Starting phenix.real_space_refine on Wed Jun 18 06:14:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh9_39285/06_2025/8yh9_39285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh9_39285/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh9_39285/06_2025/8yh9_39285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh9_39285/06_2025/8yh9_39285.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh9_39285/06_2025/8yh9_39285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh9_39285/06_2025/8yh9_39285.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.03, per 1000 atoms: 0.57 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: 4.98 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 7.47 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: 6.41 Time building geometry restraints manager: 5.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5369 1.33 - 1.45: 4403 1.45 - 1.57: 11687 1.57 - 1.69: 118 1.69 - 1.81: 159 Bond restraints: 21736 Sorted by residual: bond pdb=" CB TYR F 125 " pdb=" CG TYR F 125 " ideal model delta sigma weight residual 1.512 1.560 -0.048 2.20e-02 2.07e+03 4.70e+00 bond pdb=" N ASP I 310 " pdb=" CA ASP I 310 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.60e+00 bond pdb=" 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 50.960 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.220 ------------------------------------------------------------------------------- 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 : 7.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP E 33 HIS 0.007 0.001 HIS A 204 PHE 0.035 0.002 PHE G 200 TYR 0.031 0.002 TYR I 206 ARG 0.011 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.17592 ( 580) hydrogen bonds : angle 7.59523 ( 1662) covalent geometry : bond 0.00390 (21736) covalent geometry : angle 0.76078 (29639) *********************** 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 : 2.433 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: 0.2995 time to fit residues: 139.4300 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 : 2.188 ------------------------------------------------------------------------------- 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 209 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 0.0010 chunk 64 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 194 optimal weight: 0.0970 chunk 75 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** G 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 J 145 GLN J 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.201217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.167279 restraints weight = 35913.508| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.93 r_work: 0.3934 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21736 Z= 0.119 Angle : 0.533 9.353 29639 Z= 0.283 Chirality : 0.040 0.201 3303 Planarity : 0.004 0.072 3558 Dihedral : 14.929 179.599 3596 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.36 % Allowed : 37.13 % Favored : 58.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2416 helix: -1.08 (0.19), residues: 642 sheet: 0.00 (0.32), residues: 313 loop : -2.45 (0.14), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 33 HIS 0.004 0.001 HIS D 317 PHE 0.021 0.001 PHE G 200 TYR 0.016 0.001 TYR D 125 ARG 0.004 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 580) hydrogen bonds : angle 5.34071 ( 1662) covalent geometry : bond 0.00260 (21736) covalent geometry : angle 0.53336 (29639) *********************** 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 374 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 279 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7486 (t70) cc_final: 0.7116 (t-170) REVERT: A 184 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6279 (mp10) REVERT: I 91 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7683 (pt) REVERT: I 158 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5978 (mt) REVERT: I 198 ASP cc_start: 0.7186 (m-30) cc_final: 0.6980 (m-30) REVERT: H 47 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8029 (mp) REVERT: G 119 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6429 (m-80) outliers start: 95 outliers final: 45 residues processed: 345 average time/residue: 0.2865 time to fit residues: 160.6497 Evaluate side-chains 309 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.412 ------------------------------------------------------------------------------- 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 91 LEU Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 34 GLN Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 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 35 THR Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 239 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 204 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 107 optimal weight: 0.9980 overall best weight: 2.2144 ------------------------------------------------------------------------------- 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 I 140 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN G 34 GLN G 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN D 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.196911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163262 restraints weight = 36176.695| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.76 r_work: 0.3891 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1384 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= 0.151 Angle : 0.557 12.095 29639 Z= 0.293 Chirality : 0.041 0.191 3303 Planarity : 0.004 0.059 3558 Dihedral : 14.840 177.689 3583 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 5.97 % Allowed : 35.84 % Favored : 58.