Starting phenix.real_space_refine on Thu Dec 26 15:38:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_43729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_43729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_43729.map" model { file = "/net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_43729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w1p_43729/12_2024/8w1p_43729.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 21.63, per 1000 atoms: 0.47 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: 12.14 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 21.19 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: 21.35 Time building geometry restraints manager: 14.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22549 1.02 - 1.22: 54 1.22 - 1.42: 10253 1.42 - 1.62: 14053 1.62 - 1.82: 186 Bond restraints: 47095 Sorted by residual: bond pdb=" CA PHE B 131 " pdb=" C PHE B 131 " ideal model delta sigma weight residual 1.522 1.591 -0.069 1.72e-02 3.38e+03 1.61e+01 bond pdb=" C1' DT T 16 " pdb=" N1 DT T 16 " ideal model delta sigma weight residual 1.490 1.556 -0.066 3.00e-02 1.11e+03 4.87e+00 bond pdb=" C3' U R 54 " pdb=" C2' U R 54 " ideal model delta sigma weight residual 1.525 1.557 -0.032 1.50e-02 4.44e+03 4.45e+00 bond pdb=" CB ILE B 322 " pdb=" CG2 ILE B 322 " ideal model delta sigma weight residual 1.521 1.588 -0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB ILE D 118 " pdb=" CG2 ILE D 118 " ideal model delta sigma weight residual 1.521 1.588 -0.067 3.30e-02 9.18e+02 4.11e+00 ... (remaining 47090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 80330 1.82 - 3.64: 4247 3.64 - 5.47: 531 5.47 - 7.29: 30 7.29 - 9.11: 3 Bond angle restraints: 85141 Sorted by residual: angle pdb=" C4' DA T 23 " pdb=" C3' DA T 23 " pdb=" O3' DA T 23 " ideal model delta sigma weight residual 110.00 116.93 -6.93 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C4' U R 1 " pdb=" C3' U R 1 " pdb=" O3' U R 1 " ideal model delta sigma weight residual 109.40 115.97 -6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" C3' U R 1 " pdb=" O3' U R 1 " pdb=" P U R 2 " ideal model delta sigma weight residual 120.20 126.39 -6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" C3' DA T 23 " pdb=" O3' DA T 23 " pdb=" P DT T 24 " ideal model delta sigma weight residual 120.20 126.14 -5.94 1.50e+00 4.44e-01 1.57e+01 angle pdb=" O4' U R 19 " pdb=" C1' U R 19 " pdb=" N1 U R 19 " ideal model delta sigma weight residual 108.20 114.01 -5.81 1.50e+00 4.44e-01 1.50e+01 ... (remaining 85136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 21168 35.89 - 71.78: 828 71.78 - 107.67: 52 107.67 - 143.56: 10 143.56 - 179.45: 4 Dihedral angle restraints: 22062 sinusoidal: 12708 harmonic: 9354 Sorted by residual: dihedral pdb=" C5' U R 54 " pdb=" C4' U R 54 " pdb=" C3' U R 54 " pdb=" O3' U R 54 " ideal model delta sinusoidal sigma weight residual 147.00 92.31 54.69 1 8.00e+00 1.56e-02 6.33e+01 dihedral pdb=" O4' A R 38 " pdb=" C2' A R 38 " pdb=" C1' A R 38 " pdb=" C3' A R 38 " ideal model delta sinusoidal sigma weight residual -35.00 18.15 -53.15 1 8.00e+00 1.56e-02 6.00e+01 dihedral pdb=" C4' A R 38 " pdb=" C3' A R 38 " pdb=" C2' A R 38 " pdb=" C1' A R 38 " ideal model delta sinusoidal sigma weight residual -35.00 17.78 -52.78 1 8.00e+00 1.56e-02 5.93e+01 ... (remaining 22059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3037 0.064 - 0.127: 567 0.127 - 0.191: 112 0.191 - 0.254: 6 0.254 - 0.318: 4 Chirality restraints: 3726 Sorted by residual: chirality pdb=" C3' A R 38 " pdb=" C4' A R 38 " pdb=" O3' A R 38 " pdb=" C2' A R 38 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" C3' G R 33 " pdb=" C4' G R 33 " pdb=" O3' G R 33 " pdb=" C2' G R 33 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C3' U R 44 " pdb=" C4' U R 44 " pdb=" O3' U R 44 " pdb=" C2' U R 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 3723 not shown) Planarity restraints: 6534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 291 " 0.517 9.50e-02 1.11e+02 1.73e-01 3.30e+01 pdb=" NE ARG B 291 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 291 