Starting phenix.real_space_refine on Thu Sep 18 22:39:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh9_39285/09_2025/8yh9_39285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh9_39285/09_2025/8yh9_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_39285/09_2025/8yh9_39285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh9_39285/09_2025/8yh9_39285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yh9_39285/09_2025/8yh9_39285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh9_39285/09_2025/8yh9_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21153 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 7, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "C" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1287 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 8, 'rna3p_pur': 21, 'rna3p_pyr': 14} Link IDs: {'rna2p': 23, 'rna3p': 36} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2467 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "H" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2423 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 1 Chain: "G" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2461 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2447 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 12, 'TRANS': 287} Chain breaks: 1 Chain: "E" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2397 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2393 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Chain: "J" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1929 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 12, 'TRANS': 229} Chain breaks: 1 Time building chain proxies: 4.73, per 1000 atoms: 0.22 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: 1.77 Conformation dependent library (CDL) restraints added in 835.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.09 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: 3.55 Time building geometry restraints manager: 2.39 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=" 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 bond pdb=" CA ASN F 18 " pdb=" CB ASN F 18 " ideal model delta sigma weight residual 1.527 1.568 -0.041 2.48e-02 1.63e+03 2.72e+00 ... (remaining 21731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 28720 1.99 - 3.98: 796 3.98 - 5.98: 97 5.98 - 7.97: 16 7.97 - 9.96: 10 Bond angle restraints: 29639 Sorted by residual: 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 angle pdb=" C SER A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 121.54 128.68 -7.14 1.91e+00 2.74e-01 1.40e+01 angle pdb=" CA GLU I 278 " pdb=" CB GLU I 278 " pdb=" CG GLU I 278 " ideal model delta sigma weight residual 114.10 121.56 -7.46 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CA TYR E 112 " pdb=" CB TYR E 112 " pdb=" CG TYR E 112 " ideal model delta sigma weight residual 113.90 120.43 -6.53 1.80e+00 3.09e-01 1.32e+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: 2564 0.056 - 0.112: 609 0.112 - 0.167: 120 0.167 - 0.223: 7 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.970 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 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= 0.183 Angle : 0.761 9.959 29639 Z= 0.413 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 aren 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 covalent geometry : bond 0.00390 (21736) covalent geometry : angle 0.76078 (29639) hydrogen bonds : bond 0.17592 ( 580) hydrogen bonds : angle 7.59523 ( 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 : 0.640 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: 0.1280 time to fit residues: 60.4307 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 : 0.741 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 215 HIS B 56 ASN I 140 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 120 GLN G 190 ASN F 34 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 145 GLN J 206 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.195390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.161572 restraints weight = 36319.161| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.70 r_work: 0.3876 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21736 Z= 0.194 Angle : 0.616 11.589 29639 Z= 0.326 Chirality : 0.043 0.197 3303 Planarity : 0.005 0.072 3558 Dihedral : 15.030 177.466 3596 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 5.78 % Allowed : 36.44 % Favored : 57.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.16), residues: 2416 helix: -1.18 (0.19), residues: 634 sheet: -0.14 (0.32), residues: 313 loop : -2.51 (0.14), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 291 TYR 0.017 0.002 TYR D 125 PHE 0.021 0.002 PHE G 200 TRP 0.015 0.002 TRP F 33 HIS 0.004 0.001 HIS D 250 Details of bonding type rmsd covalent geometry : bond 0.00436 (21736) covalent geometry : angle 0.61555 (29639) hydrogen bonds : bond 0.04258 ( 580) hydrogen bonds : angle 5.55301 ( 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 400 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 274 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7524 (t70) cc_final: 0.7187 (t-170) REVERT: A 184 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6261 (mp10) REVERT: B 56 ASN cc_start: 0.6295 (OUTLIER) cc_final: 0.5937 (p0) REVERT: I 91 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7902 (pt) REVERT: I 114 TYR cc_start: 0.7896 (t80) cc_final: 0.7611 (t80) REVERT: I 158 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6299 (mt) REVERT: I 244 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: I 263 THR cc_start: 0.7919 (p) cc_final: 0.7558 (t) REVERT: H 47 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7950 (mp) REVERT: G 119 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6502 (m-80) REVERT: G 300 LEU cc_start: 0.2889 (OUTLIER) cc_final: 0.2612 (mp) REVERT: F 98 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7784 (ttmm) REVERT: F 128 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7532 (mt-10) REVERT: F 329 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: E 149 TRP cc_start: 0.7862 (m100) cc_final: 0.7345 (m100) REVERT: D 43 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.7200 (m-80) REVERT: D 125 TYR cc_start: 0.5469 (t80) cc_final: 0.5212 (t80) REVERT: D 163 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.5031 (t) outliers start: 126 outliers final: 61 residues processed: 368 average time/residue: 0.1393 time to fit residues: 83.3498 Evaluate side-chains 334 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 261 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR 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 252 CYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN 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 140 ASN Chi-restraints excluded: chain I residue 158 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 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 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 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 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 131 PHE 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 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 197 THR 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: 6.9990 chunk 132 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 217 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 34 GLN G 317 HIS F 256 ASN E 41 HIS E 151 ASN D 18 ASN D 186 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.189970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155739 restraints weight = 36566.013| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.73 r_work: 0.3792 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 21736 Z= 0.310 Angle : 0.752 16.144 29639 Z= 0.394 Chirality : 0.048 0.224 3303 Planarity : 0.005 0.063 3558 Dihedral : 15.216 176.711 3583 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 9.09 % Allowed : 34.24 % Favored : 56.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.89 (0.16), residues: 2416 helix: -1.37 (0.19), residues: 643 sheet: -0.58 (0.31), residues: 328 loop : -2.64 (0.14), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 23 TYR 0.020 0.002 TYR F 210 PHE 0.024 0.003 PHE G 95 TRP 0.016 0.002 TRP H 33 HIS 0.008 0.001 HIS H 250 Details of bonding type rmsd covalent geometry : bond 0.00700 (21736) covalent geometry : angle 0.75164 (29639) hydrogen bonds : bond 0.04879 ( 580) hydrogen bonds : angle 5.87876 ( 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 462 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 264 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7048 (tp) REVERT: A 97 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5452 (ptp) REVERT: A 156 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: A 184 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6018 (mp10) REVERT: A 249 LEU cc_start: 0.7531 (mp) cc_final: 0.6770 (tt) REVERT: B 129 MET cc_start: 0.1035 (tpp) cc_final: 0.0576 (tpp) REVERT: B 151 THR cc_start: 0.2722 (OUTLIER) cc_final: 0.2497 (t) REVERT: I 158 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6585 (mt) REVERT: I 244 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: I 263 THR cc_start: 0.7948 (p) cc_final: 0.7629 (t) REVERT: H 100 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7531 (mt) REVERT: H 104 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: H 112 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.4523 (m-10) REVERT: H 184 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: H 200 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.4999 (t80) REVERT: H 244 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: G 119 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6569 (m-80) REVERT: G 300 LEU cc_start: 0.3178 (OUTLIER) cc_final: 0.2725 (mp) REVERT: G 328 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.3900 (tpp) REVERT: F 19 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7357 (mm) REVERT: F 21 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8436 (m-80) REVERT: F 98 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: F 329 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: E 114 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6410 (t80) REVERT: E 149 TRP cc_start: 0.7936 (m100) cc_final: 0.7479 (m100) REVERT: E 151 ASN cc_start: 0.8440 (m-40) cc_final: 0.8146 (m110) REVERT: D 43 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7263 (m-80) REVERT: D 206 TYR cc_start: 0.4743 (p90) cc_final: 0.4427 (p90) REVERT: J 74 TRP cc_start: 0.6975 (t60) cc_final: 0.6660 (t60) REVERT: J 146 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6956 (t80) outliers start: 198 outliers final: 119 residues processed: 419 average time/residue: 0.1332 time to fit residues: 89.5175 Evaluate side-chains 386 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 244 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU 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 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 98 LEU 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 28 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 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 285 SER Chi-restraints excluded: chain I residue 293 ASP 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 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 184 GLU 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 85 SER Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 128 GLU 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 19 LEU Chi-restraints excluded: chain F residue 20 SER 