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.16), residues: 2416 helix: -0.73 (0.20), residues: 635 sheet: -0.12 (0.32), residues: 316 loop : -2.40 (0.14), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 33 HIS 0.006 0.001 HIS E 250 PHE 0.023 0.002 PHE G 200 TYR 0.020 0.001 TYR E 112 ARG 0.004 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 580) hydrogen bonds : angle 5.19488 ( 1662) covalent geometry : bond 0.00341 (21736) covalent geometry : angle 0.55689 (29639) *********************** 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 397 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 267 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7521 (t70) cc_final: 0.7298 (t-90) REVERT: A 184 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6178 (mp10) REVERT: I 91 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7905 (pt) REVERT: I 158 ILE cc_start: 0.6641 (OUTLIER) cc_final: 0.6203 (mt) REVERT: I 198 ASP cc_start: 0.7349 (m-30) cc_final: 0.7062 (m-30) REVERT: H 112 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.4849 (m-10) REVERT: G 328 MET cc_start: 0.4661 (OUTLIER) cc_final: 0.3266 (tpp) REVERT: F 159 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.5912 (pm20) REVERT: F 329 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: E 149 TRP cc_start: 0.7724 (m100) cc_final: 0.7318 (m100) REVERT: E 151 ASN cc_start: 0.8460 (m-40) cc_final: 0.8080 (m110) outliers start: 130 outliers final: 72 residues processed: 362 average time/residue: 0.2908 time to fit residues: 170.8944 Evaluate side-chains 330 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 251 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 252 CYS Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 49 ASP 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 91 LEU Chi-restraints excluded: chain I residue 140 ASN Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 324 ILE Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 307 LYS Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 329 PHE 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 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 136 LYS 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 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 12 optimal weight: 0.0670 chunk 185 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 51 optimal weight: 0.0370 chunk 199 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 56 ASN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN F 256 ASN E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.201262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167266 restraints weight = 36548.726| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.00 r_work: 0.3944 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21736 Z= 0.092 Angle : 0.496 10.438 29639 Z= 0.261 Chirality : 0.040 0.199 3303 Planarity : 0.004 0.051 3558 Dihedral : 14.691 178.196 3583 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.64 % Allowed : 37.17 % Favored : 58.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.16), residues: 2416 helix: -0.39 (0.20), residues: 646 sheet: 0.07 (0.32), residues: 310 loop : -2.31 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 241 HIS 0.003 0.000 HIS A 204 PHE 0.024 0.001 PHE G 200 TYR 0.012 0.001 TYR F 125 ARG 0.004 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 580) hydrogen bonds : angle 4.81849 ( 1662) covalent geometry : bond 0.00198 (21736) covalent geometry : angle 0.49596 (29639) *********************** 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 383 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 282 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 HIS cc_start: 0.7604 (t70) cc_final: 0.7378 (t-90) REVERT: A 184 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6177 (mp10) REVERT: A 222 PHE cc_start: 0.7896 (m-80) cc_final: 0.7609 (m-80) REVERT: B 129 MET cc_start: 0.1340 (tpp) cc_final: 0.0919 (tpp) REVERT: I 91 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7734 (pt) REVERT: I 198 ASP cc_start: 0.7145 (m-30) cc_final: 0.6830 (m-30) REVERT: H 100 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7436 (mt) REVERT: H 111 ASP cc_start: 0.5806 (t70) cc_final: 0.5493 (t0) REVERT: H 242 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7968 (ttmm) REVERT: G 119 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: G 157 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7420 (tt) REVERT: G 224 TYR cc_start: 0.8383 (m-80) cc_final: 0.8088 (m-80) REVERT: F 159 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5850 (pm20) REVERT: F 329 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: E 95 PHE cc_start: 0.5903 (p90) cc_final: 0.5601 (p90) REVERT: E 151 ASN cc_start: 0.8469 (m-40) cc_final: 0.8122 (m110) outliers start: 101 outliers final: 53 residues processed: 353 average time/residue: 0.3074 time to fit residues: 173.4881 Evaluate side-chains 315 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 254 time to evaluate : 2.404 ------------------------------------------------------------------------------- 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 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 293 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain H residue 242 LYS Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 284 ARG 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 35 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 264 TRP Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 329 PHE 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 131 PHE Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 212 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 118 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 21 ASN A 204 HIS ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN E 41 HIS D 18 ASN J 71 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.194282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.160279 restraints weight = 36504.378| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 2.72 r_work: 0.3853 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21736 Z= 0.199 Angle : 0.616 13.690 29639 Z= 0.322 Chirality : 0.043 0.189 3303 Planarity : 0.004 0.049 3558 Dihedral : 14.820 177.942 3583 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 6.88 % Allowed : 35.29 % Favored : 57.