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 291 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG B 291 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG B 291 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 291 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG B 291 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG B 291 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 150 " 0.332 9.50e-02 1.11e+02 1.13e-01 2.21e+01 pdb=" NE ARG E 150 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG E 150 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG E 150 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 150 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG E 150 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG E 150 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG E 150 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 150 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 115 " 0.175 9.50e-02 1.11e+02 6.36e-02 1.82e+01 pdb=" NE ARG F 115 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 115 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 115 " 0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG F 115 " -0.044 2.00e-02 2.50e+03 pdb="HH11 ARG F 115 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 115 " -0.033 2.00e-02 2.50e+03 pdb="HH21 ARG F 115 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 115 " 0.046 2.00e-02 2.50e+03 ... (remaining 6531 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4829 2.26 - 2.84: 101921 2.84 - 3.43: 118632 3.43 - 4.01: 168246 4.01 - 4.60: 260113 Nonbonded interactions: 653741 Sorted by model distance: nonbonded pdb=" HH TYR I 143 " pdb=" OP1 U R 44 " model vdw 1.669 2.450 nonbonded pdb=" H ILE F 97 " pdb=" O ILE F 209 " model vdw 1.676 2.450 nonbonded pdb=" HG1 THR I 42 " pdb=" O VAL I 97 " model vdw 1.694 2.450 nonbonded pdb=" H ILE E 97 " pdb=" O ILE E 209 " model vdw 1.702 2.450 nonbonded pdb=" H ILE B 97 " pdb=" O ILE B 209 " model vdw 1.703 2.450 ... (remaining 653736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'B' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'C' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'D' and (resid 12 through 52 or resid 79 through 332)) selection = (chain 'E' and (resid 12 through 52 or resid 79 through 332)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.710 Extract box with map and model: 1.630 Check model and map are aligned: 0.340 Set scattering table: 0.390 Process input model: 109.490 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24499 Z= 0.419 Angle : 0.936 6.930 33562 Z= 0.539 Chirality : 0.053 0.318 3726 Planarity : 0.009 0.223 3921 Dihedral : 16.666 179.449 9731 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.29 % Allowed : 2.44 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (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 TRP 0.021 0.003 TRP D 33 HIS 0.016 0.002 HIS H 215 PHE 0.031 0.003 PHE A 200 TYR 0.018 0.004 TYR G 140 ARG 0.021 0.003 ARG D 204 *********************** 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 : 3.509 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: A 112 TYR cc_start: 0.7012 (t80) cc_final: 0.6763 (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: 0.6073 (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: 0.7852 (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: 0.8341 (ttp) REVERT: E 78 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7827 (mttp) REVERT: E 169 TYR cc_start: 0.8174 (m-80) cc_final: 0.7338 (m-80) REVERT: E 269 THR cc_start: 0.8914 (t) cc_final: 0.8697 (p) REVERT: E 320 MET cc_start: 0.8013 (mmt) cc_final: 0.7686 (mmp) REVERT: F 40 ARG cc_start: 0.8400 (ptt-90) cc_final: 0.8111 (ptt90) REVERT: F 183 VAL cc_start: 0.8837 (t) cc_final: 0.8330 (m) REVERT: F 320 MET cc_start: 0.6856 (mmt) cc_final: 0.6213 (mmt) REVERT: G 94 MET cc_start: 0.6350 (mtt) cc_final: 0.6027 (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: 0.7784 (t80) REVERT: H 158 TYR cc_start: 0.7999 (m-80) cc_final: 0.7715 (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: 0.5137 (mm-40) outliers start: 7 outliers