Starting phenix.real_space_refine on Sat Jul 4 12:32:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh9_39285/07_2026/8yh9_39285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh9_39285/07_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_39285/07_2026/8yh9_39285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh9_39285/07_2026/8yh9_39285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh9_39285/07_2026/8yh9_39285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh9_39285/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.90, per 1000 atoms: 0.18 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: 1.40 Conformation dependent library (CDL) restraints added in 778.7 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: 2.37 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: 3.08 Time building geometry restraints manager: 1.83 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: 28722 1.99 - 3.98: 795 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=" 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=" C SER G 174 " pdb=" N LYS G 175 " pdb=" CA LYS G 175 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA TYR F 125 " pdb=" CB TYR F 125 " pdb=" CG TYR F 125 " ideal model delta sigma weight residual 113.90 120.75 -6.85 1.80e+00 3.09e-01 1.45e+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: 2565 0.056 - 0.112: 608 0.112 - 0.167: 121 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.230 Find NCS groups from input model: 0.390 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- 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= 0.193 Angle : 0.760 9.959 29639 Z= 0.442 Chirality : 0.049 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 0.00390 / 0.19 (21736) covalent geometry : angle 0.76042 / 0.44 (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 : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 6 residues processed: 291 average time/residue: 0.1391 time to fit residues: 65.1108 Evaluate side-chains 268 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 23 ARG 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: 4.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 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: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.198099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163618 restraints weight = 36004.600| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 3.01 r_work: 0.3890 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21736 Z= 0.191 Angle : 0.601 11.469 29639 Z= 0.324 Chirality : 0.043 0.168 3303 Planarity : 0.005 0.075 3558 Dihedral : 15.132 179.357 3596 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.47 % Rotamer: Outliers : 5.19 % Allowed : 36.44 % Favored : 58.38 % 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: -1.24 (0.19), residues: 636 sheet: -0.15 (0.32), residues: 313 loop : -2.47 (0.14), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 115 TYR 0.024 0.002 TYR D 125 PHE 0.018 0.002 PHE G 95 TRP 0.013 0.001 TRP F 33 HIS 0.006 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 (21736) covalent geometry : angle 0.60094 / 0.32 (29639) hydrogen bonds : bond 0.04515 / 2.95 ( 580) hydrogen bonds : angle 5.79690 / 4.03 ( 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 389 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 276 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7529 (t70) cc_final: 0.7113 (t-170) REVERT: A 184 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6327 (mp10) REVERT: I 91 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7832 (pt) REVERT: I 158 ILE cc_start: 0.6717 (OUTLIER) cc_final: 0.6188 (mt) REVERT: I 198 ASP cc_start: 0.7287 (m-30) cc_final: 0.7077 (m-30) REVERT: I 244 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: H 47 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8023 (mp) REVERT: H 300 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4296 (pt) REVERT: G 300 LEU cc_start: 0.2870 (OUTLIER) cc_final: 0.2658 (mp) REVERT: F 18 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7525 (t0) REVERT: F 98 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7729 (ttmm) REVERT: F 128 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7590 (mt-10) REVERT: F 198 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7731 (t0) REVERT: E 149 TRP cc_start: 0.7790 (m100) cc_final: 0.7375 (m100) outliers start: 113 outliers final: 55 residues processed: 354 average time/residue: 0.1224 time to fit residues: 71.0829 Evaluate side-chains 322 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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 184 GLN Chi-restraints excluded: chain A residue 245 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 144 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN 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 18 ASN 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 198 ASP 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 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 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 207 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 288 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 212 PHE 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: 4.9990 chunk 132 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 247 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 204 HIS A 215 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 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.195921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.162267 restraints weight = 36338.043| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.76 r_work: 0.3873 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21736 Z= 0.175 Angle : 0.586 12.006 29639 Z= 0.313 Chirality : 0.043 0.163 3303 Planarity : 0.004 0.061 3558 Dihedral : 15.018 178.030 3583 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 6.10 % Allowed : 36.07 % Favored : 57.82 % 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: -2.49 (0.16), residues: 2416 helix: -0.90 (0.20), residues: 633 sheet: -0.16 (0.31), residues: 326 loop : -2.50 (0.14), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 291 TYR 0.022 0.001 TYR D 125 PHE 0.024 0.002 PHE G 200 TRP 