Starting phenix.real_space_refine on Fri Aug 7 09:35:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh9_39285/08_2026/8yh9_39285.map" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.066 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: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 103 5.16 5 C 13307 2.51 5 N 3539 2.21 5 O 4145 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21153 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 8, 'rna3p_pur': 21, 'rna3p_pyr': 14} Link IDs: {'rna2p': 23, 'rna3p': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2467 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2423 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "G" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2461 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2447 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "E" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2397 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2393 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Chain: "J" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 4.18, per 1000 atoms: 0.20 Number of scatterers: 21153 At special positions: 0 Unit cell: (119, 153, 153.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 59 15.00 O 4145 8.00 N 3539 7.00 C 13307 6.00 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: 1.35 Conformation dependent library (CDL) restraints added in 756.9 milliseconds 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4666 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 32 sheets defined 28.4% alpha, 16.3% beta 5 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 28 through 46 removed outlier: 4.166A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 removed outlier: 4.116A pdb=" N GLU A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 4.134A pdb=" N ILE A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N HIS A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 Processing helix chain 'B' and resid 24 through 35 removed outlier: 4.743A pdb=" N SER B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 72 removed outlier: 3.732A pdb=" N LEU B 68 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.693A pdb=" N HIS B 76 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 72 through 77' Processing helix chain 'B' and resid 111 through 118 Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.796A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 129 Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.736A pdb=" N ALA I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG I 137 " --> pdb=" O THR I 133 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 177 removed outlier: 3.668A pdb=" N PHE I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 202 removed outlier: 3.994A pdb=" N THR I 199 " --> pdb=" O GLN I 195 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.847A pdb=" N ALA I 257 " --> pdb=" O LYS I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 271 Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'I' and resid 312 through 326 Processing helix chain 'H' and resid 111 through 127 Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.677A pdb=" N LYS H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG H 137 " --> pdb=" O THR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 177 removed outlier: 3.661A pdb=" N PHE H 177 " --> pdb=" O SER H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 200 Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.617A pdb=" N ILE H 254 " --> pdb=" O HIS H 250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU H 258 " --> pdb=" O ILE H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.895A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 303 removed outlier: 3.601A pdb=" N ASP H 302 " --> pdb=" O LYS H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 326 Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.689A pdb=" N GLN G 120 " --> pdb=" O THR G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.536A pdb=" N ALA G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.739A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 153 removed outlier: 3.866A pdb=" N LEU G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 201 removed outlier: 3.720A pdb=" N GLN G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE G 200 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.558A pdb=" N ILE G 254 " --> pdb=" O HIS G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 4.018A pdb=" N VAL G 319 " --> pdb=" O ASP G 315 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET G 320 " --> pdb=" O LYS G 316 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG G 325 " --> pdb=" O ALA G 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 4.370A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 116 " --> pdb=" O TYR F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.526A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.536A pdb=" N GLY F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 259 removed outlier: 4.038A pdb=" N ILE F 254 " --> pdb=" O HIS F 250 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 256 " --> pdb=" O GLN F 252 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 272 removed outlier: 3.813A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 305 removed outlier: 3.757A pdb=" N ARG F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 148 through 153 Processing helix chain 'E' and resid 187 through 201 Processing helix chain 'E' and resid 251 through 256 Processing helix chain 'E' and resid 267 through 272 Processing helix chain 'E' and resid 296 through 303 Processing helix chain 'E' and resid 313 through 326 removed outlier: 4.050A pdb=" N TYR E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 323 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 324 " --> pdb=" O MET E 320 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.638A pdb=" N MET D 106 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.614A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 148 through 152 Processing helix chain 'D' and