final: 0 residues processed: 470 average time/residue: 0.9727 time to fit residues: 695.7490 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 : 4.028 ------------------------------------------------------------------------------- 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 230 optimal weight: 0.0670 chunk 206 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 252 GLN A 256 ASN A 317 HIS B 75 ASN B 77 GLN B 195 GLN C 75 ASN C 250 HIS C 252 GLN C 256 ASN D 256 ASN D 317 HIS D 333 GLN E 250 HIS E 317 HIS F 317 HIS H 17 ASN H 20 ASN I 76 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 24499 Z= 0.306 Angle : 0.645 6.221 33562 Z= 0.361 Chirality : 0.044 0.252 3726 Planarity : 0.004 0.045 3921 Dihedral : 18.158 171.841 4298 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.18 % Allowed : 7.59 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2636 helix: 0.57 (0.17), residues: 801 sheet: -0.20 (0.24), residues: 425 loop : -0.37 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.010 0.001 HIS B 250 PHE 0.023 0.002 PHE E 273 TYR 0.018 0.002 TYR E 206 ARG 0.007 0.001 ARG G 329 *********************** 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 284 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 3.902 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: 0.8396 (OUTLIER) cc_final: 0.8170 (p) REVERT: A 174 SER cc_start: 0.9444 (p) cc_final: 0.9159 (t) REVERT: B 78 LYS cc_start: 0.6421 (mttt) cc_final: 0.6101 (tppt) REVERT: B 224 TYR cc_start: 0.8797 (m-80) cc_final: 0.8318 (m-80) REVERT: B 288 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.6979 (pp) REVERT: B 315 ASP cc_start: 0.8330 (m-30) cc_final: 0.7991 (t0) REVERT: C 331 LYS cc_start: 0.8978 (mmtt) cc_final: 0.8686 (tptm) REVERT: E 29 GLU cc_start: 0.8658 (mp0) cc_final: 0.8367 (mp0) REVERT: E 78 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7856 (mttp) REVERT: E 269 THR cc_start: 0.8918 (t) cc_final: 0.8600 (p) REVERT: F 183 VAL cc_start: 0.8969 (t) cc_final: 0.8489 (m) REVERT: G 282 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7994 (mp0) REVERT: G 321 MET cc_start: 0.7606 (mtp) cc_final: 0.7282 (mtp) REVERT: H 51 ARG cc_start: 0.7056 (mtp-110) cc_final: 0.6639 (ttm170) REVERT: H 140 ARG cc_start: 0.8474 (ttp80) cc_final: 0.7743 (ttt180) outliers start: 28 outliers final: 21 residues processed: 277 average time/residue: 0.9303 time to fit residues: 404.6356 Evaluate side-chains 235 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 3.806 ------------------------------------------------------------------------------- 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 252 GLN Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain 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 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 196 THR Chi-restraints excluded: chain G residue 324 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 268 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 333 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 24499 Z= 0.435 Angle : 0.655 9.108 33562 Z= 0.366 Chirality : 0.045 0.281 3726 Planarity : 0.004 0.056 3921 Dihedral : 18.098 169.065 4298 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.73 % Allowed : 8.93 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2636 helix: 0.54 (0.18), residues: 808 sheet: -0.52 (0.23), residues: 446 loop : -0.60 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 33 HIS 0.007 0.001 HIS B 250 PHE 0.016 0.002 PHE F 43 TYR 0.016 0.002 TYR E 206 ARG 0.006 0.001 ARG B 291 *********************** 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 263 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 4.132 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 174 SER cc_start: 0.9453 (p) cc_final: 0.9190 (t) REVERT: B 288 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7278 (pp) REVERT: C 14 SER cc_start: 0.8788 (t) cc_final: 0.8367 (m) REVERT: C 331 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8593 (tptm) REVERT: E 78 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7785 (mttp) REVERT: E 169 TYR cc_start: 0.8272 (m-80) cc_final: 0.8069 (m-80) REVERT: E 269 THR cc_start: 0.8918 (t) cc_final: 0.8604 (p) REVERT: F 183 VAL cc_start: 0.8974 (t) cc_final: 0.8516 (m) REVERT: G 263 LYS cc_start: 0.7453 (mttt) cc_final: 0.7239 (mttm) REVERT: G 282 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7965 (mp0) REVERT: G 310 GLN cc_start: 0.7127 (mm-40) cc_final: 0.6668 (mm-40) REVERT: G 321 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7070 (mtp) REVERT: H 140 ARG cc_start: 0.8560 (ttp80) cc_final: 0.7858 (ttt180) REVERT: I 1 MET cc_start: 0.7957 (tpp) cc_final: 0.7649 (tpp) REVERT: I 136 GLN cc_start: 0.8486 (mt0) cc_final: 0.8014 (tm-30) outliers start: 41 outliers final: 34 residues processed: 254 average time/residue: 0.8797 time to fit residues: 355.7002 Evaluate side-chains 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 75 ASN 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 150 ARG 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 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 99 VAL 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 26 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 83 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 0.0570 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN F 250 HIS G 143 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24499 Z= 0.236 Angle : 0.558 5.623 33562 Z= 0.310 Chirality : 0.041 0.226 3726 Planarity : 0.004 0.061 3921 Dihedral : 17.984 169.809 4298 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.47 % Allowed : 9.52 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2636 helix: 0.85 (0.18), residues: 809 sheet: -0.70 (0.23), residues: 417 loop : -0.52 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.005 0.001 HIS B 250 PHE 0.014 0.001 PHE E 273 TYR 0.012 0.001 TYR E 271 ARG 0.003 0.000 ARG G 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 3.899 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: A 174 SER cc_start: 0.9422 (p) cc_final: 0.9179 (t) REVERT: B 288 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7297 (pp) REVERT: C 14 SER cc_start: 0.8732 (t) cc_final: 0.8267 (m) REVERT: C 331 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8583 (tptm) REVERT: E 78 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7767 (mttp) REVERT: E 224 TYR cc_start: 0.9322 (m-80) cc_final: 0.9083 (m-80) REVERT: E 269 THR cc_start: 0.8900 (t) cc_final: 0.8521 (p) REVERT: F 183 VAL cc_start: 0.8917 (t) cc_final: 0.8473 (m) REVERT: G 282 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8020 (mp0) REVERT: G 310 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6617 (mm-40) REVERT: G 317 LYS cc_start: 0.8450 (mttt) cc_final: 0.8133 (mtmt) REVERT: G 321 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7107 (mtp) REVERT: H 140 ARG cc_start: 0.8567 (ttp80) cc_final: 0.7957 (ttt180) REVERT: I 136 GLN cc_start: 0.8462 (mt0) cc_final: 0.8249 (mt0) REVERT: I 137 GLN cc_start: 0.8778 (mt0) cc_final: 0.8391 (tm-30) outliers start: 35 outliers final: 28 residues processed: 250 average time/residue: 0.8104 time to fit residues: 324.7880 Evaluate side-chains 235 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 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 62 MET Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 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 I residue 83 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS C 75 ASN C 255 ASN C 333 GLN I 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24499 Z= 0.289 Angle : 0.561 6.398 33562 Z= 0.310 Chirality : 0.042 0.223 3726 Planarity : 0.004 0.055 3921 Dihedral : 17.909 171.005 4298 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.06 % Allowed : 9.