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 223 VAL 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 267 ASP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 139 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 35 THR 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 190 ASN Chi-restraints excluded: chain D residue 210 TYR 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 169 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 149 optimal weight: 8.9990 chunk 33 optimal weight: 0.0670 chunk 129 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 37 optimal weight: 40.0000 chunk 84 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 151 ASN G 190 ASN ** E 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.189153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155110 restraints weight = 36782.611| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.78 r_work: 0.3784 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 21736 Z= 0.291 Angle : 0.731 16.331 29639 Z= 0.384 Chirality : 0.047 0.201 3303 Planarity : 0.005 0.057 3558 Dihedral : 15.212 175.235 3583 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 10.05 % Allowed : 33.59 % Favored : 56.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.15), residues: 2416 helix: -1.47 (0.18), residues: 658 sheet: -0.90 (0.30), residues: 345 loop : -2.77 (0.14), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 291 TYR 0.024 0.002 TYR E 169 PHE 0.065 0.002 PHE G 131 TRP 0.032 0.002 TRP D 149 HIS 0.009 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00665 (21736) covalent geometry : angle 0.73108 (29639) hydrogen bonds : bond 0.04662 ( 580) hydrogen bonds : angle 5.86883 ( 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 467 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 248 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6917 (tp) REVERT: A 97 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.5265 (ptp) REVERT: A 156 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: A 184 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6057 (mp10) REVERT: A 249 LEU cc_start: 0.7576 (mp) cc_final: 0.6806 (tt) REVERT: B 129 MET cc_start: 0.1099 (tpp) cc_final: 0.0647 (tpp) REVERT: B 151 THR cc_start: 0.2746 (OUTLIER) cc_final: 0.2529 (t) REVERT: I 158 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6636 (mt) REVERT: I 244 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: I 263 THR cc_start: 0.7946 (p) cc_final: 0.7664 (t) REVERT: H 47 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8230 (mp) REVERT: H 100 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7572 (mt) REVERT: H 104 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.5828 (tm-30) REVERT: H 112 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.4164 (m-10) REVERT: H 200 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.4954 (t80) REVERT: H 244 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: G 300 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2591 (mp) REVERT: G 328 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4226 (tpp) REVERT: F 19 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7284 (mm) REVERT: F 21 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: F 77 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6485 (pp30) REVERT: F 98 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7838 (ttmm) REVERT: F 253 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8061 (tptm) REVERT: F 329 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: E 114 TYR cc_start: 0.7506 (OUTLIER) cc_final: 0.6427 (t80) REVERT: E 149 TRP cc_start: 0.7949 (m100) cc_final: 0.7513 (m100) REVERT: E 151 ASN cc_start: 0.8462 (m-40) cc_final: 0.8115 (m110) REVERT: E 205 GLU cc_start: 0.5967 (OUTLIER) cc_final: 0.5728 (tp30) REVERT: D 29 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: D 206 TYR cc_start: 0.4709 (p90) cc_final: 0.4420 (p90) REVERT: J 146 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6959 (t80) outliers start: 219 outliers final: 141 residues processed: 432 average time/residue: 0.1309 time to fit residues: 92.8176 Evaluate side-chains 402 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 236 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 LEU 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 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 29 HIS 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 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 41 HIS Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 28 THR 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 97 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU 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 205 GLU 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 269 THR 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 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 108 SER 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 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 19 LEU Chi-restraints excluded: chain F residue 20 SER 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 77 GLN Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR 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 253 LYS Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 267 ASP 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 301 ILE 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 28 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 38 LEU 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 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 157 ILE Chi-restraints excluded: chain E residue 205 GLU 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 306 LEU 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 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 190 ASN Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 