resid 188 through 202 removed outlier: 4.341A pdb=" N GLN D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.680A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.915A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'J' and resid 166 through 179 removed outlier: 3.837A pdb=" N SER J 174 " --> pdb=" O ASN J 170 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP J 175 " --> pdb=" O TYR J 171 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG J 179 " --> pdb=" O ASP J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 199 removed outlier: 3.662A pdb=" N ALA J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 206 removed outlier: 3.580A pdb=" N ASN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 229 Processing helix chain 'J' and resid 255 through 264 Processing helix chain 'J' and resid 283 through 291 Processing helix chain 'J' and resid 324 through 339 removed outlier: 3.895A pdb=" N GLU J 333 " --> pdb=" O GLU J 329 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA J 336 " --> pdb=" O THR J 332 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR J 338 " --> pdb=" O ALA J 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 4.106A pdb=" N GLY A 54 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 113 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 52 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLU A 219 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE A 196 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 221 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 removed outlier: 4.123A pdb=" N LYS A 10 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET A 106 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 104 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU A 14 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE A 102 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 54 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 113 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A 52 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N SER A 220 " --> pdb=" O LEU J 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.357A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.864A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 102 removed outlier: 4.010A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 158 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 106 through 109 removed outlier: 3.678A pdb=" N SER I 108 " --> pdb=" O SER I 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 25 through 27 removed outlier: 3.507A pdb=" N THR I 35 " --> pdb=" O THR I 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 94 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS I 31 " --> pdb=" O ASP I 94 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 30 through 35 current: chain 'I' and resid 161 through 164 Processing sheet with id=AB2, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.669A pdb=" N LYS I 31 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 94 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR I 35 " --> pdb=" O THR I 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 50 through 53 removed outlier: 3.975A pdb=" N SER I 79 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 25 through 27 removed outlier: 3.713A pdb=" N ARG H 92 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP H 94 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 31 " --> pdb=" O ASP H 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 25 through 27 Processing sheet with id=AB6, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AB7, first strand: chain 'G' and resid 25 through 27 Processing sheet with id=AB8, first strand: chain 'G' and resid 45 through 46 removed outlier: 3.590A pdb=" N LYS G 31 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP G 94 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE G 95 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL G 211 " --> pdb=" O PHE G 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 50 through 55 Processing sheet with id=AC1, first strand: chain 'G' and resid 163 through 164 removed outlier: 3.642A pdb=" N ILE G 164 " --> pdb=" O LYS G 167 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 21 removed outlier: 4.082A pdb=" N GLY F 327 " --> pdb=" O PHE F 21 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.549A pdb=" N LYS F 31 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE F 164 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 45 through 46 removed outlier: 5.527A pdb=" N ALA F 247 " --> pdb=" O PHE F 32 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.518A pdb=" N LYS F 52 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER F 79 " --> pdb=" O LYS F 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.568A pdb=" N MET E 249 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA E 247 " --> pdb=" O PHE E 32 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AD1, first strand: chain 'D' and resid 25 through 27 removed outlier: 3.699A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 30 through 35 current: chain 'D' and resid 158 through 163 Processing sheet with id=AD2, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.699A pdb=" N ASP D 94 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AD4, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AD5, first strand: chain 'J' and resid 185 through 186 599 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5369 1.33 - 1.45: 4403 1.45 - 1.57: 11687 1.57 - 1.69: 118 1.69 - 1.81: 159 Bond restraints: 21736 Sorted by residual: bond pdb=" CB TYR F 125 " pdb=" CG TYR F 125 " ideal model delta sigma weight residual 1.512 1.560 -0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" N ASP I 310 " pdb=" CA ASP I 310 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.60e+00 bond pdb=" N1 C C 47 " pdb=" C2 C C 47 " ideal model delta sigma weight residual 1.397 1.415 -0.018 1.00e-02 1.00e+04 3.38e+00 bond pdb=" CG1 ILE E 93 " pdb=" CD1 ILE E 93 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.90e+00 bond pdb=" C ARG B 125 " pdb=" N PRO B 126 