 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.01 % Allowed : 9.40 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2636 helix: 0.96 (0.18), residues: 811 sheet: -0.80 (0.23), residues: 419 loop : -0.50 (0.16), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 150 TYR 0.012 0.001 TYR E 271 PHE 0.016 0.001 PHE E 273 TRP 0.009 0.001 TRP D 33 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (24499) covalent geometry : angle 0.53084 / 0.30 (33562) hydrogen bonds : bond 0.04158 / 2.76 ( 768) hydrogen bonds : angle 4.86434 / 3.44 ( 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 252 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 228 time to evaluate : 1.269 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 252 GLN cc_start: 0.8887 (mp10) cc_final: 0.8678 (mp10) REVERT: B 288 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7228 (pp) REVERT: C 14 SER cc_start: 0.8344 (t) cc_final: 0.7934 (m) REVERT: C 331 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8508 (tptm) REVERT: E 221 MET cc_start: 0.8381 (mmt) cc_final: 0.8092 (mmp) REVERT: E 269 THR cc_start: 0.8656 (t) cc_final: 0.8356 (p) REVERT: F 183 VAL cc_start: 0.8941 (t) cc_final: 0.8541 (m) REVERT: F 229 MET cc_start: 0.8732 (mtp) cc_final: 0.8408 (mtt) REVERT: G 310 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6887 (mm-40) REVERT: G 321 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7305 (mtp) REVERT: H 5 TYR cc_start: 0.7856 (m-80) cc_final: 0.7426 (m-10) REVERT: I 137 GLN cc_start: 0.8741 (mt0) cc_final: 0.8427 (tm-30) outliers start: 24 outliers final: 20 residues processed: 246 average time/residue: 0.3580 time to fit residues: 142.7829 Evaluate side-chains 229 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE 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 E residue 319 VAL 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 G residue 321 MET 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 I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 62 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 252 optimal weight: 10.0000 chunk 269 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 333 GLN D 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.130304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092407 restraints weight = 90903.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095509 restraints weight = 52015.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.097451 restraints weight = 37435.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098517 restraints weight = 30751.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099189 restraints weight = 27415.506| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24499 Z= 0.204 Angle : 0.557 6.763 33562 Z= 0.317 Chirality : 0.042 0.266 3726 Planarity : 0.004 0.052 3921 Dihedral : 17.961 170.343 4298 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.35 % Allowed : 9.48 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2636 helix: 0.97 (0.18), residues: 811 sheet: -0.92 (0.23), residues: 437 loop : -0.58 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.011 0.001 TYR E 271 PHE 0.014 0.002 PHE E 273 TRP 0.011 0.001 TRP D 33 HIS 0.015 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (24499) covalent geometry : angle 0.55657 / 0.32 (33562) hydrogen bonds : bond 0.04237 / 2.82 ( 768) hydrogen bonds : angle 4.90153 / 3.47 ( 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 238 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 1.314 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: A 79 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 288 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7294 (pp) REVERT: C 14 SER cc_start: 0.8494 (t) cc_final: 0.8092 (m) REVERT: C 331 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8409 (tptm) REVERT: E 269 THR cc_start: 0.8674 (t) cc_final: 0.8365 (p) REVERT: F 183 VAL cc_start: 0.8962 (t) cc_final: 0.8619 (m) REVERT: G 317 LYS cc_start: 0.8474 (mttt) cc_final: 0.8199 (mtmt) REVERT: G 321 MET cc_start: 0.7721 (mtp) cc_final: 0.7275 (mtp) REVERT: I 137 GLN cc_start: 0.8746 (mt0) cc_final: 0.8418 (tm-30) outliers start: 32 outliers final: 26 residues processed: 231 average time/residue: 0.3588 time to fit residues: 132.9822 Evaluate side-chains 227 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER 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 288 ILE 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 166 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR 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 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 I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR 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: 10.0000 chunk 63 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 263 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN B 250 HIS C 75 ASN C 255 ASN C 333 GLN D 255 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 310 GLN I 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.092032 restraints weight = 91451.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.092325 restraints weight = 67954.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.092811 restraints weight = 54667.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093555 restraints weight = 46977.