167 THR 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 249 CYS Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 119 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 186 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 181 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN F 317 HIS ** 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 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** J 39 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 = 0.4390 r_free = 0.4390 target = 0.193627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.158992 restraints weight = 36591.140| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.84 r_work: 0.3842 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21736 Z= 0.145 Angle : 0.581 11.288 29639 Z= 0.307 Chirality : 0.042 0.205 3303 Planarity : 0.004 0.049 3558 Dihedral : 14.972 174.348 3583 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.53 % Allowed : 36.16 % Favored : 56.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.16), residues: 2416 helix: -0.91 (0.20), residues: 645 sheet: -0.67 (0.30), residues: 334 loop : -2.56 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 115 TYR 0.023 0.001 TYR E 169 PHE 0.040 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 covalent geometry : bond 0.00328 (21736) covalent geometry : angle 0.58085 (29639) hydrogen bonds : bond 0.03679 ( 580) hydrogen bonds : angle 5.36317 ( 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 434 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 270 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.6816 (tp) REVERT: A 97 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.5431 (ptp) REVERT: A 156 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: A 184 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: A 249 LEU cc_start: 0.7687 (mp) cc_final: 0.6949 (tt) REVERT: B 56 ASN cc_start: 0.5642 (OUTLIER) cc_final: 0.5197 (p0) REVERT: B 129 MET cc_start: 0.1077 (tpp) cc_final: 0.0659 (tpp) REVERT: I 158 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6428 (mt) REVERT: I 244 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: I 263 THR cc_start: 0.7970 (p) cc_final: 0.7658 (t) REVERT: H 47 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8182 (mp) REVERT: H 100 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7500 (mt) REVERT: H 112 TYR cc_start: 0.5009 (OUTLIER) cc_final: 0.4058 (m-10) REVERT: H 200 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4771 (t80) REVERT: H 229 MET cc_start: 0.4443 (OUTLIER) cc_final: 0.3721 (mtt) REVERT: G 300 LEU cc_start: 0.2819 (OUTLIER) cc_final: 0.2432 (mp) REVERT: G 328 MET cc_start: 0.5073 (OUTLIER) cc_final: 0.3834 (tpp) REVERT: F 19 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7096 (mm) REVERT: F 77 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6472 (pp30) REVERT: F 98 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7765 (ttmm) REVERT: F 159 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5944 (pm20) REVERT: F 329 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: E 98 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6860 (ttmt) REVERT: E 149 TRP cc_start: 0.7761 (m100) cc_final: 0.7457 (m100) REVERT: E 151 ASN cc_start: 0.8413 (m-40) cc_final: 0.8048 (m110) REVERT: D 34 GLN cc_start: 0.7595 (mp10) cc_final: 0.7184 (mp10) REVERT: D 150 ARG cc_start: 0.6975 (mtm180) cc_final: 0.6596 (mtm180) REVERT: D 206 TYR cc_start: 0.4620 (p90) cc_final: 0.4307 (p90) REVERT: J 146 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6843 (t80) outliers start: 164 outliers final: 100 residues processed: 398 average time/residue: 0.1399 time to fit residues: 88.3343 Evaluate side-chains 372 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 251 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 80 LEU 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 232 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN 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 157 ILE Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 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 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 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 119 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 181 THR 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 232 ASP 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 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 99 VAL Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 258 LEU 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 19 LEU Chi-restraints excluded: chain F residue 20 SER 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 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 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 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 190 ASN 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 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 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 186 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 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE 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 146 PHE Chi-restraints excluded: chain J residue 164 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 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 143 optimal weight: 0.0040 chunk 196 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 242 optimal weight: 20.0000 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS ** 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 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 ** J 39 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 = 0.4425 r_free = 0.4425 target = 0.196998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162569 restraints weight = 