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.80e+00 ... (remaining 21731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 28611 1.99 - 3.98: 906 3.98 - 5.98: 96 5.98 - 7.97: 16 7.97 - 9.96: 10 Bond angle restraints: 29639 Sorted by residual: angle pdb=" N1 U C 44 " pdb=" C2 U C 44 " pdb=" O2 U C 44 " ideal model delta sigma weight residual 122.80 125.75 -2.95 7.00e-01 2.04e+00 1.77e+01 angle pdb=" O5' U C 2 " pdb=" C5' U C 2 " pdb=" C4' U C 2 " ideal model delta sigma weight residual 109.40 112.63 -3.23 8.00e-01 1.56e+00 1.63e+01 angle pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sigma weight residual 117.70 122.54 -4.84 1.20e+00 6.94e-01 1.63e+01 angle pdb=" O2 U C 44 " pdb=" C2 U C 44 " pdb=" N3 U C 44 " ideal model delta sigma weight residual 122.20 119.43 2.77 7.00e-01 2.04e+00 1.56e+01 angle pdb=" O5' U C 19 " pdb=" C5' U C 19 " pdb=" C4' U C 19 " ideal model delta sigma weight residual 109.40 112.54 -3.14 8.00e-01 1.56e+00 1.54e+01 ... (remaining 29634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 12342 35.97 - 71.94: 781 71.94 - 107.92: 50 107.92 - 143.89: 0 143.89 - 179.86: 2 Dihedral angle restraints: 13175 sinusoidal: 5951 harmonic: 7224 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual -128.00 51.86 -179.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U C 44 " pdb=" C1' U C 44 " pdb=" N1 U C 44 " pdb=" C2 U C 44 " ideal model delta sinusoidal sigma weight residual 232.00 54.13 177.87 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -160.00 -84.86 -75.14 1 1.50e+01 4.44e-03 3.17e+01 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2507 0.056 - 0.112: 628 0.112 - 0.167: 159 0.167 - 0.223: 6 0.223 - 0.279: 3 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CB ILE E 93 " pdb=" CA ILE E 93 " pdb=" CG1 ILE E 93 " pdb=" CG2 ILE E 93 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB ILE I 93 " pdb=" CA ILE I 93 " pdb=" CG1 ILE I 93 " pdb=" CG2 ILE I 93 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE E 97 " pdb=" CA ILE E 97 " pdb=" CG1 ILE E 97 " pdb=" CG2 ILE E 97 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 3300 not shown) Planarity restraints: 3558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 9 " -0.070 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO B 10 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER G 174 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER G 174 " 0.053 2.00e-02 2.50e+03 pdb=" O SER G 174 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 175 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU J 256 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO J 257 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO J 257 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 257 " 0.043 5.00e-02 4.00e+02 ... (remaining 3555 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5084 2.79 - 3.32: 18147 3.32 - 3.84: 35903 3.84 - 4.37: 39871 4.37 - 4.90: 68785 Nonbonded interactions: 167790 Sorted by model distance: nonbonded pdb=" O LEU A 80 " pdb=" O2' A C 7 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR F 265 " pdb=" O PHE F 273 " model vdw 2.268 3.040 nonbonded pdb=" O ALA F 143 " pdb=" OG SER F 174 " model vdw 2.269 3.040 nonbonded pdb=" OG SER B 148 " pdb=" O THR B 151 " model vdw 2.275 3.040 nonbonded pdb=" O THR D 28 " pdb=" OG SER D 251 " model vdw 2.277 3.040 ... (remaining 167785 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 'D' and resid 18 through 330) selection = (chain 'E' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'F' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'G' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'H' and (resid 18 through 53 or resid 79 through 330)) selection = (chain 'I' and (resid 18 through 53 or resid 79 through 330)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 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 : 0.004 0.066 21736 Z= 0.196 Angle : 0.779 9.959 29639 Z= 0.468 Chirality : 0.052 0.279 3303 Planarity : 0.006 0.107 3558 Dihedral : 20.726 179.860 8509 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.65 % Allowed : 39.19 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2416 helix: -1.97 (0.17), residues: 616 sheet: -0.29 (0.29), residues: 357 loop : -2.52 (0.14), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 115 TYR 0.031 0.002 TYR I 206 PHE 0.035 0.002 PHE G 200 TRP 0.018 0.002 TRP E 33 HIS 0.007 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (21736) covalent geometry : angle 0.77877 / 0.47 (29639) hydrogen bonds : bond 0.17592 / 12.18 ( 580) hydrogen bonds : angle 7.59523 / 5.28 ( 1662) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 291 average time/residue: 0.1226 time to fit residues: 58.1276 Evaluate side-chains 267 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 151 ASN Chi-restraints excluded: chain D residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS A 215 HIS B 56 ASN ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 ASN F 34 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.194877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.161033 restraints weight = 36163.807| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.91 r_work: 0.3873 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21736 Z= 0.223 Angle : 0.652 12.227 29639 Z= 0.346 Chirality : 0.045 0.241 3303 Planarity : 0.005 0.077 3558 Dihedral : 15.093 178.375 3594 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.23 % Favored : 90.73 % Rotamer: Outliers : 5.64 % Allowed : 36.21 % Favored : 58.