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093762 restraints weight = 42458.307| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 24499 Z= 0.290 Angle : 0.613 7.119 33562 Z= 0.348 Chirality : 0.044 0.265 3726 Planarity : 0.004 0.063 3921 Dihedral : 17.992 171.144 4298 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.98 % Allowed : 9.52 % 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 are not related in a simple way. whole: -0.64 (0.16), residues: 2636 helix: 0.70 (0.18), residues: 805 sheet: -1.07 (0.23), residues: 424 loop : -0.84 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.016 0.002 TYR D 271 PHE 0.020 0.002 PHE G 150 TRP 0.017 0.002 TRP D 33 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.29 (24499) covalent geometry : angle 0.61330 / 0.35 (33562) hydrogen bonds : bond 0.04731 / 3.14 ( 768) hydrogen bonds : angle 5.11365 / 3.63 ( 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 256 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 209 time to evaluate : 1.025 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: B 288 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7365 (pp) REVERT: E 269 THR cc_start: 0.8569 (t) cc_final: 0.8339 (p) REVERT: F 183 VAL cc_start: 0.8918 (t) cc_final: 0.8645 (m) REVERT: G 317 LYS cc_start: 0.8384 (mttt) cc_final: 0.8172 (mtmt) REVERT: G 321 MET cc_start: 0.7404 (mtp) cc_final: 0.7182 (mtp) outliers start: 47 outliers final: 35 residues processed: 244 average time/residue: 0.2808 time to fit residues: 109.7988 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 : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR 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 288 ILE 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 181 THR Chi-restraints excluded: chain D residue 226 SER Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 252 GLN 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 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 264 ARG 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 I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 248 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN C 75 ASN C 333 GLN D 195 GLN D 255 ASN E 333 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.093319 restraints weight = 90362.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.096455 restraints weight = 51041.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098370 restraints weight = 36505.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099452 restraints weight = 29978.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.100276 restraints weight = 26666.408| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3744 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= 0.118 Angle : 0.525 6.922 33562 Z= 0.296 Chirality : 0.041 0.259 3726 Planarity : 0.003 0.057 3921 Dihedral : 17.971 171.291 4298 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.31 % Allowed : 10.28 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.16), residues: 2636 helix: 1.05 (0.18), residues: 803 sheet: -1.08 (0.23), residues: 422 loop : -0.65 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.012 0.001 TYR E 271 PHE 0.012 0.001 PHE D 231 TRP 0.009 0.001 TRP D 33 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (24499) covalent geometry : angle 0.52471 / 0.30 (33562) hydrogen bonds : bond 0.03956 / 2.62 ( 768) hydrogen bonds : angle 4.74626 / 3.37 ( 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 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.942 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: 0.8845 (OUTLIER) cc_final: 0.8562 (p) REVERT: C 141 ASN cc_start: 0.8028 (m-40) cc_final: 0.7790 (m-40) REVERT: E 269 THR cc_start: 0.8625 (t) cc_final: 0.8337 (p) REVERT: F 183 VAL cc_start: 0.8924 (t) cc_final: 0.8595 (m) REVERT: G 317 LYS cc_start: 0.8454 (mttt) cc_final: 0.8171 (mtmt) REVERT: G 321 MET cc_start: 0.7367 (mtp) cc_final: 0.6997 (mtp) REVERT: I 137 GLN cc_start: 0.8710 (mt0) cc_final: 0.8397 (tm-30) outliers start: 31 outliers final: 27 residues processed: 236 average time/residue: 0.2999 time to fit residues: 114.8636 Evaluate side-chains 229 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER 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 75 ASN 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 255 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 301 ILE Chi-restraints excluded: chain F residue 322 ILE 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 H residue 233 LEU Chi-restraints excluded: chain H residue 249 LEU Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 208 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 222 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 ASN A 144 ASN C 75 ASN C 333 GLN E 140 ASN G 50 ASN ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092676 restraints weight = 90038.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.095778 restraints weight = 51118.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.097688 restraints weight = 36680.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.098867 restraints weight = 30141.