36508.220| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.87 r_work: 0.3887 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21736 Z= 0.110 Angle : 0.543 9.458 29639 Z= 0.284 Chirality : 0.041 0.195 3303 Planarity : 0.004 0.051 3558 Dihedral : 14.797 176.346 3583 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 6.65 % Allowed : 36.48 % 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 aren not related in a simple way. whole: -2.34 (0.16), residues: 2416 helix: -0.52 (0.20), residues: 646 sheet: -0.52 (0.31), residues: 322 loop : -2.41 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 115 TYR 0.019 0.001 TYR E 169 PHE 0.020 0.001 PHE G 131 TRP 0.013 0.001 TRP I 149 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00247 (21736) covalent geometry : angle 0.54282 (29639) hydrogen bonds : bond 0.03250 ( 580) hydrogen bonds : angle 5.05360 ( 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 416 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 271 time to evaluate : 0.811 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 97 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5214 (ptp) REVERT: A 99 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: A 184 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.5893 (mp10) REVERT: A 249 LEU cc_start: 0.7662 (mp) cc_final: 0.6915 (tt) REVERT: B 56 ASN cc_start: 0.5590 (OUTLIER) cc_final: 0.5138 (p0) REVERT: B 129 MET cc_start: 0.1146 (tpp) cc_final: 0.0822 (tpp) REVERT: I 158 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6141 (mt) REVERT: I 244 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: I 263 THR cc_start: 0.8008 (p) cc_final: 0.7679 (t) REVERT: H 47 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8099 (mp) REVERT: H 100 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7463 (mt) REVERT: H 112 TYR cc_start: 0.4878 (OUTLIER) cc_final: 0.3976 (m-10) REVERT: H 200 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4469 (t80) REVERT: H 229 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.3745 (mtt) REVERT: G 300 LEU cc_start: 0.2903 (OUTLIER) cc_final: 0.2617 (mp) REVERT: G 328 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.3490 (tpp) REVERT: F 21 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: F 77 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6454 (pp30) REVERT: F 98 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7697 (ttmm) REVERT: F 159 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.5854 (pm20) REVERT: E 149 TRP cc_start: 0.7608 (m100) cc_final: 0.7393 (m100) REVERT: E 151 ASN cc_start: 0.8399 (m-40) cc_final: 0.8052 (m110) REVERT: E 205 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.5625 (tp30) REVERT: D 206 TYR cc_start: 0.4607 (p90) cc_final: 0.4239 (p90) outliers start: 145 outliers final: 88 residues processed: 383 average time/residue: 0.1304 time to fit residues: 80.5958 Evaluate side-chains 364 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 258 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 190 ASN 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 270 THR Chi-restraints excluded: chain I residue 293 ASP 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 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 296 SER Chi-restraints excluded: chain H residue 328 MET 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 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 300 LEU 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 77 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain E residue 28 THR 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 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 139 VAL 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 288 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 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 Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 219 optimal weight: 9.9990 chunk 146 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 209 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 120 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 256 ASN ** 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 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4392 r_free = 0.4392 target = 0.193797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159412 restraints weight = 36683.675| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.85 r_work: 0.3843 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21736 Z= 0.167 Angle : 0.595 11.604 29639 Z= 0.310 Chirality : 0.043 0.186 3303 Planarity : 0.004 0.053 3558 Dihedral : 14.828 175.748 3583 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 7.99 % Allowed : 35.43 % 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 aren not related in a simple way. whole: -2.38 (0.16), residues: 2416 helix: -0.57 (0.20), residues: 640 sheet: -0.56 (0.30), residues: 342 loop : -2.45 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 137 TYR 0.017 0.001 TYR E 169 PHE 0.032 0.002 PHE G 131 TRP 0.017 0.001 TRP E 33 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00384 (21736) covalent geometry : angle 0.59494 (29639) hydrogen bonds : bond 0.03667 ( 580) hydrogen bonds : angle 5.18981 ( 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 431 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 257 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7003 (tp) REVERT: A 97 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5293 (ptp) REVERT: A 99 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: A 184 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.5960 (mp10) REVERT: A 249 LEU cc_start: 0.7737 (mp) cc_final: 0.6980 (tt) REVERT: B 56 ASN cc_start: 0.5527 (OUTLIER) cc_final: 0.5068 (p0) REVERT: B 129 MET cc_start: 0.1168 (tpp) cc_final: 0.0776 (tpp) REVERT: I 158 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6529 (mt) REVERT: I 244 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7194 (mt-10) REVERT: I 263 THR cc_start: 0.8023 (p) cc_final: 0.7696 (t) REVERT: H 47 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8061 (mp) REVERT: H 100 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7574 (mt) REVERT: H 112 TYR cc_start: 0.5020 (OUTLIER) cc_final: 0.4094 (m-10) REVERT: H 200 PHE cc_start: 0.5301 (OUTLIER) cc_final: 0.4531 (t80) REVERT: H 229 MET cc_start: 0.4423 (OUTLIER) cc_final: 0.3696 (mtt) REVERT: H 244 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: G 300 LEU cc_start: 0.2945 (OUTLIER) cc_final: 0.2579 (mp) REVERT: G 328 MET cc_start: 0.4939 (OUTLIER) cc_final: 0.3735 (tpp) REVERT: F 21 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: F 77 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6492 (pp30) REVERT: F 98 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7729 (ttmm) REVERT: F 159 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.5933 (pm20) REVERT: F 239 LYS cc_start: 0.7123 (mttp) cc_final: 0.6799 (mtpp) REVERT: F 329 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: E 23 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7926 (ttm-80) REVERT: E 149 TRP cc_start: 0.7761 (m100) cc_final: 0.7399 (m100) REVERT: E 151 ASN cc_start: 0.8407 (m-40) cc_final: 0.8049 (m110) REVERT: E 205 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5609 (tp30) REVERT: D 206 TYR cc_start: 0.4572 (p90) cc_final: 0.4279 (p90) REVERT: J 146 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6800 (t80) outliers start: 174 outliers final: 122 residues processed: 398 average time/residue: 0.1289 time to fit residues: 83.5782 Evaluate side-chains 394 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 250 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 80 LEU 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 174 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 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 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 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 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 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE 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 261 ILE 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 27 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 252 GLN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 297 PHE Chi-restraints excluded: chain G residue 300 LEU 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 77 GLN Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR 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 94 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 36 ASP 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 186 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 261 ILE Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 198 optimal weight: 0.1980 chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 235 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.197382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.162727 restraints weight = 36313.266| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.95 r_work: 0.3894 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21736 Z= 0.108 Angle : 0.552 10.507 29639 Z= 0.287 Chirality : 0.041 0.280 3303 Planarity : 0.004 0.054 3558 Dihedral : 14.728 176.405 3583 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 6.29 % Allowed : 37.13 % 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 aren not related in a simple way. whole: -2.19 (0.16), residues: 2416 helix: -0.36 (0.21), residues: 641 sheet: -0.43 (0.30), residues: 340 loop : -2.35 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 150 TYR 0.026 0.001 TYR E 169 PHE 0.030 0.001 PHE D 32 TRP 0.013 0.001 TRP E 33 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00243 (21736) covalent geometry : angle 0.55197 (29639) hydrogen bonds : bond 0.03214 ( 580) hydrogen bonds : angle 4.96639 ( 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 397 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 260 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.5576 (OUTLIER) cc_final: 0.5215 (ptp) REVERT: A 99 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: A 184 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.5904 (mp10) REVERT: A 249 LEU cc_start: 0.7610 (mp) cc_final: 0.6882 (tt) REVERT: B 56 ASN cc_start: 0.5496 (OUTLIER) cc_final: 0.5033 (p0) REVERT: B 129 MET cc_start: 0.1146 (tpp) cc_final: 0.0817 (tpp) REVERT: I 158 ILE cc_start: 0.6498 (OUTLIER) cc_final: 0.6259 (mt) REVERT: I 244 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: I 263 THR cc_start: 0.8035 (p) cc_final: 0.7700 (t) REVERT: H 47 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8084 (mp) REVERT: H 100 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (mt) REVERT: H 112 TYR cc_start: 0.4868 (OUTLIER) cc_final: 0.3980 (m-10) REVERT: H 200 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.4344 (t80) REVERT: H 229 MET cc_start: 0.4419 (OUTLIER) cc_final: 0.3745 (mtt) REVERT: G 300 LEU cc_start: 0.2810 (OUTLIER) cc_final: 0.2516 (mp) REVERT: G 328 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.3369 (tpp) REVERT: F 21 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: F 98 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7739 (ttmm) REVERT: F 159 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: E 151 ASN cc_start: 0.8381 (m-40) cc_final: 0.8036 (m110) REVERT: D 206 TYR cc_start: 0.4612 (p90) cc_final: 0.4241 (p90) outliers start: 137 outliers final: 102 residues processed: 371 average time/residue: 0.1251 time to fit residues: 75.4487 Evaluate side-chains 370 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 252 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 68 LYS 