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.16), residues: 2416 helix: -0.60 (0.20), residues: 643 sheet: -0.24 (0.31), residues: 325 loop : -2.37 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 149 HIS 0.007 0.001 HIS E 250 PHE 0.023 0.002 PHE G 200 TYR 0.020 0.002 TYR E 112 ARG 0.005 0.001 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 580) hydrogen bonds : angle 5.17636 ( 1662) covalent geometry : bond 0.00453 (21736) covalent geometry : angle 0.61578 (29639) *********************** 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 416 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 266 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.6929 (tp) REVERT: A 181 HIS cc_start: 0.7601 (t70) cc_final: 0.7381 (t-90) REVERT: A 184 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6111 (mp10) REVERT: B 56 ASN cc_start: 0.5635 (OUTLIER) cc_final: 0.5135 (p0) REVERT: B 129 MET cc_start: 0.1366 (tpp) cc_final: 0.0934 (tpp) REVERT: I 158 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6539 (mt) REVERT: I 198 ASP cc_start: 0.7468 (m-30) cc_final: 0.7156 (m-30) REVERT: I 244 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: H 77 GLN cc_start: 0.7141 (tt0) cc_final: 0.6791 (tt0) REVERT: H 100 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7523 (mt) REVERT: H 112 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4654 (m-10) REVERT: H 200 PHE cc_start: 0.5274 (OUTLIER) cc_final: 0.4826 (t80) REVERT: H 244 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: G 119 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6846 (m-80) REVERT: G 328 MET cc_start: 0.4972 (OUTLIER) cc_final: 0.3581 (tpp) REVERT: F 19 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7302 (mm) REVERT: F 21 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: F 159 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6040 (pm20) REVERT: F 329 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: E 98 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6785 (ttmp) REVERT: E 149 TRP cc_start: 0.7835 (m100) cc_final: 0.7459 (m100) REVERT: E 151 ASN cc_start: 0.8499 (m-40) cc_final: 0.8168 (m110) REVERT: J 43 PHE cc_start: 0.6698 (t80) cc_final: 0.6485 (t80) REVERT: J 146 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6868 (t80) outliers start: 150 outliers final: 91 residues processed: 379 average time/residue: 0.3012 time to fit residues: 180.7071 Evaluate side-chains 362 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 254 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 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 H residue 23 ARG Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 81 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 298 TYR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 140 ASN 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 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 50 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 178 ASN Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 219 CYS Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 231 PHE Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 301 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 23 ARG 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 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 177 PHE Chi-restraints excluded: chain D residue 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 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 275 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 38 optimal weight: 20.0000 chunk 52 optimal weight: 0.0050 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 157 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- 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 80 GLN ** I 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 317 HIS F 256 ASN E 41 HIS ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.194080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159894 restraints weight = 36306.589| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.76 r_work: 0.3847 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21736 Z= 0.188 Angle : 0.608 14.192 29639 Z= 0.318 Chirality : 0.043 0.187 3303 Planarity : 0.004 0.045 3558 Dihedral : 14.865 176.565 3583 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 7.02 % Allowed : 35.61 % Favored : 57.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.16), residues: 2416 helix: -0.66 (0.20), residues: 647 sheet: -0.26 (0.31), residues: 319 loop : -2.41 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 33 HIS 0.005 0.001 HIS E 250 PHE 0.054 0.002 PHE G 131 TYR 0.030 0.002 TYR E 169 ARG 0.005 0.000 ARG E 23 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 580) hydrogen bonds : angle 5.19436 ( 1662) covalent geometry : bond 0.00429 (21736) covalent geometry : angle 0.60840 (29639) *********************** 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: 153 poor density : 263 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.6929 (tp) REVERT: A 99 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 181 HIS cc_start: 0.7734 (t70) cc_final: 0.7526 (t-90) REVERT: A 184 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6060 (mp10) REVERT: B 56 ASN cc_start: 0.5475 (OUTLIER) cc_final: 0.4961 (p0) REVERT: B 129 MET cc_start: 0.1243 (tpp) cc_final: 0.0769 (tpp) REVERT: I 158 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6488 (mt) REVERT: I 198 ASP cc_start: 0.7493 (m-30) cc_final: 0.7187 (m-30) REVERT: I 244 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: H 100 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7562 (mt) REVERT: H 112 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4364 (m-10) REVERT: H 200 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.4805 (t80) REVERT: H 207 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5920 (tt) REVERT: H 244 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: G 119 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: G 328 MET cc_start: 0.4897 (OUTLIER) cc_final: 0.3544 (tpp) REVERT: F 19 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7309 (mm) REVERT: F 159 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.5951 (pm20) REVERT: F 329 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: E 149 TRP cc_start: 0.7844 (m100) cc_final: 0.7431 (m100) REVERT: E 151 ASN cc_start: 0.8520 (m-40) cc_final: 0.8172 (m110) REVERT: J 146 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6931 (t80) outliers start: 153 outliers final: 100 residues processed: 378 average time/residue: 0.3111 time to fit residues: 191.2930 Evaluate side-chains 370 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 253 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 98 LEU 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 163 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 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 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 83 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 140 ASN Chi-restraints excluded: chain G residue 258 LEU Chi-restraints excluded: chain G residue 264 TRP 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 19 LEU Chi-restraints excluded: chain F residue 20 SER Chi-restraints excluded: chain F residue 50 THR 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 199 THR 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 232 ASP 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 93 ILE 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 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 136 LYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 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 324 ILE Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS 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 10 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 238 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 218 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 0.0030 chunk 231 optimal weight: 9.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- 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 F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.196761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.162013 restraints weight = 36321.192| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.87 r_work: 0.3874 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1984 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= 0.126 Angle : 0.554 12.582 29639 Z= 0.287 Chirality : 0.041 0.196 3303 Planarity : 0.004 0.046 3558 Dihedral : 14.743 175.788 3583 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 5.97 % Allowed : 36.85 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2416 helix: -0.43 (0.20), residues: 644 sheet: -0.26 (0.31), residues: 326 loop : -2.33 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 149 HIS 0.003 0.001 HIS E 250 PHE 0.027 0.001 PHE G 131 TYR 0.027 0.001 TYR E 169 ARG 0.004 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03364 ( 580) hydrogen bonds : angle 5.00280 ( 1662) covalent geometry : bond 0.00286 (21736) covalent geometry : angle 0.55423 (29639) *********************** 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 397 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 267 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASN cc_start: 0.5406 (m110) cc_final: 0.4779 (t0) REVERT: A 99 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: A 181 HIS cc_start: 0.7725 (t70) cc_final: 0.7443 (t-90) REVERT: A 184 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5970 (mp10) REVERT: B 56 ASN cc_start: 0.5568 (OUTLIER) cc_final: 0.5070 (p0) REVERT: B 129 MET cc_start: 0.1176 (tpp) cc_final: 0.0772 (tpp) REVERT: I 114 TYR cc_start: 0.7939 (t80) cc_final: 0.7650 (t80) REVERT: I 158 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6314 (mt) REVERT: I 198 ASP cc_start: 0.7323 (m-30) cc_final: 0.6984 (m-30) REVERT: I 244 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7039 (mt-10) REVERT: I 310 ASP cc_start: 0.6860 (m-30) cc_final: 0.6645 (p0) REVERT: H 100 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7544 (mt) REVERT: H 112 TYR cc_start: 0.4981 (OUTLIER) cc_final: 0.4165 (m-10) REVERT: H 200 PHE cc_start: 0.5177 (OUTLIER) cc_final: 0.4608 (t80) REVERT: H 229 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3738 (mtt) REVERT: H 244 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: G 119 TYR cc_start: 0.7210 (OUTLIER) cc_final: 0.6712 (m-80) REVERT: G 304 MET cc_start: 0.6342 (mpp) cc_final: 0.5532 (mpp) REVERT: G 328 MET cc_start: 0.4722 (OUTLIER) cc_final: 0.3448 (tpp) REVERT: F 19 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7097 (mm) REVERT: F 21 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: F 159 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5945 (pm20) REVERT: F 329 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: E 149 TRP cc_start: 0.7714 (m100) cc_final: 0.7472 (m100) REVERT: E 151 ASN cc_start: 0.8546 (m-40) cc_final: 0.8199 (m110) outliers start: 130 outliers final: 89 residues processed: 366 average time/residue: 0.3048 time to fit residues: 178.1317 Evaluate