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099507 restraints weight = 26804.002| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24499 Z= 0.167 Angle : 0.530 7.104 33562 Z= 0.300 Chirality : 0.041 0.264 3726 Planarity : 0.004 0.058 3921 Dihedral : 17.940 171.469 4296 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.24 % Rotamer: Outliers : 1.26 % Allowed : 10.54 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.16), residues: 2636 helix: 1.05 (0.18), residues: 803 sheet: -1.11 (0.23), residues: 427 loop : -0.64 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 264 TYR 0.011 0.001 TYR E 271 PHE 0.014 0.001 PHE E 273 TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (24499) covalent geometry : angle 0.52986 / 0.30 (33562) hydrogen bonds : bond 0.04030 / 2.66 ( 768) hydrogen bonds : angle 4.75583 / 3.37 ( 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 232 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.787 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: A 79 SER cc_start: 0.8859 (OUTLIER) cc_final: 0.8575 (p) REVERT: C 141 ASN cc_start: 0.8061 (m-40) cc_final: 0.7829 (m-40) REVERT: E 269 THR cc_start: 0.8595 (t) cc_final: 0.8336 (p) REVERT: F 183 VAL cc_start: 0.8928 (t) cc_final: 0.8597 (m) REVERT: G 317 LYS cc_start: 0.8463 (mttt) cc_final: 0.8173 (mtmt) REVERT: G 321 MET cc_start: 0.7359 (mtp) cc_final: 0.6986 (mtp) outliers start: 30 outliers final: 28 residues processed: 226 average time/residue: 0.2784 time to fit residues: 100.9352 Evaluate side-chains 231 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER 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 230 THR 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 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 249 LEU Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.092628 restraints weight = 90677.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095724 restraints weight = 51384.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097682 restraints weight = 36843.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.098826 restraints weight = 30175.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099498 restraints weight = 26842.837| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 24499 Z= 0.206 Angle : 0.667 59.142 33562 Z= 0.396 Chirality : 0.042 0.264 3726 Planarity : 0.004 0.058 3921 Dihedral : 17.939 171.470 4296 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.22 % Allowed : 10.66 % Favored : 88.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2636 helix: 1.04 (0.18), residues: 803 sheet: -1.12 (0.23), residues: 427 loop : -0.64 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 264 TYR 0.011 0.001 TYR E 271 PHE 0.014 0.001 PHE E 273 TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (24499) covalent geometry : angle 0.66743 / 0.40 (33562) hydrogen bonds : bond 0.04030 / 2.65 ( 768) hydrogen bonds : angle 4.75563 / 3.37 ( 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 231 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.768 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: A 79 SER cc_start: 0.8860 (OUTLIER) cc_final: 0.8576 (p) REVERT: C 141 ASN cc_start: 0.8061 (m-40) cc_final: 0.7833 (m-40) REVERT: E 269 THR cc_start: 0.8597 (t) cc_final: 0.8340 (p) REVERT: F 183 VAL cc_start: 0.8928 (t) cc_final: 0.8597 (m) REVERT: G 317 LYS cc_start: 0.8465 (mttt) cc_final: 0.8173 (mtmt) REVERT: G 321 MET cc_start: 0.7365 (mtp) cc_final: 0.6985 (mtp) outliers start: 29 outliers final: 27 residues processed: 225 average time/residue: 0.3193 time to fit residues: 114.7949 Evaluate side-chains 229 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 SER 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 230 THR 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 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 249 LEU Chi-restraints excluded: chain I residue 83 TYR 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: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 125 optimal weight: 0.0980 chunk 206 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 216 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.092628 restraints weight = 90516.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.095740 restraints weight = 51357.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.097666 restraints weight = 36744.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098801 restraints weight = 30216.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.099550 restraints weight = 26839.751| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.261 24499 Z= 0.206 Angle : 0.667 59.198 33562 Z= 0.396 Chirality : 0.042 0.264 3726 Planarity : 0.004 0.058 3921 Dihedral : 17.939 171.470 4296 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.21 % Rotamer: Outliers : 1.18 % Allowed : 10.70 % Favored : 88.12 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.16), residues: 2636 helix: 1.04 (0.18), residues: 803 sheet: -1.12 (0.23), residues: 427 loop : -0.64 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 264 TYR 0.011 0.001 TYR E 271 PHE 0.014 0.001 PHE E 273 TRP 0.010 0.001 TRP D 33 HIS 0.003 0.001 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.21 (24499) covalent geometry : angle 0.66749 / 0.40 (33562) hydrogen bonds : bond 0.04030 / 2.65 ( 768) hydrogen bonds : angle 4.75562 / 3.37 ( 1984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6428.13 seconds wall clock time: 110 minutes 43.83 seconds (6643.83 seconds total)