0.011 0.001 TRP F 33 HIS 0.005 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (21736) covalent geometry : angle 0.58570 / 0.31 (29639) hydrogen bonds : bond 0.04182 / 2.74 ( 580) hydrogen bonds : angle 5.55005 / 3.85 ( 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 399 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 266 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8711 (mp0) cc_final: 0.8452 (mp0) REVERT: A 181 HIS cc_start: 0.7516 (t70) cc_final: 0.7167 (t-170) REVERT: A 184 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6273 (mp10) REVERT: A 186 GLU cc_start: 0.7751 (tp30) cc_final: 0.7550 (tp30) REVERT: I 91 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7932 (pt) REVERT: I 158 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6196 (mt) REVERT: I 198 ASP cc_start: 0.7361 (m-30) cc_final: 0.7078 (m-30) REVERT: I 244 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: H 100 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7472 (mt) REVERT: G 119 TYR cc_start: 0.6944 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: G 300 LEU cc_start: 0.2813 (OUTLIER) cc_final: 0.2559 (mp) REVERT: G 328 MET cc_start: 0.4866 (OUTLIER) cc_final: 0.3730 (tpp) REVERT: F 98 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7714 (ttmm) REVERT: F 128 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7553 (mt-10) REVERT: E 149 TRP cc_start: 0.7777 (m100) cc_final: 0.7319 (m100) REVERT: E 151 ASN cc_start: 0.8490 (m-40) cc_final: 0.8157 (m110) REVERT: D 43 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.7104 (m-80) outliers start: 133 outliers final: 83 residues processed: 362 average time/residue: 0.1370 time to fit residues: 80.6655 Evaluate side-chains 345 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 252 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 55 VAL 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 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 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 189 ILE Chi-restraints excluded: chain I residue 219 CYS 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 23 ARG 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 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 199 THR 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 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 18 ASN 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 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain E residue 23 ARG 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 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 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP 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 207 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 258 LEU 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 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 192 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 149 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 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: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN A 204 HIS B 29 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 G 317 HIS F 34 GLN F 256 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.187833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.153308 restraints weight = 36995.428| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.84 r_work: 0.3763 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.109 21736 Z= 0.421 Angle : 0.883 16.935 29639 Z= 0.468 Chirality : 0.053 0.300 3303 Planarity : 0.006 0.070 3558 Dihedral : 15.370 178.384 3583 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 10.19 % Allowed : 32.95 % Favored : 56.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.21 (0.15), residues: 2416 helix: -1.54 (0.19), residues: 640 sheet: -0.94 (0.30), residues: 341 loop : -2.86 (0.14), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 23 TYR 0.029 0.003 TYR H 224 PHE 0.032 0.003 PHE G 95 TRP 0.021 0.003 TRP F 33 HIS 0.014 0.002 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00955 / 0.42 (21736) covalent geometry : angle 0.88274 / 0.47 (29639) hydrogen bonds : bond 0.05539 / 3.59 ( 580) hydrogen bonds : angle 6.20295 / 4.31 ( 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 482 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 260 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7758 (OUTLIER) cc_final: 0.7216 (tp) REVERT: A 156 TYR cc_start: 0.7551 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: B 105 GLU cc_start: 0.0116 (OUTLIER) cc_final: -0.0162 (tt0) REVERT: B 151 THR cc_start: 0.2703 (OUTLIER) cc_final: 0.2457 (t) REVERT: I 91 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8275 (pt) REVERT: I 158 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6687 (mt) REVERT: I 198 ASP cc_start: 0.7782 (m-30) cc_final: 0.7534 (m-30) REVERT: I 244 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: I 263 THR cc_start: 0.7974 (p) cc_final: 0.7662 (t) REVERT: H 47 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8278 (mp) REVERT: H 100 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7616 (mt) REVERT: H 112 TYR cc_start: 0.5788 (OUTLIER) cc_final: 0.4995 (m-10) REVERT: H 200 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.5133 (t80) REVERT: H 207 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6026 (tt) REVERT: H 244 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: G 300 LEU cc_start: 0.3158 (OUTLIER) cc_final: 0.2681 (mp) REVERT: G 328 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.3992 (tpp) REVERT: F 77 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: F 98 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7882 (ttmm) REVERT: F 329 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: E 114 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6457 (t80) REVERT: E 146 ARG cc_start: 0.6873 (mpt180) cc_final: 0.6608 (mmt-90) REVERT: E 149 TRP cc_start: 0.8100 (m100) cc_final: 0.7613 (m100) REVERT: E 151 ASN cc_start: 0.8508 (m-40) cc_final: 0.8182 (m110) REVERT: E 205 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5705 (tp30) REVERT: D 29 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: D 43 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: D 206 TYR cc_start: 