side-chains 365 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 260 time to evaluate : 2.467 ------------------------------------------------------------------------------- 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 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 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 158 ILE Chi-restraints excluded: chain I residue 163 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 190 ASN Chi-restraints excluded: chain I residue 219 CYS Chi-restraints excluded: chain I residue 229 MET 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 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 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 284 ARG 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 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN 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 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 21 PHE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain E residue 28 THR 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 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS Chi-restraints excluded: chain J residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 153 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 204 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 133 optimal weight: 0.0470 overall best weight: 2.1282 ------------------------------------------------------------------------------- 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** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.195706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161656 restraints weight = 36391.987| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.78 r_work: 0.3866 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21736 Z= 0.148 Angle : 0.577 12.684 29639 Z= 0.298 Chirality : 0.042 0.190 3303 Planarity : 0.004 0.048 3558 Dihedral : 14.742 176.296 3583 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 6.75 % Allowed : 35.89 % Favored : 57.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.16), residues: 2416 helix: -0.42 (0.20), residues: 641 sheet: -0.29 (0.30), residues: 331 loop : -2.33 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 149 HIS 0.004 0.001 HIS E 250 PHE 0.022 0.001 PHE G 131 TYR 0.033 0.001 TYR E 169 ARG 0.005 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 580) hydrogen bonds : angle 5.03928 ( 1662) covalent geometry : bond 0.00338 (21736) covalent geometry : angle 0.57671 (29639) *********************** 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 404 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 257 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.6912 (tp) REVERT: A 99 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: A 181 HIS cc_start: 0.7726 (t70) cc_final: 0.7458 (t-90) REVERT: A 184 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.5969 (mp10) REVERT: B 56 ASN cc_start: 0.5448 (OUTLIER) cc_final: 0.4935 (p0) REVERT: B 129 MET cc_start: 0.1262 (tpp) cc_final: 0.0896 (tpp) REVERT: I 114 TYR cc_start: 0.7975 (t80) cc_final: 0.7654 (t80) REVERT: I 158 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6396 (mt) REVERT: I 198 ASP cc_start: 0.7397 (m-30) cc_final: 0.7060 (m-30) REVERT: I 244 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: H 77 GLN cc_start: 0.7058 (tt0) cc_final: 0.6841 (tt0) REVERT: H 100 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7599 (mt) REVERT: H 104 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5779 (tm-30) REVERT: H 112 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.4232 (m-10) REVERT: H 200 PHE cc_start: 0.5245 (OUTLIER) cc_final: 0.4617 (t80) REVERT: H 207 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5832 (tt) REVERT: H 229 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.3789 (mtt) REVERT: H 244 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: G 119 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: G 304 MET cc_start: 0.6373 (mpp) cc_final: 0.5574 (mpp) REVERT: G 328 MET cc_start: 0.4763 (OUTLIER) cc_final: 0.3510 (tpp) REVERT: F 19 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7162 (mm) REVERT: F 21 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8483 (m-80) REVERT: F 159 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5984 (pm20) REVERT: E 151 ASN cc_start: 0.8483 (m-40) cc_final: 0.8139 (m110) REVERT: J 146 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6845 (t80) outliers start: 147 outliers final: 107 residues processed: 370 average time/residue: 0.2955 time to fit residues: 177.5197 Evaluate side-chains 379 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 253 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 250 TYR 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 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 190 ASN 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 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 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 284 ARG Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN 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 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 50 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 256 ASN Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS 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 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS 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 122 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 0.0050 chunk 40 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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** F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.196305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.162237 restraints weight = 