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2636 helix: 0.94 (0.18), residues: 811 sheet: -0.86 (0.23), residues: 427 loop : -0.59 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 33 HIS 0.005 0.001 HIS B 250 PHE 0.018 0.001 PHE E 273 TYR 0.019 0.001 TYR E 271 ARG 0.004 0.000 ARG C 259 *********************** 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 267 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 3.610 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 174 SER cc_start: 0.9423 (p) cc_final: 0.9198 (t) REVERT: B 288 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7448 (pp) REVERT: C 14 SER cc_start: 0.8771 (t) cc_final: 0.8293 (p) REVERT: E 78 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7835 (mttp) REVERT: E 269 THR cc_start: 0.8894 (t) cc_final: 0.8542 (p) REVERT: F 183 VAL cc_start: 0.8920 (t) cc_final: 0.8543 (m) REVERT: F 290 PHE cc_start: 0.8680 (m-80) cc_final: 0.8439 (m-80) REVERT: G 310 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6501 (mm-40) REVERT: G 317 LYS cc_start: 0.8458 (mttt) cc_final: 0.8128 (mtmt) REVERT: G 321 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7024 (mtp) REVERT: H 140 ARG cc_start: 0.8574 (ttp80) cc_final: 0.7981 (ttt180) REVERT: I 1 MET cc_start: 0.7957 (tpp) cc_final: 0.7584 (tpp) outliers start: 49 outliers final: 37 residues processed: 256 average time/residue: 0.8549 time to fit residues: 349.1084 Evaluate side-chains 243 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 3.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 288 ILE 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 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 62 MET 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 150 ARG Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 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 Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN C 333 GLN D 255 ASN E 333 GLN I 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3724 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= 0.251 Angle : 0.539 5.234 33562 Z= 0.298 Chirality : 0.041 0.220 3726 Planarity : 0.004 0.062 3921 Dihedral : 17.885 170.709 4298 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.81 % Allowed : 9.86 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2636 helix: 1.07 (0.18), residues: 804 sheet: -0.95 (0.23), residues: 427 loop : -0.58 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.004 0.001 HIS B 250 PHE 0.014 0.001 PHE E 273 TYR 0.014 0.001 TYR G 291 ARG 0.004 0.000 ARG E 150 *********************** 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 256 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 3.688 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 174 SER cc_start: 0.9419 (p) cc_final: 0.9185 (t) REVERT: C 14 SER cc_start: 0.8786 (t) cc_final: 0.8306 (p) REVERT: E 78 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7769 (mttt) REVERT: E 269 THR cc_start: 0.8866 (t) cc_final: 0.8519 (p) REVERT: F 183 VAL cc_start: 0.8907 (t) cc_final: 0.8534 (m) REVERT: F 290 PHE cc_start: 0.8669 (m-80) cc_final: 0.8414 (m-80) REVERT: G 310 GLN cc_start: 0.7063 (mm-40) cc_final: 0.6585 (mm-40) REVERT: G 317 LYS cc_start: 0.8449 (mttt) cc_final: 0.8109 (mtmt) REVERT: G 321 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6815 (mtp) REVERT: H 140 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8001 (ttt180) REVERT: I 1 MET cc_start: 0.7972 (tpp) cc_final: 0.7705 (tpp) outliers start: 43 outliers final: 36 residues processed: 245 average time/residue: 0.8505 time to fit residues: 330.4634 Evaluate side-chains 245 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 263 LYS 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 I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 121 optimal weight: 0.0270 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN I 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24499 Z= 0.248 Angle : 0.531 5.645 33562 Z= 0.293 Chirality : 0.041 0.220 3726 Planarity : 0.003 0.054 3921 Dihedral : 17.838 170.494 4296 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.69 % Allowed : 10.28 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2636 helix: 1.16 (0.18), residues: 804 sheet: -0.98 (0.23), residues: 427 loop : -0.60 (0.17), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.004 0.001 HIS B 250 PHE 0.014 0.001 PHE E 273 TYR 0.011 0.001 TYR E 271 ARG 0.002 0.000 ARG C 259 *********************** 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 251 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 3.907 