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.16), residues: 2416 helix: -1.30 (0.19), residues: 635 sheet: -0.22 (0.31), residues: 325 loop : -2.52 (0.14), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 23 TYR 0.025 0.002 TYR D 125 PHE 0.021 0.002 PHE G 95 TRP 0.014 0.002 TRP F 33 HIS 0.007 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (21736) covalent geometry : angle 0.65194 / 0.35 (29639) hydrogen bonds : bond 0.04903 / 3.20 ( 580) hydrogen bonds : angle 5.90231 / 4.10 ( 1662) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 274 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.6051 (p0) REVERT: B 151 THR cc_start: 0.2580 (OUTLIER) cc_final: 0.2334 (t) REVERT: I 91 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7865 (pt) REVERT: I 114 TYR cc_start: 0.7885 (t80) cc_final: 0.7655 (t80) REVERT: I 158 ILE cc_start: 0.6688 (OUTLIER) cc_final: 0.6211 (mt) REVERT: I 198 ASP cc_start: 0.7374 (m-30) cc_final: 0.7154 (m-30) REVERT: I 244 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7216 (mt-10) REVERT: H 47 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.7971 (mp) REVERT: H 300 LEU cc_start: 0.4577 (OUTLIER) cc_final: 0.4367 (pt) REVERT: G 300 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2572 (mp) REVERT: F 98 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7771 (ttmm) REVERT: F 128 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 149 TRP cc_start: 0.7880 (m100) cc_final: 0.7365 (m100) REVERT: D 163 THR cc_start: 0.4833 (OUTLIER) cc_final: 0.4598 (t) outliers start: 123 outliers final: 67 residues processed: 361 average time/residue: 0.1290 time to fit residues: 76.7837 Evaluate side-chains 338 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 261 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 251 SER Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 227 optimal weight: 5.9990 chunk 132 optimal weight: 0.0040 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 29 optimal weight: 40.0000 chunk 217 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 3.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 204 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN G 317 HIS F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.193748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.159992 restraints weight = 36565.812| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.70 r_work: 0.3848 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 21736 Z= 0.222 Angle : 0.645 13.048 29639 Z= 0.341 Chirality : 0.045 0.226 3303 Planarity : 0.005 0.059 3558 Dihedral : 15.042 177.932 3583 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 6.70 % Allowed : 35.84 % Favored : 57.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2416 helix: -1.05 (0.20), residues: 632 sheet: -0.35 (0.31), residues: 333 loop : -2.53 (0.14), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 291 TYR 0.023 0.002 TYR D 125 PHE 0.026 0.002 PHE G 200 TRP 0.013 0.001 TRP F 33 HIS 0.007 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (21736) covalent geometry : angle 0.64461 / 0.34 (29639) hydrogen bonds : bond 0.04470 / 2.93 ( 580) hydrogen bonds : angle 5.69924 / 3.95 ( 1662) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 262 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7796 (t-170) cc_final: 0.7356 (t-90) REVERT: A 184 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.6451 (mp10) REVERT: A 186 GLU cc_start: 0.7857 (tp30) cc_final: 0.7647 (tp30) REVERT: I 91 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8057 (pt) REVERT: I 158 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6390 (mt) REVERT: I 198 ASP cc_start: 0.7427 (m-30) cc_final: 0.7160 (m-30) REVERT: I 244 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: I 263 THR cc_start: 0.7927 (p) cc_final: 0.7551 (t) REVERT: H 100 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7488 (mt) REVERT: G 119 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: G 300 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2652 (mp) REVERT: G 328 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.3871 (tpp) REVERT: F 18 ASN cc_start: 0.7938 (t0) cc_final: 0.7708 (t0) REVERT: F 98 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7761 (ttmm) REVERT: E 149 TRP cc_start: 0.7846 (m100) cc_final: 0.7350 (m100) REVERT: E 151 ASN cc_start: 0.8472 (m-40) cc_final: 0.8101 (m110) REVERT: D 43 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7066 (m-80) outliers start: 146 outliers final: 90 residues processed: 374 average time/residue: 0.1310 time to fit residues: 80.9944 Evaluate side-chains 347 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 247 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 149 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 133 optimal weight: 0.0370 chunk 85 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 ASN H 34 GLN G 120 GLN F 18 ASN F 317 HIS E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 186 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.191969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157858 restraints weight = 36651.655| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.72 r_work: 0.3820 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21736 Z= 0.252 Angle : 0.679 14.593 29639 Z= 0.358 Chirality : 0.047 0.227 3303 Planarity : 0.005 0.052 3558 Dihedral : 15.057 177.698 3583 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 9.13 % Allowed : 33.64 % Favored : 57.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2416 helix: -1.07 (0.20), residues: 633 sheet: -0.59 (0.31), residues: 333 loop : -2.59 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 291 TYR 0.018 0.002 TYR D 125 PHE 0.026 0.002 PHE G 200 TRP 0.013 0.002 TRP F 33 HIS 0.007 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (21736) covalent geometry : angle 0.67921 / 0.36 (29639) hydrogen bonds : bond 0.04460 / 2.92 ( 580) hydrogen bonds : angle 5.71685 / 3.96 ( 1662) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 259 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7033 (tp) REVERT: A 156 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7274 (m-80) REVERT: A 181 HIS cc_start: 0.7962 (t-90) cc_final: 0.7635 (t-90) REVERT: A 184 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6258 (mp10) REVERT: I 91 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (pt) REVERT: I 158 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6482 (mt) REVERT: I 198 ASP cc_start: 0.7567 (m-30) cc_final: 0.7250 (m-30) REVERT: I 244 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: I 263 THR cc_start: 0.7953 (p) cc_final: 0.7610 (t) REVERT: H 47 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8206 (mp) REVERT: H 100 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7470 (mt) REVERT: H 104 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5822 (tm-30) REVERT: H 112 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.4665 (m-10) REVERT: H 207 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5892 (tt) REVERT: H 244 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: G 291 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6777 (ttt90) REVERT: G 300 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2524 (mp) REVERT: G 328 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.3908 (tpp) REVERT: F 18 ASN cc_start: 0.8238 (t0) cc_final: 0.8002 (t0) REVERT: F 77 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6546 (pp30) REVERT: F 98 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7776 (ttmm) REVERT: F 329 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: E 149 TRP cc_start: 0.7890 (m100) cc_final: 0.7422 (m100) REVERT: E 151 ASN cc_start: 0.8517 (m-40) cc_final: 0.8145 (m110) REVERT: E 249 MET cc_start: 0.7280 (tpt) cc_final: 0.6924 (tpt) REVERT: D 29 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: D 43 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7250 (m-80) REVERT: J 146 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6913 (t80) outliers start: 199 outliers final: 131 residues processed: 411 average time/residue: 0.1348 time to fit residues: 90.7972 Evaluate side-chains 406 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 254 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 156 TYR Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 291 ARG Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.194582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159685 restraints weight = 36376.579| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.18 r_work: 0.3836 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21736 Z= 0.153 Angle : 0.580 12.830 29639 Z= 0.309 Chirality : 0.043 0.218 3303 Planarity : 0.004 0.049 3558 Dihedral : 14.975 176.981 3583 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 7.30 % Allowed : 35.89 % Favored : 56.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.16), residues: 2416 helix: -0.84 (0.20), residues: 637 sheet: -0.49 (0.31), residues: 333 loop : -2.52 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 115 TYR 0.015 0.001 TYR D 125 PHE 0.055 0.002 PHE G 131 TRP 0.034 0.002 TRP D 149 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (21736) covalent geometry : angle 0.58044 / 0.31 (29639) hydrogen bonds : bond 0.03884 / 2.59 ( 580) hydrogen bonds : angle 5.44956 / 3.78 ( 1662) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 263 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.8101 (t-90) cc_final: 0.7725 (t-90) REVERT: A 184 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6264 (mp10) REVERT: I 158 ILE cc_start: 0.6652 (OUTLIER) cc_final: 0.6325 (mt) REVERT: I 198 ASP cc_start: 0.7489 (m-30) cc_final: 0.7130 (m-30) REVERT: I 244 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: I 263 THR cc_start: 0.7954 (p) cc_final: 0.7591 (t) REVERT: H 100 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7448 (mt) REVERT: H 112 TYR cc_start: 0.5392 (OUTLIER) cc_final: 0.4607 (m-10) REVERT: H 229 MET cc_start: 0.4401 (OUTLIER) cc_final: 0.3752 (mtt) REVERT: H 244 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: G 119 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6534 (m-80) REVERT: G 120 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: G 300 LEU cc_start: 0.2746 (OUTLIER) cc_final: 0.2315 (mp) REVERT: G 328 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3637 (tpp) REVERT: F 94 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8230 (m-30) REVERT: F 98 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7781 (ttmm) REVERT: F 329 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: E 98 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6821 (ttmt) REVERT: E 149 TRP cc_start: 0.7786 (m100) cc_final: 0.7368 (m100) REVERT: E 151 ASN cc_start: 0.8504 (m-40) cc_final: 0.8146 (m110) REVERT: E 205 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5604 (tp30) REVERT: D 29 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 43 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7169 (m-80) REVERT: D 125 TYR cc_start: 0.5374 (t80) cc_final: 0.5151 (t80) outliers start: 159 outliers final: 97 residues processed: 384 average time/residue: 0.1338 time to fit residues: 84.4632 Evaluate side-chains 363 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 248 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 298 TYR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 143 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 186 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.192698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158175 restraints weight = 36559.264| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.80 r_work: 0.3822 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21736 Z= 0.216 Angle : 0.645 14.663 29639 Z= 0.339 Chirality : 0.045 0.212 3303 Planarity : 0.004 0.048 3558 Dihedral : 14.996 177.057 3583 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 9.50 % Allowed : 34.19 % Favored : 56.