36386.247| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 2.82 r_work: 0.3875 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21736 Z= 0.135 Angle : 0.574 12.479 29639 Z= 0.296 Chirality : 0.042 0.188 3303 Planarity : 0.004 0.052 3558 Dihedral : 14.712 176.114 3583 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.65 % Allowed : 36.21 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.16), residues: 2416 helix: -0.36 (0.20), residues: 641 sheet: -0.27 (0.31), residues: 331 loop : -2.31 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 149 HIS 0.004 0.001 HIS E 250 PHE 0.028 0.001 PHE G 200 TYR 0.032 0.001 TYR E 169 ARG 0.005 0.000 ARG H 115 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 580) hydrogen bonds : angle 4.99533 ( 1662) covalent geometry : bond 0.00309 (21736) covalent geometry : angle 0.57400 (29639) *********************** 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 404 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 259 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ASN cc_start: 0.5368 (m110) cc_final: 0.4812 (t0) REVERT: A 22 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.6940 (tp) REVERT: A 99 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: A 181 HIS cc_start: 0.7676 (t70) cc_final: 0.7396 (t-90) REVERT: A 184 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.5974 (mp10) REVERT: A 249 LEU cc_start: 0.7489 (mp) cc_final: 0.6843 (tt) REVERT: B 56 ASN cc_start: 0.5480 (OUTLIER) cc_final: 0.4984 (p0) REVERT: B 129 MET cc_start: 0.1223 (tpp) cc_final: 0.0829 (tpp) REVERT: I 114 TYR cc_start: 0.7972 (t80) cc_final: 0.7655 (t80) REVERT: I 158 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6385 (mt) REVERT: I 198 ASP cc_start: 0.7353 (m-30) cc_final: 0.7031 (m-30) REVERT: I 244 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7049 (mt-10) REVERT: H 100 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7575 (mt) REVERT: H 104 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5754 (tm-30) REVERT: H 112 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.4112 (m-10) REVERT: H 200 PHE cc_start: 0.5259 (OUTLIER) cc_final: 0.4629 (t80) REVERT: H 207 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5794 (tt) REVERT: H 229 MET cc_start: 0.4501 (OUTLIER) cc_final: 0.3809 (mtt) REVERT: H 244 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: G 119 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6671 (m-80) REVERT: G 304 MET cc_start: 0.6346 (mpp) cc_final: 0.5561 (mpp) REVERT: G 328 MET cc_start: 0.4689 (OUTLIER) cc_final: 0.3401 (tpp) REVERT: F 19 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7235 (mm) REVERT: F 21 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8512 (m-80) REVERT: F 159 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5995 (pm20) REVERT: E 149 TRP cc_start: 0.7694 (m100) cc_final: 0.7393 (m100) REVERT: E 151 ASN cc_start: 0.8471 (m-40) cc_final: 0.8110 (m110) REVERT: J 146 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6710 (t80) outliers start: 145 outliers final: 113 residues processed: 371 average time/residue: 0.3045 time to fit residues: 181.9255 Evaluate side-chains 387 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 255 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 250 TYR 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 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 190 ASN 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 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 99 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 229 MET Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 140 ASN 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 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 13 LYS 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 50 THR Chi-restraints excluded: chain F residue 106 MET Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 171 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 294 THR Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 316 LYS Chi-restraints excluded: chain 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 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 172 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 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 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 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 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 87 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 199 optimal weight: 0.0570 overall best weight: 2.8104 ------------------------------------------------------------------------------- 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** G 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.193777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159206 restraints weight = 36437.786| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.85 r_work: 0.3836 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 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 : 0.004 0.053 21736 Z= 0.182 Angle : 0.620 13.776 29639 Z= 0.320 Chirality : 0.043 0.187 3303 Planarity : 0.004 0.053 3558 Dihedral : 14.800 176.346 3583 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 6.65 % Allowed : 36.16 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.16), residues: 2416 helix: -0.50 (0.20), residues: 642 sheet: -0.48 (0.30), residues: 340 loop : -2.34 (0.15), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 149 HIS 0.004 0.001 HIS E 250 PHE 0.021 0.002 PHE G 131 TYR 0.036 0.002 TYR E 169 ARG 0.005 0.000 ARG D 303 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 580) hydrogen bonds : angle 5.17193 ( 1662) covalent geometry : bond 0.00418 (21736) covalent geometry : angle 0.61970 (29639) ********************** 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 