0.4796 (p90) cc_final: 0.4467 (p90) REVERT: J 146 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.7051 (t80) REVERT: J 213 GLN cc_start: 0.8754 (pp30) cc_final: 0.8501 (pp30) outliers start: 222 outliers final: 138 residues processed: 438 average time/residue: 0.1384 time to fit residues: 98.6922 Evaluate side-chains 408 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 247 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 156 TYR Chi-restraints excluded: chain A residue 161 THR 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 29 HIS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 THR 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 124 GLU 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 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 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 108 SER Chi-restraints excluded: chain H residue 112 TYR 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 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 200 PHE 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 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 42 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 89 ASP 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 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 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 256 ASN 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 F residue 330 SER 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 114 TYR 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 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 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 47 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 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 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 161 LEU 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 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 275 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 119 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 186 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 151 ASN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 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 186 ASN ** D 250 HIS ** 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 = 0.4399 r_free = 0.4399 target = 0.194434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159776 restraints weight = 36392.425| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.84 r_work: 0.3842 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21736 Z= 0.142 Angle : 0.594 13.355 29639 Z= 0.320 Chirality : 0.043 0.181 3303 Planarity : 0.004 0.050 3558 Dihedral : 15.124 176.573 3583 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 7.21 % Allowed : 36.21 % Favored : 56.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.16), residues: 2416 helix: -1.00 (0.20), residues: 638 sheet: -0.62 (0.30), residues: 334 loop : -2.57 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 23 TYR 0.024 0.001 TYR D 224 PHE 0.053 0.002 PHE G 131 TRP 0.038 0.002 TRP D 149 HIS 0.010 0.001 HIS B 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (21736) covalent geometry : angle 0.59448 / 0.32 (29639) hydrogen bonds : bond 0.03977 / 2.65 ( 580) hydrogen bonds : angle 5.57788 / 3.87 ( 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 417 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 260 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6192 (mp10) REVERT: I 158 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6429 (mt) REVERT: I 198 ASP cc_start: 0.7543 (m-30) cc_final: 0.7240 (m-30) REVERT: I 244 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: I 263 THR cc_start: 0.7940 (p) cc_final: 0.7581 (t) REVERT: H 100 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7522 (mt) REVERT: H 104 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5846 (tm-30) REVERT: H 112 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4457 (m-10) REVERT: H 200 PHE cc_start: 0.5376 (OUTLIER) cc_final: 0.4792 (t80) REVERT: H 244 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8346 (mt-10) REVERT: G 119 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: G 300 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.2593 (mp) REVERT: G 328 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.3683 (tpp) REVERT: F 21 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: F 98 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7778 (ttmm) REVERT: F 329 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: E 149 TRP cc_start: 0.7764 (m100) cc_final: 0.7454 (m100) REVERT: E 151 ASN cc_start: 0.8476 (m-40) cc_final: 0.8124 (m110) REVERT: D 43 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7215 (m-80) outliers start: 157 outliers final: 95 residues processed: 383 average time/residue: 0.1367 time to fit residues: 85.3948 Evaluate side-chains 358 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 248 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 109 LEU 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 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 29 HIS 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 158 ILE Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 189 ILE 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 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 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 200 PHE 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 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 328 MET Chi-restraints excluded: chain F residue 21 PHE 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 159 GLU Chi-restraints excluded: chain F residue 178 ASN 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 270 THR 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 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 200 PHE 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 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 186 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 324 ILE Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 67 LEU 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: 0.0770 chunk 196 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 256 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159155 