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 174 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 41 HIS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 270 THR Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 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 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 294 THR 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 99 VAL Chi-restraints excluded: chain G residue 108 SER Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 189 ILE 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 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 223 VAL 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 35 THR Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 139 VAL 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 288 ILE 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 167 THR Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 120 GLN F 256 ASN ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 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 = 0.4422 r_free = 0.4422 target = 0.196814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.161842 restraints weight = 36218.644| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.30 r_work: 0.3876 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21736 Z= 0.122 Angle : 0.562 10.582 29639 Z= 0.292 Chirality : 0.041 0.287 3303 Planarity : 0.004 0.062 3558 Dihedral : 14.704 176.165 3583 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 6.98 % Allowed : 36.58 % Favored : 56.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.16), residues: 2416 helix: -0.32 (0.21), residues: 642 sheet: -0.45 (0.30), residues: 345 loop : -2.31 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 150 TYR 0.044 0.001 TYR E 169 PHE 0.026 0.001 PHE D 32 TRP 0.020 0.001 TRP E 33 HIS 0.003 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00279 (21736) covalent geometry : angle 0.56225 (29639) hydrogen bonds : bond 0.03238 ( 580) hydrogen bonds : angle 4.94353 ( 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 410 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 258 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.5658 (OUTLIER) cc_final: 0.5296 (ptp) REVERT: A 99 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: A 177 ASP cc_start: 0.7244 (m-30) cc_final: 0.6941 (p0) REVERT: A 184 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.5972 (mp10) REVERT: A 249 LEU cc_start: 0.7661 (mp) cc_final: 0.6879 (tt) REVERT: B 56 ASN cc_start: 0.5509 (OUTLIER) cc_final: 0.5049 (p0) REVERT: B 129 MET cc_start: 0.1181 (tpp) cc_final: 0.0839 (tpp) REVERT: I 158 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6279 (mt) REVERT: I 244 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7036 (mt-10) REVERT: I 263 THR cc_start: 0.8052 (p) cc_final: 0.7704 (t) REVERT: H 47 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8119 (mp) REVERT: H 112 TYR cc_start: 0.4900 (OUTLIER) cc_final: 0.4006 (m-10) REVERT: H 200 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4421 (t80) REVERT: H 229 MET cc_start: 0.4451 (OUTLIER) cc_final: 0.3780 (mtt) REVERT: G 300 LEU cc_start: 0.2916 (OUTLIER) cc_final: 0.2597 (mp) REVERT: G 328 MET cc_start: 0.4729 (OUTLIER) cc_final: 0.3427 (tpp) REVERT: F 21 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8434 (m-80) REVERT: F 29 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: F 77 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6421 (pp30) REVERT: F 98 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7692 (ttmm) REVERT: F 159 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.5874 (pm20) REVERT: E 151 ASN cc_start: 0.8517 (m-40) cc_final: 0.8191 (m110) REVERT: D 206 TYR cc_start: 0.4568 (p90) cc_final: 0.4197 (p90) REVERT: J 146 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6719 (t80) outliers start: 152 outliers final: 116 residues processed: 377 average time/residue: 0.1306 time to fit residues: 80.2207 Evaluate side-chains 383 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 249 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 68 LYS Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 80 LEU 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 174 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE 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 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 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 23 ARG Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 288 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 108 SER 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 189 ILE 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 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 77 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR 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 313 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 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 37 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 139 VAL 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 288 ILE 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 146 PHE Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 45 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 71 optimal weight: 0.0030 chunk 156 optimal weight: 0.6980 chunk 245 optimal weight: 30.0000 chunk 229 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 120 GLN F 256 ASN D 18 ASN ** D 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 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 = 0.4428 r_free = 0.4428 target = 0.197455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163325 restraints weight = 36542.631| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 2.90 r_work: 0.3894 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21736 Z= 0.113 Angle : 0.557 10.645 29639 Z= 0.288 Chirality : 0.041 0.289 3303 Planarity : 0.004 0.068 3558 Dihedral : 14.669 176.374 3583 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 6.61 % Allowed : 36.76 % Favored : 56.