402 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 257 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7018 (tp) REVERT: A 41 ARG cc_start: 0.7332 (mtp85) cc_final: 0.6999 (mtm110) REVERT: A 99 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: A 181 HIS cc_start: 0.7813 (t70) cc_final: 0.7584 (t-90) REVERT: A 184 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.5926 (mp10) REVERT: A 249 LEU cc_start: 0.7472 (mp) cc_final: 0.6857 (tt) REVERT: B 56 ASN cc_start: 0.5488 (OUTLIER) cc_final: 0.5016 (p0) REVERT: B 129 MET cc_start: 0.1247 (tpp) cc_final: 0.0843 (tpp) REVERT: I 114 TYR cc_start: 0.7985 (t80) cc_final: 0.7632 (t80) REVERT: I 158 ILE cc_start: 0.6747 (OUTLIER) cc_final: 0.6483 (mt) REVERT: I 198 ASP cc_start: 0.7468 (m-30) cc_final: 0.7143 (m-30) REVERT: I 244 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: H 100 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7594 (mt) REVERT: H 104 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5750 (tm-30) REVERT: H 112 TYR cc_start: 0.5085 (OUTLIER) cc_final: 0.4365 (m-10) REVERT: H 200 PHE cc_start: 0.5386 (OUTLIER) cc_final: 0.4698 (t80) REVERT: H 207 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5895 (tt) REVERT: H 244 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: G 119 TYR cc_start: 0.7226 (OUTLIER) cc_final: 0.6656 (m-80) REVERT: G 304 MET cc_start: 0.6435 (mpp) cc_final: 0.5645 (mpp) REVERT: G 328 MET cc_start: 0.5038 (OUTLIER) cc_final: 0.3808 (tpp) REVERT: F 19 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7201 (mm) REVERT: F 21 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8426 (m-80) REVERT: F 159 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5936 (pm20) REVERT: E 149 TRP cc_start: 0.7867 (m100) cc_final: 0.7488 (m100) REVERT: E 151 ASN cc_start: 0.8507 (m-40) cc_final: 0.8126 (m110) REVERT: D 206 TYR cc_start: 0.4618 (p90) cc_final: 0.4290 (p90) REVERT: J 74 TRP cc_start: 0.6906 (t60) cc_final: 0.6557 (t60) REVERT: J 146 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6877 (t80) outliers start: 145 outliers final: 115 residues processed: 369 average time/residue: 0.2944 time to fit residues: 176.0646 Evaluate side-chains 385 residues out of total 2179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 252 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 56 ASN Chi-restraints excluded: chain B residue 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 163 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 190 ASN 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 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 103 LYS Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 144 ASN Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 194 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 244 GLU Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain H residue 261 ILE Chi-restraints excluded: chain H residue 294 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain H residue 328 MET Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 41 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 120 GLN Chi-restraints excluded: chain G residue 140 ASN 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 307 LYS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 328 MET Chi-restraints excluded: chain F residue 13 LYS 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 50 THR 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 199 THR Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 222 GLU Chi-restraints excluded: chain F residue 223 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 264 TRP 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 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 100 LEU Chi-restraints excluded: chain E residue 131 PHE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 270 THR Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 293 ASP Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 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 217 ILE Chi-restraints excluded: chain D residue 223 VAL Chi-restraints excluded: chain D residue 251 SER Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 146 PHE Chi-restraints excluded: chain J residue 211 VAL Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 239 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 260 ILE Chi-restraints excluded: chain J residue 275 HIS 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 48 optimal weight: 0.6980 chunk 188 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 235 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- 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** G 120 GLN F 256 ASN ** E 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.193955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159989 restraints weight = 36375.257| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.73 r_work: 0.3845 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21736 Z= 0.175 Angle : 0.615 13.837 29639 Z= 0.318 Chirality : 0.043 0.186 3303 Planarity : 0.004 0.054 3558 Dihedral : 14.807 175.799 3583 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 6.75 % Allowed : 36.12 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2416 helix: -0.53 (0.20), residues: 643 sheet: -0.53 (0.30), residues: 347 loop : -2.38 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 149 HIS 0.004 0.001 HIS H 250 PHE 0.027 0.002 PHE G 200 TYR 0.036 0.001 TYR E 169 ARG 0.004 0.000 ARG E 137 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 580) hydrogen bonds : angle 5.17524 ( 1662) covalent geometry : bond 0.00403 (21736) covalent geometry : angle 0.61498 (29639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10959.76 seconds wall clock time: 189 minutes 7.30 seconds (11347.30 seconds total)