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: A 174 SER cc_start: 0.9419 (p) cc_final: 0.9191 (t) REVERT: C 14 SER cc_start: 0.8796 (t) cc_final: 0.8320 (p) REVERT: E 78 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7756 (mttt) REVERT: E 269 THR cc_start: 0.8853 (t) cc_final: 0.8512 (p) REVERT: F 183 VAL cc_start: 0.8894 (t) cc_final: 0.8532 (m) REVERT: G 317 LYS cc_start: 0.8459 (mttt) cc_final: 0.8105 (mtmt) REVERT: G 321 MET cc_start: 0.7283 (mtp) cc_final: 0.6816 (mtp) REVERT: H 140 ARG cc_start: 0.8587 (ttp80) cc_final: 0.7995 (ttt180) outliers start: 40 outliers final: 33 residues processed: 240 average time/residue: 0.8260 time to fit residues: 315.4329 Evaluate side-chains 235 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 263 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 79 optimal weight: 0.0670 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN D 252 GLN G 310 GLN I 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24499 Z= 0.250 Angle : 0.526 6.006 33562 Z= 0.290 Chirality : 0.041 0.217 3726 Planarity : 0.003 0.054 3921 Dihedral : 17.809 170.975 4296 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.69 % Allowed : 10.58 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2636 helix: 1.20 (0.18), residues: 816 sheet: -0.97 (0.23), residues: 428 loop : -0.64 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 33 HIS 0.004 0.001 HIS G 105 PHE 0.013 0.001 PHE E 273 TYR 0.016 0.001 TYR F 265 ARG 0.003 0.000 ARG C 150 *********************** 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 258 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 3.485 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 174 SER cc_start: 0.9421 (p) cc_final: 0.9197 (t) REVERT: D 72 MET cc_start: 0.6891 (mmm) cc_final: 0.6456 (mtm) REVERT: D 157 ILE cc_start: 0.8959 (mt) cc_final: 0.8753 (mm) REVERT: E 78 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7767 (mttt) REVERT: E 269 THR cc_start: 0.8962 (t) cc_final: 0.8600 (p) REVERT: F 183 VAL cc_start: 0.8887 (t) cc_final: 0.8527 (m) REVERT: G 310 GLN cc_start: 0.7696 (mm110) cc_final: 0.7314 (mm-40) REVERT: G 317 LYS cc_start: 0.8450 (mttt) cc_final: 0.8121 (mtmt) REVERT: G 321 MET cc_start: 0.7290 (mtp) cc_final: 0.6839 (mtp) REVERT: H 140 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8101 (ttt180) outliers start: 40 outliers final: 38 residues processed: 249 average time/residue: 0.8281 time to fit residues: 328.8134 Evaluate side-chains 245 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 109 CYS 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 144 GLN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 263 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.1980 chunk 252 optimal weight: 8.9990 chunk 229 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN B 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24499 Z= 0.190 Angle : 0.501 6.050 33562 Z= 0.275 Chirality : 0.040 0.211 3726 Planarity : 0.003 0.054 3921 Dihedral : 17.765 170.756 4296 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.60 % Allowed : 10.66 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2636 helix: 1.31 (0.18), residues: 822 sheet: -0.99 (0.23), residues: 449 loop : -0.56 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 33 HIS 0.004 0.001 HIS B 250 PHE 0.013 0.001 PHE E 273 TYR 0.010 0.001 TYR H 142 ARG 0.003 0.000 ARG B 150 *********************** 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 267 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 3.669 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 174 SER cc_start: 0.9402 (p) cc_final: 0.9190 (t) REVERT: C 140 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.7602 (m110) REVERT: D 157 ILE cc_start: 0.8955 (mt) cc_final: 0.8741 (mm) REVERT: E 78 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7786 (mttt) REVERT: E 232 ASP cc_start: 0.8089 (t0) cc_final: 0.7796 (t0) REVERT: E 269 THR cc_start: 0.8945 (t) cc_final: 0.8586 (p) REVERT: F 183 VAL cc_start: 0.8861 (t) cc_final: 0.8506 (m) REVERT: G 39 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8756 (m) REVERT: G 317 LYS cc_start: 0.8422 (mttt) cc_final: 0.8088 (mtmt) REVERT: G 321 MET cc_start: 0.7224 (mtp) cc_final: 0.6826 (mtp) REVERT: H 140 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8117 (ttt180) outliers start: 38 outliers final: 32 residues processed: 257 average time/residue: 0.7597 time to fit residues: 311.9827 Evaluate side-chains 247 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 3.