restraints weight = 36472.804| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.78 r_work: 0.3840 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21736 Z= 0.164 Angle : 0.596 14.042 29639 Z= 0.318 Chirality : 0.043 0.188 3303 Planarity : 0.004 0.049 3558 Dihedral : 15.075 176.535 3583 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 7.43 % Allowed : 36.03 % Favored : 56.54 % 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: -2.60 (0.16), residues: 2416 helix: -0.89 (0.20), residues: 639 sheet: -0.58 (0.30), residues: 335 loop : -2.54 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 23 TYR 0.027 0.001 TYR D 224 PHE 0.059 0.002 PHE G 131 TRP 0.017 0.001 TRP D 149 HIS 0.004 0.001 HIS E 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21736) covalent geometry : angle 0.59648 / 0.32 (29639) hydrogen bonds : bond 0.03955 / 2.61 ( 580) hydrogen bonds : angle 5.46685 / 3.79 ( 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 418 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 256 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.6815 (tp) REVERT: A 156 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: A 184 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6019 (mp10) REVERT: B 129 MET cc_start: 0.1106 (tpp) cc_final: 0.0745 (tpp) REVERT: I 158 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6439 (mt) REVERT: I 198 ASP cc_start: 0.7551 (m-30) cc_final: 0.7222 (m-30) REVERT: I 244 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: I 263 THR cc_start: 0.7961 (p) cc_final: 0.7599 (t) REVERT: H 100 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7528 (mt) REVERT: H 104 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5839 (tm-30) REVERT: H 112 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4322 (m-10) REVERT: H 200 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4759 (t80) REVERT: H 229 MET cc_start: 0.4448 (OUTLIER) cc_final: 0.3724 (mtt) REVERT: H 244 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: G 119 TYR cc_start: 0.7077 (OUTLIER) cc_final: 0.6467 (m-80) REVERT: G 300 LEU cc_start: 0.2832 (OUTLIER) cc_final: 0.2506 (mp) REVERT: G 328 MET cc_start: 0.5021 (OUTLIER) cc_final: 0.3693 (tpp) REVERT: F 21 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: F 98 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7777 (ttmm) REVERT: F 329 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: E 98 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6805 (ttmt) REVERT: E 151 ASN cc_start: 0.8478 (m-40) cc_final: 0.8134 (m110) REVERT: E 179 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7168 (mm) REVERT: D 43 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: D 100 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4928 (pp) REVERT: J 146 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6861 (t80) outliers start: 162 outliers final: 107 residues processed: 386 average time/residue: 0.1401 time to fit residues: 87.4946 Evaluate side-chains 376 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 247 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 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 156 TYR 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 29 HIS Chi-restraints excluded: chain B residue 49 ASP 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 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER 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 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 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE 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 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 119 TYR Chi-restraints excluded: chain G residue 128 GLU 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 21 PHE 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 215 VAL 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 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 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 200 PHE 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 286 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 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 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 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 211 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 219 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 209 optimal weight: 0.3980 chunk 45 optimal weight: 50.0000 chunk 151 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 256 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.192662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158167 restraints weight = 36604.071| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.81 r_work: 0.3821 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21736 Z= 0.200 Angle : 0.631 14.190 29639 Z= 0.335 Chirality : 0.044 0.182 3303 Planarity : 0.004 0.056 3558 Dihedral : 15.069 176.728 3583 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 7.94 % Allowed : 35.20 % 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: -2.66 (0.16), residues: 2416 helix: -0.90 (0.20), residues: 639 sheet: -0.71 (0.30), residues: 329 loop : -2.56 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 146 TYR 0.036 0.002 TYR E 169 PHE 0.041 0.002 PHE G 131 TRP 0.016 0.002 TRP D 149 HIS 0.006 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (21736) covalent geometry : angle 0.63113 / 0.33 (29639) hydrogen bonds : bond 0.04115 / 2.71 ( 580) hydrogen bonds : angle 5.48480 / 3.80 ( 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 432 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 259 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6851 (tp) REVERT: A 156 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.7214 (m-80) REVERT: A 184 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6064 (mp10) REVERT: B 125 ARG cc_start: 0.0504 (OUTLIER) cc_final: -0.0421 (ttt180) REVERT: I 158 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6564 (mt) REVERT: I 198 ASP cc_start: 0.7552 (m-30) cc_final: 0.7256 (m-30) REVERT: I 244 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: I 263 THR cc_start: 0.7973 (p) cc_final: 0.7624 (t) REVERT: H 100 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7539 (mt) REVERT: H 104 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.5830 (tm-30) REVERT: H 112 TYR cc_start: 0.5233 (OUTLIER) cc_final: 0.4312 (m-10) REVERT: H 200 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.4809 (t80) REVERT: H 207 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5904 (tt) REVERT: H 244 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: G 300 LEU cc_start: 0.2955 (OUTLIER) cc_final: 0.2589 (mp) REVERT: G 328 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.3725 (tpp) REVERT: F 21 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: F 98 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7772 (ttmm) REVERT: F 329 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7288 (m-80) REVERT: E 149 TRP cc_start: 0.7859 (m100) cc_final: 0.7526 (m100) REVERT: E 151 ASN cc_start: 0.8519 (m-40) cc_final: 0.8209 (m110) REVERT: E 179 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7148 (mm) REVERT: D 43 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: D 100 LEU cc_start: 0.5257 (OUTLIER) cc_final: 0.5040 (pp) REVERT: D 206 TYR cc_start: 0.4623 (p90) cc_final: 0.4302 (p90) REVERT: J 146 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6856 (t80) outliers start: 173 outliers final: 126 residues processed: 395 average time/residue: 0.1406 time to fit residues: 90.2023 Evaluate side-chains 394 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 247 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 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 156 TYR 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 125 ARG Chi-restraints excluded: chain B residue 146 VAL 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 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER 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 34 GLN 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 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 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE 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 288 ILE Chi-restraints excluded: chain H residue 294 THR 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 99 VAL Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU 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 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 80 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 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN 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 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 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 235 ASP Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 286 ILE 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 100 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 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 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 169 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 136 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS ** 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** F 80 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 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** ** 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 = 0.4389 r_free = 0.4389 target = 0.193545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.159569 restraints weight = 36461.856| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.73 r_work: 0.3842 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21736 Z= 0.163 Angle : 0.605 11.668 29639 Z= 0.321 Chirality : 0.043 0.183 3303 Planarity : 0.004 0.055 3558 Dihedral : 15.035 176.477 3583 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 7.25 % Allowed : 35.98 % Favored : 56.77 % 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: -2.60 (0.16), residues: 2416 helix: -0.85 (0.20), residues: 645 sheet: -0.68 (0.30), residues: 326 loop : -2.53 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 146 TYR 0.052 0.002 TYR E 169 PHE 0.031 0.002 PHE G 131 TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (21736) covalent geometry : angle 0.60521 / 0.32 (29639) hydrogen bonds : bond 0.03884 / 2.58 ( 580) hydrogen bonds : angle 5.40536 / 3.75 ( 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 412 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 254 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6775 (tp) REVERT: A 156 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7166 (m-80) REVERT: A 184 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: I 158 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6549 (mt) REVERT: I 198 ASP cc_start: 0.7541 (m-30) cc_final: 0.7218 (m-30) REVERT: I 244 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: I 263 THR cc_start: 0.7967 (p) cc_final: 0.7621 (t) REVERT: H 100 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7564 (mt) REVERT: H 104 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5843 (tm-30) REVERT: H 112 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4265 (m-10) REVERT: H 200 PHE cc_start: 0.5364 (OUTLIER) cc_final: 0.4673 (t80) REVERT: H 207 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5845 (tt) REVERT: H 229 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.3662 (mtt) REVERT: H 244 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: G 119 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: G 300 LEU cc_start: 0.2899 (OUTLIER) cc_final: 0.2546 (mp) REVERT: G 328 MET cc_start: 0.5035 (OUTLIER) cc_final: 0.3714 (tpp) REVERT: F 21 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: F 29 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: F 98 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7779 (ttmm) REVERT: F 329 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7393 (m-80) REVERT: E 151 ASN cc_start: 0.8524 (m-40) cc_final: 0.8209 (m110) REVERT: E 179 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7023 (mm) REVERT: D 43 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7094 (m-80) REVERT: D 100 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.4985 (pp) REVERT: D 206 TYR cc_start: 0.4661 (p90) cc_final: 0.4313 (p90) REVERT: J 74 TRP cc_start: 0.6921 (t60) cc_final: 0.6583 (t60) REVERT: J 146 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6836 (t80) outliers