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.16), residues: 2416 helix: -0.93 (0.20), residues: 639 sheet: -0.56 (0.30), residues: 334 loop : -2.55 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 146 TYR 0.020 0.002 TYR F 210 PHE 0.062 0.002 PHE G 131 TRP 0.020 0.002 TRP D 149 HIS 0.006 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (21736) covalent geometry : angle 0.64530 / 0.34 (29639) hydrogen bonds : bond 0.04158 / 2.74 ( 580) hydrogen bonds : angle 5.52389 / 3.83 ( 1662) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 249 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6840 (tp) REVERT: A 181 HIS cc_start: 0.8078 (t-90) cc_final: 0.7713 (t-90) REVERT: A 184 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: I 158 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6491 (mt) REVERT: I 198 ASP cc_start: 0.7527 (m-30) cc_final: 0.7228 (m-30) REVERT: I 244 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: I 263 THR cc_start: 0.7977 (p) cc_final: 0.7627 (t) REVERT: H 100 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7487 (mt) REVERT: H 104 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5848 (tm-30) REVERT: H 112 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.4347 (m-10) REVERT: H 207 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5976 (tt) REVERT: H 244 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: G 119 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: G 300 LEU cc_start: 0.2924 (OUTLIER) cc_final: 0.2579 (mp) REVERT: G 328 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.3695 (tpp) REVERT: F 98 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7788 (ttmm) REVERT: F 329 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: E 98 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6908 (ttmt) REVERT: E 151 ASN cc_start: 0.8539 (m-40) cc_final: 0.8195 (m110) REVERT: E 179 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7174 (mm) REVERT: E 205 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5652 (tp30) REVERT: D 29 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7129 (mp0) REVERT: D 43 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: D 100 LEU cc_start: 0.5228 (OUTLIER) cc_final: 0.4986 (pp) REVERT: J 146 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.7026 (t80) outliers start: 207 outliers final: 136 residues processed: 413 average time/residue: 0.1166 time to fit residues: 79.1486 Evaluate side-chains 404 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 247 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 219 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 45 optimal weight: 50.0000 chunk 151 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 208 optimal weight: 0.0370 chunk 70 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 120 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.194937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160700 restraints weight = 36541.695| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.85 r_work: 0.3855 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21736 Z= 0.140 Angle : 0.579 11.693 29639 Z= 0.306 Chirality : 0.043 0.192 3303 Planarity : 0.004 0.048 3558 Dihedral : 14.925 176.611 3583 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 7.39 % Allowed : 35.29 % Favored : 57.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.16), residues: 2416 helix: -0.75 (0.20), residues: 645 sheet: -0.54 (0.30), residues: 334 loop : -2.47 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 115 TYR 0.037 0.001 TYR E 169 PHE 0.034 0.001 PHE G 131 TRP 0.016 0.001 TRP D 149 HIS 0.003 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (21736) covalent geometry : angle 0.57944 / 0.31 (29639) hydrogen bonds : bond 0.03777 / 2.51 ( 580) hydrogen bonds : angle 5.33026 / 3.70 ( 1662) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 265 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6655 (tp) REVERT: A 99 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: A 181 HIS cc_start: 0.8033 (t-90) cc_final: 0.7637 (t-90) REVERT: A 184 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6191 (mp10) REVERT: B 125 ARG cc_start: 0.0536 (OUTLIER) cc_final: 0.0021 (tmt170) REVERT: B 129 MET cc_start: 0.1410 (tpp) cc_final: 0.1158 (tpp) REVERT: I 158 ILE cc_start: 0.6685 (OUTLIER) cc_final: 0.6329 (mt) REVERT: I 198 ASP cc_start: 0.7525 (m-30) cc_final: 0.7183 (m-30) REVERT: I 244 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7184 (mt-10) REVERT: I 263 THR cc_start: 0.7993 (p) cc_final: 0.7654 (t) REVERT: H 100 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7414 (mt) REVERT: H 112 TYR cc_start: 0.5104 (OUTLIER) cc_final: 0.4213 (m-10) REVERT: H 207 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5840 (tt) REVERT: H 229 MET cc_start: 0.4438 (OUTLIER) cc_final: 0.3727 (mtt) REVERT: H 244 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: G 119 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.6539 (m-80) REVERT: G 300 LEU cc_start: 0.2768 (OUTLIER) cc_final: 0.2452 (mp) REVERT: G 328 MET cc_start: 0.4943 (OUTLIER) cc_final: 0.3685 (tpp) REVERT: F 29 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: F 98 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7749 (ttmm) REVERT: F 329 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: E 98 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6847 (ttmt) REVERT: E 149 TRP cc_start: 0.7756 (m100) cc_final: 0.7407 (m100) REVERT: E 151 ASN cc_start: 0.8542 (m-40) cc_final: 0.8186 (m110) REVERT: E 205 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5598 (tp30) REVERT: D 34 GLN cc_start: 0.7593 (mp10) cc_final: 0.7327 (mp10) REVERT: D 43 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: J 74 TRP cc_start: 0.6889 (t60) cc_final: 0.6612 (t60) REVERT: J 146 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.6852 (t80) outliers start: 161 outliers final: 109 residues processed: 390 average time/residue: 0.1313 time to fit residues: 82.5559 Evaluate side-chains 385 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 255 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 88 CYS Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 298 TYR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 0.9980 chunk 168 optimal weight: 0.0470 chunk 174 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 235 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN F 80 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.196439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.162394 restraints weight = 36399.040| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.82 r_work: 0.3878 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21736 Z= 0.118 Angle : 0.560 10.529 29639 Z= 0.296 Chirality : 0.042 0.178 3303 Planarity : 0.004 0.054 3558 Dihedral : 14.855 176.452 3583 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 6.42 % Allowed : 36.03 % Favored : 57.