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 181 THR 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 C residue 140 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 118 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 144 GLN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 263 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 3.9990 chunk 259 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 216 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24499 Z= 0.363 Angle : 0.564 5.629 33562 Z= 0.311 Chirality : 0.042 0.215 3726 Planarity : 0.004 0.059 3921 Dihedral : 17.734 171.406 4296 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.60 % Allowed : 10.83 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2636 helix: 1.13 (0.18), residues: 816 sheet: -1.08 (0.24), residues: 437 loop : -0.71 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 33 HIS 0.006 0.001 HIS D 250 PHE 0.019 0.002 PHE G 338 TYR 0.012 0.002 TYR E 271 ARG 0.004 0.001 ARG C 259 ********************** 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 255 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8322 (ttmm) REVERT: A 174 SER cc_start: 0.9434 (p) cc_final: 0.9208 (t) REVERT: C 140 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.7734 (m110) REVERT: D 157 ILE cc_start: 0.9001 (mt) cc_final: 0.8781 (mm) REVERT: E 78 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7788 (mttt) REVERT: E 269 THR cc_start: 0.8956 (t) cc_final: 0.8629 (p) REVERT: F 224 TYR cc_start: 0.8826 (m-80) cc_final: 0.8603 (m-80) REVERT: G 4 LYS cc_start: 0.8519 (mttt) cc_final: 0.8042 (mtmt) REVERT: G 39 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8786 (m) REVERT: G 317 LYS cc_start: 0.8478 (mttt) cc_final: 0.8163 (mtmt) REVERT: G 321 MET cc_start: 0.7244 (mtp) cc_final: 0.6799 (mtp) REVERT: H 140 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8085 (ttt180) outliers start: 38 outliers final: 33 residues processed: 247 average time/residue: 0.7999 time to fit residues: 316.4921 Evaluate side-chains 249 residues out of total 2373 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 3.587 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 181 THR 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 C residue 140 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 118 ILE Chi-restraints excluded: chain D residue 150 ARG Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 322 ILE Chi-restraints excluded: chain G residue 24 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 263 LYS Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 219 GLU Chi-restraints excluded: chain I residue 83 TYR Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.0670 chunk 230 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 222 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.090808 restraints weight = 92490.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095048 restraints weight = 40452.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097668 restraints weight = 25487.909| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 24499 Z= 0.152 Angle : 0.492 5.967 33562 Z= 0.269 Chirality : 0.040 0.204 3726 Planarity : 0.003 0.055 3921 Dihedral : 17.689 171.258 4296 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 1.31 % Allowed : 11.08 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2636 helix: 1.38 (0.18), residues: 822 sheet: -1.05 (0.24), residues: 439 loop : -0.55 (0.17), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 33 HIS 0.003 0.001 HIS G 105 PHE 0.013 0.001 PHE E 273 TYR 0.016 0.001 TYR E 224 ARG 0.004 0.000 ARG E 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9252.20 seconds wall clock time: 165 minutes 46.35 seconds (9946.35 seconds total)