start: 158 outliers final: 117 residues processed: 379 average time/residue: 0.1333 time to fit residues: 83.4280 Evaluate side-chains 390 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 250 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 156 TYR Chi-restraints excluded: chain A residue 184 GLN 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 146 VAL 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 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 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 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 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 200 PHE 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 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 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 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 21 PHE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 80 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 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 215 VAL 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 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 235 ASP Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 286 ILE 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 47 LEU Chi-restraints excluded: chain D residue 100 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 0.9980 chunk 190 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 5 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** G 120 GLN F 80 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.194853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.160997 restraints weight = 36479.145| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.74 r_work: 0.3862 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21736 Z= 0.130 Angle : 0.577 10.611 29639 Z= 0.306 Chirality : 0.042 0.190 3303 Planarity : 0.004 0.058 3558 Dihedral : 14.979 176.233 3583 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 6.98 % Allowed : 36.26 % Favored : 56.77 % 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: -0.71 (0.20), residues: 646 sheet: -0.56 (0.30), residues: 332 loop : -2.49 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 115 TYR 0.046 0.001 TYR E 169 PHE 0.030 0.001 PHE G 200 TRP 0.014 0.001 TRP D 149 HIS 0.004 0.001 HIS J 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21736) covalent geometry : angle 0.57735 / 0.31 (29639) hydrogen bonds : bond 0.03647 / 2.44 ( 580) hydrogen bonds : angle 5.27549 / 3.66 ( 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 414 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 262 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6847 (tp) REVERT: A 99 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: A 184 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6060 (mp10) REVERT: I 114 TYR cc_start: 0.7950 (t80) cc_final: 0.7574 (t80) REVERT: I 158 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6470 (mt) REVERT: I 198 ASP cc_start: 0.7464 (m-30) cc_final: 0.7149 (m-30) REVERT: I 244 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: I 263 THR cc_start: 0.7942 (p) cc_final: 0.7576 (t) REVERT: H 100 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7462 (mt) REVERT: H 104 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5903 (tm-30) REVERT: H 112 TYR cc_start: 0.5115 (OUTLIER) cc_final: 0.4176 (m-10) REVERT: H 200 PHE cc_start: 0.5271 (OUTLIER) cc_final: 0.4577 (t80) REVERT: H 207 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5728 (tt) REVERT: H 229 MET cc_start: 0.4407 (OUTLIER) cc_final: 0.3658 (mtt) REVERT: H 244 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: G 119 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: G 300 LEU cc_start: 0.2794 (OUTLIER) cc_final: 0.2453 (mp) REVERT: G 328 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.3626 (tpp) REVERT: F 21 PHE cc_start: 0.8814 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: F 29 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: F 98 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7722 (ttmm) REVERT: F 159 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: F 329 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: E 98 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6723 (ttmt) REVERT: E 149 TRP cc_start: 0.7718 (m100) cc_final: 0.7445 (m100) REVERT: E 151 ASN cc_start: 0.8465 (m-40) cc_final: 0.8109 (m110) REVERT: D 43 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7077 (m-80) REVERT: D 206 TYR cc_start: 0.4656 (p90) cc_final: 0.4296 (p90) REVERT: J 74 TRP cc_start: 0.6868 (t60) cc_final: 0.6546 (t60) REVERT: J 146 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6747 (t80) outliers start: 152 outliers final: 109 residues processed: 384 average time/residue: 0.1352 time to fit residues: 85.0222 Evaluate side-chains 386 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 254 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 73 GLN Chi-restraints excluded: chain A residue 96 ILE 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 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 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 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 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 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 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU 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 200 PHE Chi-restraints excluded: chain H residue 207 LEU 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 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 108 SER 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 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 80 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 215 VAL 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 316 LYS Chi-restraints excluded: chain F residue 329 PHE 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 148 LEU Chi-restraints excluded: chain E residue 157 ILE 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 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 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 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 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 