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.16), residues: 2416 helix: -0.25 (0.21), residues: 642 sheet: -0.43 (0.30), residues: 333 loop : -2.27 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 150 TYR 0.045 0.001 TYR E 169 PHE 0.030 0.001 PHE G 200 TRP 0.024 0.001 TRP E 33 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00258 (21736) covalent geometry : angle 0.55674 (29639) hydrogen bonds : bond 0.03183 ( 580) hydrogen bonds : angle 4.90658 ( 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 401 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 257 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5302 (ptp) REVERT: A 99 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: A 177 ASP cc_start: 0.7225 (m-30) cc_final: 0.6922 (p0) REVERT: A 184 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.5985 (mp10) REVERT: A 249 LEU cc_start: 0.7650 (mp) cc_final: 0.6852 (tt) REVERT: B 56 ASN cc_start: 0.5494 (OUTLIER) cc_final: 0.5040 (p0) REVERT: B 129 MET cc_start: 0.1216 (tpp) cc_final: 0.0784 (tpp) REVERT: I 158 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6222 (mt) REVERT: I 244 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: I 263 THR cc_start: 0.8044 (p) cc_final: 0.7697 (t) REVERT: H 100 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7472 (mt) REVERT: H 112 TYR cc_start: 0.4865 (OUTLIER) cc_final: 0.3972 (m-10) REVERT: H 200 PHE cc_start: 0.5086 (OUTLIER) cc_final: 0.4378 (t80) REVERT: H 229 MET cc_start: 0.4469 (OUTLIER) cc_final: 0.3810 (mtt) REVERT: G 300 LEU cc_start: 0.2869 (OUTLIER) cc_final: 0.2552 (mp) REVERT: G 328 MET cc_start: 0.4647 (OUTLIER) cc_final: 0.3277 (tpp) REVERT: F 21 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: F 29 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: F 77 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.6410 (pp30) REVERT: F 98 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7714 (ttmm) REVERT: F 159 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5880 (pm20) REVERT: E 151 ASN cc_start: 0.8537 (m-40) cc_final: 0.8257 (m110) REVERT: D 206 TYR cc_start: 0.4578 (p90) cc_final: 0.4209 (p90) REVERT: D 303 ARG cc_start: 0.5509 (ttp80) cc_final: 0.4997 (ttt180) REVERT: J 146 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6661 (t80) outliers start: 144 outliers final: 114 residues processed: 370 average time/residue: 0.1421 time to fit residues: 85.1909 Evaluate side-chains 380 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 248 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 68 LYS 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 174 ASP Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 164 ILE 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 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 VAL Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 244 GLU Chi-restraints excluded: chain I residue 246 SER Chi-restraints excluded: chain I residue 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 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 102 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE 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 252 GLN Chi-restraints excluded: chain H residue 261 ILE 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 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 120 GLN Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 189 ILE 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 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 77 GLN Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 120 GLN Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR 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 313 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 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 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 217 ILE Chi-restraints excluded: chain D residue 223 VAL 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 146 PHE Chi-restraints excluded: chain J residue 174 SER Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 249 CYS Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 135 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 0.0070 chunk 183 optimal weight: 5.9990 chunk 143 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 199 optimal weight: 0.3980 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** J 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 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 = 0.4427 r_free = 0.4427 target = 0.197333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162291 restraints weight = 36291.917| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 3.26 r_work: 0.3884 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2300 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= 0.115 Angle : 0.561 10.585 29639 Z= 0.290 Chirality : 0.041 0.271 3303 Planarity : 0.004 0.072 3558 Dihedral : 14.646 176.388 3583 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 6.65 % Allowed : 36.44 % Favored : 56.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.16), residues: 2416 helix: -0.21 (0.21), residues: 642 sheet: -0.42 (0.30), residues: 333 loop : -2.26 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 150 TYR 0.041 0.001 TYR E 169 PHE 0.030 0.001 PHE G 200 TRP 0.023 0.001 TRP E 33 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00264 (21736) covalent geometry : angle 0.56065 (29639) hydrogen bonds : bond 0.03178 ( 580) hydrogen bonds : angle 4.88193 ( 1662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5372.84 seconds wall clock time: 92 minutes 55.68 seconds (5575.68 seconds total)