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2416 helix: -0.61 (0.20), residues: 650 sheet: -0.46 (0.31), residues: 316 loop : -2.40 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 303 TYR 0.044 0.001 TYR E 169 PHE 0.025 0.001 PHE G 131 TRP 0.014 0.001 TRP D 149 HIS 0.003 0.001 HIS D 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (21736) covalent geometry : angle 0.56041 / 0.30 (29639) hydrogen bonds : bond 0.03526 / 2.36 ( 580) hydrogen bonds : angle 5.18328 / 3.60 ( 1662) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 270 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6699 (tp) REVERT: A 99 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 181 HIS cc_start: 0.7993 (t-90) cc_final: 0.7600 (t-90) REVERT: A 184 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6184 (mp10) REVERT: B 125 ARG cc_start: 0.0411 (OUTLIER) cc_final: -0.0115 (tmt170) REVERT: B 129 MET cc_start: 0.1186 (tpp) cc_final: 0.0909 (tpp) REVERT: I 114 TYR cc_start: 0.8013 (t80) cc_final: 0.7532 (t80) REVERT: I 158 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6300 (mt) REVERT: I 198 ASP cc_start: 0.7410 (m-30) cc_final: 0.7070 (m-30) REVERT: I 244 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7044 (mt-10) REVERT: I 263 THR cc_start: 0.7992 (p) cc_final: 0.7643 (t) REVERT: H 100 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7407 (mt) REVERT: H 104 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5884 (tm-30) REVERT: H 111 ASP cc_start: 0.6026 (t70) cc_final: 0.5740 (t0) REVERT: H 112 TYR cc_start: 0.5016 (OUTLIER) cc_final: 0.4214 (m-10) REVERT: H 207 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5794 (tt) REVERT: H 229 MET cc_start: 0.4382 (OUTLIER) cc_final: 0.3688 (mtt) REVERT: H 244 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8306 (mt-10) REVERT: G 119 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: G 300 LEU cc_start: 0.2826 (OUTLIER) cc_final: 0.2537 (mp) REVERT: G 328 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.3547 (tpp) REVERT: F 29 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: F 77 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6306 (pp30) REVERT: F 98 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7701 (ttmm) REVERT: F 329 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7306 (m-80) REVERT: E 98 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6689 (ttmt) REVERT: E 149 TRP cc_start: 0.7661 (m100) cc_final: 0.7442 (m100) REVERT: E 151 ASN cc_start: 0.8515 (m-40) cc_final: 0.8152 (m110) REVERT: E 179 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6897 (mm) REVERT: D 43 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: J 74 TRP cc_start: 0.6849 (t60) cc_final: 0.6583 (t60) REVERT: J 146 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6814 (t80) outliers start: 140 outliers final: 102 residues processed: 378 average time/residue: 0.1157 time to fit residues: 71.5361 Evaluate side-chains 388 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 263 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 298 TYR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 chunk 24 optimal weight: 30.0000 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN F 80 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.195933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.162320 restraints weight = 36483.202| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.69 r_work: 0.3878 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21736 Z= 0.131 Angle : 0.568 10.785 29639 Z= 0.298 Chirality : 0.042 0.170 3303 Planarity : 0.004 0.061 3558 Dihedral : 14.822 176.620 3583 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 7.30 % Allowed : 35.61 % Favored : 57.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2416 helix: -0.55 (0.20), residues: 644 sheet: -0.45 (0.31), residues: 316 loop : -2.40 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 303 TYR 0.043 0.001 TYR E 169 PHE 0.030 0.001 PHE G 200 TRP 0.013 0.001 TRP D 149 HIS 0.003 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (21736) covalent geometry : angle 0.56845 / 0.30 (29639) hydrogen bonds : bond 0.03566 / 2.38 ( 580) hydrogen bonds : angle 5.14967 / 3.57 ( 1662) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 261 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6732 (tp) REVERT: A 99 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: A 184 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6234 (mp10) REVERT: B 125 ARG cc_start: 0.0494 (OUTLIER) cc_final: 0.0035 (tmt170) REVERT: B 129 MET cc_start: 0.1223 (tpp) cc_final: 0.0922 (tpp) REVERT: I 114 TYR cc_start: 0.7991 (t80) cc_final: 0.7515 (t80) REVERT: I 158 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6331 (mt) REVERT: I 198 ASP cc_start: 0.7441 (m-30) cc_final: 0.7095 (m-30) REVERT: I 244 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: I 263 THR cc_start: 0.7997 (p) cc_final: 0.7648 (t) REVERT: H 100 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7449 (mt) REVERT: H 104 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5891 (tm-30) REVERT: H 111 ASP cc_start: 0.6066 (t70) cc_final: 0.5785 (t0) REVERT: H 112 TYR cc_start: 0.5048 (OUTLIER) cc_final: 0.4190 (m-10) REVERT: H 207 LEU cc_start: 0.6084 (OUTLIER) cc_final: 0.5794 (tt) REVERT: H 229 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.3801 (mtt) REVERT: H 244 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: G 119 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: G 300 LEU cc_start: 0.2882 (OUTLIER) cc_final: 0.2583 (mp) REVERT: G 328 MET cc_start: 0.4842 (OUTLIER) cc_final: 0.3522 (tpp) REVERT: F 21 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8432 (m-80) REVERT: F 29 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: F 77 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6369 (pp30) REVERT: F 98 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7727 (ttmm) REVERT: F 159 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6064 (pm20) REVERT: F 329 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: E 98 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6735 (ttmt) REVERT: E 151 ASN cc_start: 0.8462 (m-40) cc_final: 0.8095 (m110) REVERT: E 179 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6893 (mm) REVERT: D 43 PHE cc_start: 0.7419 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: J 74 TRP cc_start: 0.6834 (t60) cc_final: 0.6543 (t60) REVERT: J 146 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.6788 (t80) outliers start: 159 outliers final: 115 residues processed: 391 average time/residue: 0.1200 time to fit residues: 76.9683 Evaluate side-chains 400 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 260 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 298 TYR Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 45 optimal weight: 50.0000 chunk 20 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 120 GLN F 80 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 113 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.194077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159604 restraints weight = 36578.169| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.81 r_work: 0.3843 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21736 Z= 0.191 Angle : 0.623 11.671 29639 Z= 0.325 Chirality : 0.044 0.200 3303 Planarity : 0.004 0.064 3558 Dihedral : 14.850 176.909 3583 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 7.25 % Allowed : 35.80 % Favored : 56.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.16), residues: 2416 helix: -0.63 (0.20), residues: 641 sheet: -0.46 (0.30), residues: 328 loop : -2.46 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 303 TYR 0.040 0.002 TYR E 169 PHE 0.029 0.002 PHE G 131 TRP 0.027 0.002 TRP E 149 HIS 0.006 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (21736) covalent geometry : angle 0.62273 / 0.32 (29639) hydrogen bonds : bond 0.03825 / 2.54 ( 580) hydrogen bonds : angle 5.25772 / 3.65 ( 1662) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4832 Ramachandran restraints generated. 2416 Oldfield, 0 Emsley, 2416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 261 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6879 (tp) REVERT: A 99 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 184 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6213 (mp10) REVERT: B 125 ARG cc_start: 0.0462 (OUTLIER) cc_final: -0.0025 (tmt170) REVERT: B 129 MET cc_start: 0.1274 (tpp) cc_final: 0.0950 (tpp) REVERT: I 114 TYR cc_start: 0.8024 (t80) cc_final: 0.7526 (t80) REVERT: I 158 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6394 (mt) REVERT: I 198 ASP cc_start: 0.7507 (m-30) cc_final: 0.7172 (m-30) REVERT: I 244 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: I 263 THR cc_start: 0.8002 (p) cc_final: 0.7646 (t) REVERT: H 100 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7450 (mt) REVERT: H 104 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: H 112 TYR cc_start: 0.5136 (OUTLIER) cc_final: 0.4152 (m-10) REVERT: H 207 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5891 (tt) REVERT: H 229 MET cc_start: 0.4470 (OUTLIER) cc_final: 0.3727 (mtt) REVERT: H 244 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8304 (mt-10) REVERT: G 119 TYR cc_start: 0.7082 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: G 300 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2514 (mp) REVERT: G 328 MET cc_start: 0.4918 (OUTLIER) cc_final: 0.3649 (tpp) REVERT: F 21 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: F 29 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: F 77 GLN cc_start: 0.6795 (OUTLIER) cc_final: 0.6439 (pp30) REVERT: F 98 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7723 (ttmm) REVERT: F 159 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5957 (pm20) REVERT: F 329 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: E 98 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6715 (ttmt) REVERT: E 151 ASN cc_start: 0.8500 (m-40) cc_final: 0.8173 (m110) REVERT: E 179 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6888 (mm) REVERT: E 205 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: D 43 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7118 (m-80) REVERT: D 206 TYR cc_start: 0.4689 (p90) cc_final: 0.4341 (p90) REVERT: J 74 TRP cc_start: 0.6932 (t60) cc_final: 0.6645 (t60) REVERT: J 146 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6799 (t80) outliers start: 158 outliers final: 119 residues processed: 389 average time/residue: 0.1272 time to fit residues: 80.4293 Evaluate side-chains 402 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 257 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 21 PHE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 77 GLN Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 192 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 135 optimal weight: 0.0980 chunk 236 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 0.1980 chunk 183 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 158 optimal weight: 0.3980 chunk 199 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 250 HIS J 206 ASN ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.197701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164425 restraints weight = 36307.709| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.69 r_work: 0.3905 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21736 Z= 0.107 Angle : 0.569 11.111 29639 Z= 0.298 Chirality : 0.042 0.175 3303 Planarity : 0.004 0.068 3558 Dihedral : 14.785 176.888 3583 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.09 % Allowed : 38.04 % Favored : 56.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.16), residues: 2416 helix: -0.43 (0.20), residues: 641 sheet: -0.39 (0.31), residues: 316 loop : -2.36 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 303 TYR 0.037 0.001 TYR E 169 PHE 0.032 0.001 PHE G 200 TRP 0.015 0.002 TRP E 149 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (21736) covalent geometry : angle 0.56871 / 0.30 (29639) hydrogen bonds : bond 0.03393 / 2.27 ( 580) hydrogen bonds : angle 5.07645 / 3.51 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.62 seconds wall clock time: 83 minutes 28.02 seconds (5008.02 seconds total)