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: 9.9990 chunk 71 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN F 80 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.192684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.158072 restraints weight = 36789.403| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.84 r_work: 0.3821 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21736 Z= 0.214 Angle : 0.639 12.282 29639 Z= 0.337 Chirality : 0.044 0.179 3303 Planarity : 0.005 0.061 3558 Dihedral : 14.994 176.621 3583 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 6.98 % Allowed : 36.26 % Favored : 56.77 % 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: -2.58 (0.16), residues: 2416 helix: -0.81 (0.20), residues: 645 sheet: -0.76 (0.30), residues: 333 loop : -2.51 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 146 TYR 0.043 0.002 TYR E 169 PHE 0.029 0.002 PHE G 131 TRP 0.017 0.002 TRP E 33 HIS 0.006 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (21736) covalent geometry : angle 0.63942 / 0.34 (29639) hydrogen bonds : bond 0.03981 / 2.63 ( 580) hydrogen bonds : angle 5.40810 / 3.76 ( 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 404 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 252 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.6919 (tp) REVERT: A 99 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: A 184 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6050 (mp10) REVERT: B 125 ARG cc_start: 0.0501 (OUTLIER) cc_final: -0.0367 (ttt180) REVERT: I 158 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6582 (mt) REVERT: I 198 ASP cc_start: 0.7554 (m-30) cc_final: 0.7238 (m-30) REVERT: I 244 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: I 263 THR cc_start: 0.8001 (p) cc_final: 0.7651 (t) REVERT: I 310 ASP cc_start: 0.6954 (m-30) cc_final: 0.6660 (p0) REVERT: H 100 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7552 (mt) REVERT: H 104 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: H 112 TYR cc_start: 0.5081 (OUTLIER) cc_final: 0.4188 (m-10) REVERT: H 200 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.4744 (t80) REVERT: H 207 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5829 (tt) REVERT: H 229 MET cc_start: 0.4548 (OUTLIER) cc_final: 0.3757 (mtt) REVERT: H 244 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: G 119 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6662 (m-80) REVERT: G 300 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.2443 (mp) REVERT: G 328 MET cc_start: 0.5039 (OUTLIER) cc_final: 0.3723 (tpp) REVERT: F 21 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.8387 (m-80) REVERT: F 29 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: F 98 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7757 (ttmm) REVERT: F 329 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: E 98 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6573 (ttmt) REVERT: E 149 TRP cc_start: 0.7849 (m100) cc_final: 0.7515 (m100) REVERT: E 151 ASN cc_start: 0.8505 (m-40) cc_final: 0.8148 (m110) REVERT: D 43 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7135 (m-80) REVERT: D 206 TYR cc_start: 0.4668 (p90) cc_final: 0.4315 (p90) REVERT: J 146 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6803 (t80) outliers start: 152 outliers final: 119 residues processed: 374 average time/residue: 0.1359 time to fit residues: 83.3838 Evaluate side-chains 393 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 251 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 245 THR Chi-restraints excluded: chain B residue 1 MET 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 179 LEU 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 252 GLN 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 34 GLN 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 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU 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 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 99 VAL Chi-restraints excluded: chain G residue 108 SER 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 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 13 LYS 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 80 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 178 ASN Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 215 VAL 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 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 148 LEU Chi-restraints excluded: chain E residue 157 ILE 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 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 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 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 169 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 135 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 158 optimal weight: 0.0970 chunk 199 optimal weight: 0.0010 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 GLN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN D 186 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 = 0.4379 r_free = 0.4379 target = 0.192593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.158634 restraints weight = 36455.847| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.69 r_work: 0.3828 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.266 21736 Z= 0.264 Angle : 0.825 59.194 29639 Z= 0.474 Chirality : 0.053 1.797 3303 Planarity : 0.006 0.198 3558 Dihedral : 14.992 176.598 3583 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 7.07 % Allowed : 36.07 % Favored : 56.86 % Cbeta Deviations : 0.09 % 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: -2.58 (0.16), residues: 2416 helix: -0.80 (0.20), residues: 645 sheet: -0.76 (0.30), residues: 333 loop : -2.51 (0.15), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 146 TYR 0.041 0.002 TYR E 169 PHE 0.027 0.002 PHE G 131 TRP 0.014 0.002 TRP E 33 HIS 0.005 0.001 HIS H 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 (21736) covalent geometry : angle 0.82479 / 0.47 (29639) hydrogen bonds : bond 0.03946 / 2.59 ( 580) hydrogen bonds : angle 5.42303 / 3.76 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5192.64 seconds wall clock time: 90 minutes 16.67 seconds (5416.67 seconds total)